Starting phenix.real_space_refine on Wed Jan 22 21:40:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8usc_42507/01_2025/8usc_42507.cif Found real_map, /net/cci-nas-00/data/ceres_data/8usc_42507/01_2025/8usc_42507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8usc_42507/01_2025/8usc_42507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8usc_42507/01_2025/8usc_42507.map" model { file = "/net/cci-nas-00/data/ceres_data/8usc_42507/01_2025/8usc_42507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8usc_42507/01_2025/8usc_42507.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 15 5.49 5 Mg 5 5.21 5 S 375 5.16 5 C 44317 2.51 5 N 12063 2.21 5 O 13285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 70061 Number of models: 1 Model: "" Number of chains: 35 Chain: "H" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1813 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain: "Y" Number of atoms: 3127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3127 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 371} Chain: "f" Number of atoms: 6512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 6512 Classifications: {'peptide': 842} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 811} Chain breaks: 1 Chain: "X" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2994 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 10, 'TRANS': 367} Chain: "U" Number of atoms: 6559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6559 Classifications: {'peptide': 841} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 812} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "A" Number of atoms: 3261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3261 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 24, 'TRANS': 390} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3122 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3051 Classifications: {'peptide': 386} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 369} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3040 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 362} Chain: "E" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2859 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 18, 'TRANS': 341} Chain breaks: 2 Chain: "F" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2850 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "v" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1820 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 1911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1911 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1749 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "K" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1733 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 355 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "e" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 353 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 1 Chain: "d" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2188 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain: "W" Number of atoms: 3570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3570 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 8, 'TRANS': 429} Chain: "g" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 771 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "V" Number of atoms: 3593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3593 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 16, 'TRANS': 424} Chain: "c" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2150 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 263} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY Z 30 " occ=0.73 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.73 Time building chain proxies: 28.97, per 1000 atoms: 0.41 Number of scatterers: 70061 At special positions: 0 Unit cell: (191.784, 223.224, 217.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 375 16.00 P 15 15.00 Mg 5 11.99 O 13285 8.00 N 12063 7.00 C 44317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 137 " - pdb=" SG CYS H 213 " distance=2.04 Simple disulfide: pdb=" SG CYS U 633 " - pdb=" SG CYS U 659 " distance=2.03 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 154 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.35 Conformation dependent library (CDL) restraints added in 8.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 113 " 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16724 Finding SS restraints... Secondary structure from input PDB file: 393 helices and 39 sheets defined 60.0% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.89 Creating SS restraints... Processing helix chain 'H' and resid 3 through 7 removed outlier: 3.502A pdb=" N TYR H 6 " --> pdb=" O GLU H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 31 removed outlier: 3.521A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 102 removed outlier: 3.594A pdb=" N ARG H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL H 85 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 121 removed outlier: 3.812A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 174 Processing helix chain 'H' and resid 183 through 197 Processing helix chain 'H' and resid 222 through 234 Processing helix chain 'Y' and resid 16 through 28 removed outlier: 3.673A pdb=" N ALA Y 20 " --> pdb=" O ASP Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 33 removed outlier: 4.305A pdb=" N GLY Y 33 " --> pdb=" O PRO Y 29 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 49 Processing helix chain 'Y' and resid 50 through 62 Processing helix chain 'Y' and resid 66 through 95 Processing helix chain 'Y' and resid 96 through 114 removed outlier: 3.502A pdb=" N ILE Y 100 " --> pdb=" O GLY Y 96 " (cutoff:3.500A) Processing helix chain 'Y' and resid 117 through 131 Processing helix chain 'Y' and resid 133 through 152 Processing helix chain 'Y' and resid 153 through 171 Processing helix chain 'Y' and resid 173 through 191 Processing helix chain 'Y' and resid 193 through 205 Processing helix chain 'Y' and resid 215 through 231 Processing helix chain 'Y' and resid 232 through 240 Processing helix chain 'Y' and resid 243 through 251 Processing helix chain 'Y' and resid 253 through 265 removed outlier: 3.966A pdb=" N LEU Y 263 " --> pdb=" O TYR Y 259 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR Y 264 " --> pdb=" O LEU Y 260 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 285 removed outlier: 3.769A pdb=" N LYS Y 284 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 291 through 310 removed outlier: 4.115A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 323 Processing helix chain 'Y' and resid 326 through 340 Processing helix chain 'Y' and resid 360 through 388 Processing helix chain 'f' and resid 46 through 62 Processing helix chain 'f' and resid 63 through 65 No H-bonds generated for 'chain 'f' and resid 63 through 65' Processing helix chain 'f' and resid 67 through 87 removed outlier: 4.281A pdb=" N TYR f 71 " --> pdb=" O ASP f 67 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARG f 72 " --> pdb=" O THR f 68 " (cutoff:3.500A) Proline residue: f 73 - end of helix Processing helix chain 'f' and resid 93 through 99 Processing helix chain 'f' and resid 103 through 113 Processing helix chain 'f' and resid 116 through 133 removed outlier: 4.026A pdb=" N ARG f 120 " --> pdb=" O GLY f 116 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR f 132 " --> pdb=" O VAL f 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET f 133 " --> pdb=" O LEU f 129 " (cutoff:3.500A) Processing helix chain 'f' and resid 135 through 146 removed outlier: 3.811A pdb=" N ARG f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) Processing helix chain 'f' and resid 155 through 173 Processing helix chain 'f' and resid 180 through 198 removed outlier: 3.576A pdb=" N LEU f 184 " --> pdb=" O GLN f 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU f 190 " --> pdb=" O THR f 186 " (cutoff:3.500A) Proline residue: f 193 - end of helix Processing helix chain 'f' and resid 200 through 211 Processing helix chain 'f' and resid 215 through 221 removed outlier: 4.019A pdb=" N LYS f 219 " --> pdb=" O ASP f 215 " (cutoff:3.500A) Processing helix chain 'f' and resid 225 through 237 Processing helix chain 'f' and resid 243 through 259 removed outlier: 3.526A pdb=" N ALA f 247 " --> pdb=" O PRO f 243 " (cutoff:3.500A) Processing helix chain 'f' and resid 261 through 273 Processing helix chain 'f' and resid 274 through 285 removed outlier: 3.707A pdb=" N VAL f 278 " --> pdb=" O ASP f 274 " (cutoff:3.500A) Processing helix chain 'f' and resid 287 through 302 Processing helix chain 'f' and resid 313 through 322 Processing helix chain 'f' and resid 325 through 338 Processing helix chain 'f' and resid 344 through 350 Processing helix chain 'f' and resid 367 through 381 Processing helix chain 'f' and resid 394 through 400 Processing helix chain 'f' and resid 404 through 417 removed outlier: 3.519A pdb=" N GLY f 415 " --> pdb=" O ALA f 411 " (cutoff:3.500A) Processing helix chain 'f' and resid 421 through 434 removed outlier: 3.746A pdb=" N GLN f 428 " --> pdb=" O GLY f 424 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 439 No H-bonds generated for 'chain 'f' and resid 437 through 439' Processing helix chain 'f' and resid 440 through 452 Processing helix chain 'f' and resid 460 through 468 removed outlier: 4.368A pdb=" N ASP f 468 " --> pdb=" O ALA f 464 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 489 Processing helix chain 'f' and resid 494 through 507 Proline residue: f 503 - end of helix removed outlier: 3.951A pdb=" N GLY f 506 " --> pdb=" O LEU f 502 " (cutoff:3.500A) Processing helix chain 'f' and resid 511 through 526 Processing helix chain 'f' and resid 531 through 545 Processing helix chain 'f' and resid 546 through 551 Processing helix chain 'f' and resid 553 through 555 No H-bonds generated for 'chain 'f' and resid 553 through 555' Processing helix chain 'f' and resid 556 through 565 removed outlier: 3.665A pdb=" N LEU f 560 " --> pdb=" O ARG f 556 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY f 561 " --> pdb=" O TRP f 557 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU f 562 " --> pdb=" O LEU f 558 " (cutoff:3.500A) Processing helix chain 'f' and resid 572 through 581 removed outlier: 3.892A pdb=" N ILE f 576 " --> pdb=" O ALA f 572 " (cutoff:3.500A) Processing helix chain 'f' and resid 586 through 600 Processing helix chain 'f' and resid 605 through 618 Processing helix chain 'f' and resid 645 through 662 removed outlier: 4.037A pdb=" N HIS f 649 " --> pdb=" O ASP f 645 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN f 650 " --> pdb=" O MET f 646 " (cutoff:3.500A) Processing helix chain 'f' and resid 664 through 682 removed outlier: 3.650A pdb=" N ARG f 673 " --> pdb=" O GLU f 669 " (cutoff:3.500A) Processing helix chain 'f' and resid 683 through 698 Proline residue: f 691 - end of helix Processing helix chain 'f' and resid 703 through 714 Processing helix chain 'f' and resid 718 through 733 Processing helix chain 'f' and resid 738 through 752 Processing helix chain 'f' and resid 755 through 770 Processing helix chain 'f' and resid 771 through 774 Processing helix chain 'f' and resid 789 through 804 Processing helix chain 'f' and resid 814 through 818 Processing helix chain 'f' and resid 819 through 824 removed outlier: 3.864A pdb=" N ALA f 823 " --> pdb=" O TYR f 819 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA f 824 " --> pdb=" O GLY f 820 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 819 through 824' Processing helix chain 'X' and resid 45 through 61 Processing helix chain 'X' and resid 62 through 73 Processing helix chain 'X' and resid 73 through 79 removed outlier: 3.860A pdb=" N ASN X 78 " --> pdb=" O ARG X 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER X 79 " --> pdb=" O PRO X 75 " (cutoff:3.500A) Processing helix chain 'X' and resid 81 through 99 removed outlier: 4.061A pdb=" N MET X 99 " --> pdb=" O LEU X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 121 Processing helix chain 'X' and resid 122 through 140 Processing helix chain 'X' and resid 142 through 160 removed outlier: 4.278A pdb=" N ARG X 155 " --> pdb=" O SER X 151 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU X 156 " --> pdb=" O GLN X 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 180 Processing helix chain 'X' and resid 182 through 198 Processing helix chain 'X' and resid 203 through 221 Processing helix chain 'X' and resid 225 through 242 removed outlier: 3.679A pdb=" N ILE X 242 " --> pdb=" O GLY X 238 " (cutoff:3.500A) Processing helix chain 'X' and resid 243 through 245 No H-bonds generated for 'chain 'X' and resid 243 through 245' Processing helix chain 'X' and resid 246 through 261 removed outlier: 3.533A pdb=" N LEU X 261 " --> pdb=" O CYS X 257 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 272 removed outlier: 3.993A pdb=" N GLN X 268 " --> pdb=" O PRO X 264 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 297 Processing helix chain 'X' and resid 298 through 309 Processing helix chain 'X' and resid 309 through 314 Processing helix chain 'X' and resid 316 through 338 Processing helix chain 'X' and resid 346 through 355 Processing helix chain 'X' and resid 357 through 371 Processing helix chain 'X' and resid 394 through 417 removed outlier: 3.532A pdb=" N GLU X 398 " --> pdb=" O ASP X 394 " (cutoff:3.500A) Processing helix chain 'U' and resid 6 through 14 removed outlier: 3.728A pdb=" N ILE U 9 " --> pdb=" O ALA U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 42 removed outlier: 3.679A pdb=" N LYS U 20 " --> pdb=" O GLU U 16 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASN U 32 " --> pdb=" O ASN U 28 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE U 34 " --> pdb=" O VAL U 30 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP U 35 " --> pdb=" O VAL U 31 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ALA U 36 " --> pdb=" O ASN U 32 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLU U 37 " --> pdb=" O ASP U 33 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE U 38 " --> pdb=" O PHE U 34 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL U 42 " --> pdb=" O ILE U 38 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 51 removed outlier: 3.925A pdb=" N LEU U 48 " --> pdb=" O LYS U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 84 removed outlier: 4.248A pdb=" N ASN U 79 " --> pdb=" O GLU U 75 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 118 Processing helix chain 'U' and resid 127 through 145 removed outlier: 3.720A pdb=" N HIS U 145 " --> pdb=" O CYS U 141 " (cutoff:3.500A) Processing helix chain 'U' and resid 149 through 157 Processing helix chain 'U' and resid 159 through 169 Processing helix chain 'U' and resid 174 through 187 removed outlier: 3.572A pdb=" N ALA U 178 " --> pdb=" O PRO U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 208 removed outlier: 3.695A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 4.186A pdb=" N PHE U 222 " --> pdb=" O GLN U 218 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 239 Processing helix chain 'U' and resid 242 through 256 Processing helix chain 'U' and resid 257 through 270 Processing helix chain 'U' and resid 321 through 331 Processing helix chain 'U' and resid 331 through 345 Processing helix chain 'U' and resid 349 through 358 removed outlier: 4.052A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) Processing helix chain 'U' and resid 364 through 377 removed outlier: 4.244A pdb=" N ALA U 368 " --> pdb=" O VAL U 364 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER U 374 " --> pdb=" O VAL U 370 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 389 Processing helix chain 'U' and resid 398 through 412 removed outlier: 3.704A pdb=" N PHE U 402 " --> pdb=" O ASN U 398 " (cutoff:3.500A) Processing helix chain 'U' and resid 415 through 417 No H-bonds generated for 'chain 'U' and resid 415 through 417' Processing helix chain 'U' and resid 418 through 427 removed outlier: 3.945A pdb=" N ALA U 424 " --> pdb=" O LEU U 420 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR U 426 " --> pdb=" O LEU U 422 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 450 Processing helix chain 'U' and resid 455 through 467 removed outlier: 3.670A pdb=" N ASP U 459 " --> pdb=" O GLY U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 485 Processing helix chain 'U' and resid 490 through 504 removed outlier: 4.015A pdb=" N ASP U 504 " --> pdb=" O ASN U 500 " (cutoff:3.500A) Processing helix chain 'U' and resid 506 through 520 removed outlier: 3.754A pdb=" N LEU U 514 " --> pdb=" O GLU U 510 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 537 Processing helix chain 'U' and resid 541 through 555 removed outlier: 3.680A pdb=" N VAL U 550 " --> pdb=" O ARG U 546 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL U 555 " --> pdb=" O GLY U 551 " (cutoff:3.500A) Processing helix chain 'U' and resid 559 through 563 removed outlier: 4.580A pdb=" N ALA U 563 " --> pdb=" O MET U 560 " (cutoff:3.500A) Processing helix chain 'U' and resid 564 through 573 Processing helix chain 'U' and resid 575 through 590 Processing helix chain 'U' and resid 595 through 609 Processing helix chain 'U' and resid 611 through 627 removed outlier: 4.004A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) Processing helix chain 'U' and resid 631 through 641 removed outlier: 4.234A pdb=" N SER U 635 " --> pdb=" O GLU U 631 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER U 641 " --> pdb=" O VAL U 637 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 660 removed outlier: 3.626A pdb=" N ARG U 649 " --> pdb=" O ASN U 645 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N CYS U 660 " --> pdb=" O LEU U 656 " (cutoff:3.500A) Processing helix chain 'U' and resid 667 through 676 Proline residue: U 674 - end of helix Processing helix chain 'U' and resid 680 through 695 removed outlier: 3.714A pdb=" N ARG U 684 " --> pdb=" O VAL U 680 " (cutoff:3.500A) Processing helix chain 'U' and resid 705 through 718 Processing helix chain 'U' and resid 723 through 738 removed outlier: 3.637A pdb=" N ASP U 738 " --> pdb=" O GLN U 734 " (cutoff:3.500A) Processing helix chain 'U' and resid 756 through 768 Processing helix chain 'U' and resid 772 through 781 removed outlier: 3.722A pdb=" N HIS U 777 " --> pdb=" O PRO U 774 " (cutoff:3.500A) Processing helix chain 'U' and resid 835 through 851 Processing helix chain 'U' and resid 885 through 889 removed outlier: 3.533A pdb=" N LEU U 889 " --> pdb=" O PRO U 886 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 28 removed outlier: 3.780A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 removed outlier: 3.821A pdb=" N LEU Z 75 " --> pdb=" O ASP Z 71 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 116 removed outlier: 3.830A pdb=" N ILE Z 108 " --> pdb=" O ASN Z 104 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 177 Processing helix chain 'Z' and resid 185 through 217 removed outlier: 3.799A pdb=" N GLN Z 189 " --> pdb=" O GLY Z 185 " (cutoff:3.500A) Processing helix chain 'Z' and resid 226 through 236 Processing helix chain 'Z' and resid 242 through 290 removed outlier: 3.756A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY Z 290 " --> pdb=" O GLU Z 286 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 11 Processing helix chain 'a' and resid 17 through 31 removed outlier: 4.079A pdb=" N TRP a 22 " --> pdb=" O GLN a 18 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG a 24 " --> pdb=" O ALA a 20 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU a 25 " --> pdb=" O VAL a 21 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU a 28 " --> pdb=" O ARG a 24 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS a 31 " --> pdb=" O GLU a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 35 through 46 Processing helix chain 'a' and resid 53 through 67 removed outlier: 4.451A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE a 67 " --> pdb=" O PHE a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 88 removed outlier: 3.764A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 104 removed outlier: 3.578A pdb=" N LEU a 94 " --> pdb=" O PRO a 90 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL a 104 " --> pdb=" O THR a 100 " (cutoff:3.500A) Processing helix chain 'a' and resid 110 through 123 Processing helix chain 'a' and resid 130 through 142 Processing helix chain 'a' and resid 150 through 162 Processing helix chain 'a' and resid 169 through 183 Processing helix chain 'a' and resid 189 through 207 Processing helix chain 'a' and resid 219 through 225 Processing helix chain 'a' and resid 231 through 243 removed outlier: 3.755A pdb=" N ASP a 235 " --> pdb=" O GLN a 231 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 256 removed outlier: 3.873A pdb=" N GLY a 256 " --> pdb=" O LYS a 252 " (cutoff:3.500A) Processing helix chain 'a' and resid 264 through 283 Processing helix chain 'a' and resid 292 through 300 removed outlier: 3.691A pdb=" N ILE a 296 " --> pdb=" O THR a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 306 through 318 Processing helix chain 'a' and resid 342 through 371 Processing helix chain 'a' and resid 371 through 376 removed outlier: 4.127A pdb=" N THR a 376 " --> pdb=" O HIS a 372 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 17 Processing helix chain 'b' and resid 24 through 44 Processing helix chain 'b' and resid 67 through 76 removed outlier: 4.479A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS b 76 " --> pdb=" O LEU b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 98 removed outlier: 3.590A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 135 Processing helix chain 'b' and resid 150 through 161 removed outlier: 3.998A pdb=" N ASN b 161 " --> pdb=" O VAL b 157 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 186 removed outlier: 3.868A pdb=" N SER b 186 " --> pdb=" O ALA b 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.680A pdb=" N TRP A 78 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 158 through 164 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.614A pdb=" N ASP A 176 " --> pdb=" O THR A 173 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 177 " --> pdb=" O TYR A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.598A pdb=" N VAL A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.594A pdb=" N ASN A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 232 Processing helix chain 'A' and resid 251 through 267 Processing helix chain 'A' and resid 293 through 307 Processing helix chain 'A' and resid 323 through 327 removed outlier: 3.964A pdb=" N THR A 326 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 347 through 359 Processing helix chain 'A' and resid 369 through 376 Processing helix chain 'A' and resid 381 through 399 removed outlier: 3.691A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 417 through 422 removed outlier: 4.651A pdb=" N LYS A 422 " --> pdb=" O LYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'B' and resid 58 through 85 removed outlier: 4.459A pdb=" N GLU B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 104 removed outlier: 3.711A pdb=" N ASP B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.596A pdb=" N ILE B 187 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.643A pdb=" N TYR B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 243 Processing helix chain 'B' and resid 261 through 277 removed outlier: 3.512A pdb=" N LYS B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 removed outlier: 3.670A pdb=" N THR B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.770A pdb=" N GLU B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 380 through 385 Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 415 through 428 removed outlier: 3.531A pdb=" N GLU B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B 428 " --> pdb=" O GLU B 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 68 removed outlier: 3.619A pdb=" N GLU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 154 through 166 removed outlier: 3.883A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 171 through 179 removed outlier: 4.231A pdb=" N PHE C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 206 Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 267 through 281 Processing helix chain 'C' and resid 297 through 301 removed outlier: 3.873A pdb=" N LEU C 301 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.652A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 373 removed outlier: 3.520A pdb=" N LYS C 360 " --> pdb=" O GLY C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 391 Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'D' and resid 40 through 83 removed outlier: 3.915A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 182 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'D' and resid 187 through 195 removed outlier: 4.136A pdb=" N TYR D 191 " --> pdb=" O HIS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 242 through 257 Processing helix chain 'D' and resid 279 through 297 Processing helix chain 'D' and resid 339 through 350 Processing helix chain 'D' and resid 360 through 365 Processing helix chain 'D' and resid 371 through 389 Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 412 through 416 removed outlier: 4.081A pdb=" N GLU D 415 " --> pdb=" O GLN D 412 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE D 416 " --> pdb=" O GLU D 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 412 through 416' Processing helix chain 'E' and resid 16 through 51 removed outlier: 3.702A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'E' and resid 138 through 155 removed outlier: 5.189A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 156 through 163 removed outlier: 3.847A pdb=" N GLN E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 192 Processing helix chain 'E' and resid 212 through 222 removed outlier: 3.760A pdb=" N ALA E 222 " --> pdb=" O MET E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 265 Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 305 through 318 Processing helix chain 'E' and resid 327 through 334 removed outlier: 3.933A pdb=" N ILE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 357 Processing helix chain 'E' and resid 363 through 373 removed outlier: 4.569A pdb=" N LYS E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 385 Processing helix chain 'F' and resid 53 through 85 removed outlier: 3.581A pdb=" N THR F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 176 removed outlier: 3.846A pdb=" N GLU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 192 through 203 Processing helix chain 'F' and resid 203 through 208 Processing helix chain 'F' and resid 209 through 216 removed outlier: 3.807A pdb=" N GLU F 213 " --> pdb=" O LYS F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 243 Processing helix chain 'F' and resid 262 through 278 Processing helix chain 'F' and resid 302 through 320 removed outlier: 4.019A pdb=" N PHE F 320 " --> pdb=" O GLN F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 344 removed outlier: 3.957A pdb=" N LEU F 343 " --> pdb=" O ASP F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 370 Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 392 through 410 Processing helix chain 'F' and resid 416 through 428 removed outlier: 3.558A pdb=" N GLN F 428 " --> pdb=" O ILE F 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 33 removed outlier: 4.061A pdb=" N ASN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 36 No H-bonds generated for 'chain 'G' and resid 34 through 36' Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 Processing helix chain 'G' and resid 171 through 183 removed outlier: 3.539A pdb=" N SER G 175 " --> pdb=" O LYS G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 231 through 244 Processing helix chain 'I' and resid 18 through 28 Processing helix chain 'I' and resid 29 through 31 No H-bonds generated for 'chain 'I' and resid 29 through 31' Processing helix chain 'I' and resid 80 through 102 Processing helix chain 'I' and resid 107 through 122 Processing helix chain 'I' and resid 167 through 178 Processing helix chain 'I' and resid 185 through 201 Processing helix chain 'I' and resid 207 through 209 No H-bonds generated for 'chain 'I' and resid 207 through 209' Processing helix chain 'I' and resid 229 through 249 removed outlier: 3.550A pdb=" N VAL I 233 " --> pdb=" O LYS I 229 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG I 249 " --> pdb=" O ALA I 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 28 removed outlier: 3.716A pdb=" N GLN J 23 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA J 25 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL J 26 " --> pdb=" O ALA J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 98 Processing helix chain 'J' and resid 103 through 118 Processing helix chain 'J' and resid 165 through 174 removed outlier: 4.059A pdb=" N LYS J 174 " --> pdb=" O GLU J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 197 Processing helix chain 'J' and resid 223 through 237 Processing helix chain 'J' and resid 238 through 240 No H-bonds generated for 'chain 'J' and resid 238 through 240' Processing helix chain 'K' and resid 23 through 33 removed outlier: 3.609A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 81 through 104 Processing helix chain 'K' and resid 108 through 121 Processing helix chain 'K' and resid 122 through 125 removed outlier: 3.798A pdb=" N GLU K 125 " --> pdb=" O GLN K 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 122 through 125' Processing helix chain 'K' and resid 173 through 185 Processing helix chain 'K' and resid 190 through 205 Processing helix chain 'K' and resid 233 through 239 removed outlier: 3.515A pdb=" N VAL K 237 " --> pdb=" O GLU K 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.634A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 99 Processing helix chain 'L' and resid 104 through 118 removed outlier: 3.691A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 121 No H-bonds generated for 'chain 'L' and resid 119 through 121' Processing helix chain 'L' and resid 165 through 176 Processing helix chain 'L' and resid 177 through 179 No H-bonds generated for 'chain 'L' and resid 177 through 179' Processing helix chain 'L' and resid 183 through 199 removed outlier: 3.725A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 234 Processing helix chain 'M' and resid 20 through 31 Processing helix chain 'M' and resid 80 through 103 Processing helix chain 'M' and resid 107 through 121 Processing helix chain 'M' and resid 122 through 124 No H-bonds generated for 'chain 'M' and resid 122 through 124' Processing helix chain 'M' and resid 168 through 177 removed outlier: 3.620A pdb=" N GLU M 175 " --> pdb=" O ALA M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 201 removed outlier: 3.510A pdb=" N ILE M 189 " --> pdb=" O THR M 185 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 202 through 207 Processing helix chain 'M' and resid 219 through 221 No H-bonds generated for 'chain 'M' and resid 219 through 221' Processing helix chain 'M' and resid 228 through 241 Processing helix chain 'O' and resid 52 through 71 Processing helix chain 'O' and resid 75 through 90 Processing helix chain 'e' and resid 42 through 47 removed outlier: 4.025A pdb=" N ASP e 46 " --> pdb=" O ASN e 42 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN e 47 " --> pdb=" O TRP e 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 42 through 47' Processing helix chain 'e' and resid 51 through 65 removed outlier: 3.686A pdb=" N TYR e 65 " --> pdb=" O GLU e 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 83 through 104 removed outlier: 3.826A pdb=" N ARG d 104 " --> pdb=" O GLY d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 127 Processing helix chain 'd' and resid 137 through 156 removed outlier: 3.753A pdb=" N ILE d 156 " --> pdb=" O ALA d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 157 through 159 No H-bonds generated for 'chain 'd' and resid 157 through 159' Processing helix chain 'd' and resid 160 through 178 removed outlier: 4.027A pdb=" N CYS d 173 " --> pdb=" O ALA d 169 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR d 174 " --> pdb=" O GLN d 170 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR d 178 " --> pdb=" O TYR d 174 " (cutoff:3.500A) Processing helix chain 'd' and resid 185 through 203 removed outlier: 4.319A pdb=" N HIS d 189 " --> pdb=" O SER d 185 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 215 Processing helix chain 'd' and resid 216 through 222 removed outlier: 3.545A pdb=" N ILE d 220 " --> pdb=" O PRO d 216 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN d 221 " --> pdb=" O ALA d 217 " (cutoff:3.500A) Processing helix chain 'd' and resid 223 through 238 Proline residue: d 229 - end of helix Processing helix chain 'd' and resid 240 through 248 Processing helix chain 'd' and resid 249 through 251 No H-bonds generated for 'chain 'd' and resid 249 through 251' Processing helix chain 'd' and resid 253 through 279 removed outlier: 4.027A pdb=" N PHE d 259 " --> pdb=" O SER d 255 " (cutoff:3.500A) Processing helix chain 'd' and resid 284 through 291 removed outlier: 3.862A pdb=" N ARG d 289 " --> pdb=" O THR d 285 " (cutoff:3.500A) Processing helix chain 'd' and resid 295 through 306 removed outlier: 3.576A pdb=" N MET d 299 " --> pdb=" O THR d 295 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR d 302 " --> pdb=" O LYS d 298 " (cutoff:3.500A) Processing helix chain 'd' and resid 318 through 323 removed outlier: 3.940A pdb=" N GLN d 322 " --> pdb=" O PHE d 318 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN d 323 " --> pdb=" O ALA d 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 318 through 323' Processing helix chain 'd' and resid 332 through 348 Processing helix chain 'W' and resid 20 through 38 removed outlier: 3.826A pdb=" N GLN W 26 " --> pdb=" O ALA W 22 " (cutoff:3.500A) Proline residue: W 29 - end of helix removed outlier: 4.216A pdb=" N LEU W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 57 Processing helix chain 'W' and resid 59 through 78 Processing helix chain 'W' and resid 79 through 92 Processing helix chain 'W' and resid 97 through 115 removed outlier: 4.024A pdb=" N GLU W 113 " --> pdb=" O CYS W 109 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLU W 114 " --> pdb=" O THR W 110 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE W 115 " --> pdb=" O TYR W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 Processing helix chain 'W' and resid 138 through 156 Processing helix chain 'W' and resid 158 through 168 removed outlier: 3.676A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 178 through 196 Processing helix chain 'W' and resid 198 through 209 Processing helix chain 'W' and resid 219 through 238 Processing helix chain 'W' and resid 239 through 252 Processing helix chain 'W' and resid 253 through 259 Processing helix chain 'W' and resid 259 through 277 Processing helix chain 'W' and resid 280 through 292 Processing helix chain 'W' and resid 293 through 298 removed outlier: 3.593A pdb=" N LEU W 296 " --> pdb=" O ASP W 293 " (cutoff:3.500A) Processing helix chain 'W' and resid 299 through 311 removed outlier: 3.632A pdb=" N PHE W 309 " --> pdb=" O LEU W 305 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR W 310 " --> pdb=" O LEU W 306 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 329 removed outlier: 6.084A pdb=" N MET W 326 " --> pdb=" O GLU W 322 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLU W 327 " --> pdb=" O ASP W 323 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 369 Processing helix chain 'W' and resid 374 through 383 Processing helix chain 'W' and resid 385 through 399 Processing helix chain 'W' and resid 420 through 453 Processing helix chain 'g' and resid 108 through 121 Processing helix chain 'g' and resid 123 through 125 No H-bonds generated for 'chain 'g' and resid 123 through 125' Processing helix chain 'g' and resid 142 through 146 removed outlier: 3.543A pdb=" N GLY g 146 " --> pdb=" O GLU g 143 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 172 removed outlier: 3.837A pdb=" N GLU g 172 " --> pdb=" O ASN g 168 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 89 Processing helix chain 'V' and resid 91 through 105 Proline residue: V 102 - end of helix Processing helix chain 'V' and resid 109 through 120 Processing helix chain 'V' and resid 125 through 132 removed outlier: 3.771A pdb=" N ASP V 129 " --> pdb=" O ASN V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 157 Processing helix chain 'V' and resid 160 through 178 Processing helix chain 'V' and resid 180 through 198 removed outlier: 3.572A pdb=" N ALA V 184 " --> pdb=" O ARG V 180 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS V 186 " --> pdb=" O LYS V 182 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE V 187 " --> pdb=" O GLU V 183 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR V 197 " --> pdb=" O GLN V 193 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN V 198 " --> pdb=" O LYS V 194 " (cutoff:3.500A) Processing helix chain 'V' and resid 200 through 222 removed outlier: 3.952A pdb=" N LEU V 205 " --> pdb=" O ARG V 201 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL V 206 " --> pdb=" O ALA V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 227 through 241 Processing helix chain 'V' and resid 244 through 261 Processing helix chain 'V' and resid 263 through 274 Processing helix chain 'V' and resid 281 through 299 Processing helix chain 'V' and resid 301 through 315 Processing helix chain 'V' and resid 321 through 340 Processing helix chain 'V' and resid 345 through 350 removed outlier: 3.789A pdb=" N ARG V 349 " --> pdb=" O ARG V 345 " (cutoff:3.500A) Processing helix chain 'V' and resid 353 through 370 Proline residue: V 359 - end of helix Processing helix chain 'V' and resid 371 through 390 removed outlier: 5.211A pdb=" N GLU V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LYS V 385 " --> pdb=" O GLN V 381 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE V 386 " --> pdb=" O PHE V 382 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN V 387 " --> pdb=" O GLY V 383 " (cutoff:3.500A) Processing helix chain 'V' and resid 391 through 400 Processing helix chain 'V' and resid 402 through 414 removed outlier: 3.757A pdb=" N GLY V 406 " --> pdb=" O VAL V 402 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 426 Processing helix chain 'V' and resid 430 through 444 Processing helix chain 'V' and resid 465 through 469 Processing helix chain 'V' and resid 470 through 494 removed outlier: 3.610A pdb=" N ALA V 493 " --> pdb=" O MET V 489 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET V 494 " --> pdb=" O SER V 490 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 49 Processing helix chain 'c' and resid 83 through 87 Processing helix chain 'c' and resid 88 through 103 Processing helix chain 'c' and resid 123 through 137 removed outlier: 4.091A pdb=" N LEU c 136 " --> pdb=" O SER c 132 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 170 removed outlier: 3.820A pdb=" N MET c 168 " --> pdb=" O ASN c 164 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 194 removed outlier: 3.633A pdb=" N LEU c 192 " --> pdb=" O SER c 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 195 through 199 removed outlier: 3.853A pdb=" N HIS c 199 " --> pdb=" O GLY c 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 195 through 199' Processing helix chain 'c' and resid 210 through 219 Processing helix chain 'c' and resid 224 through 230 removed outlier: 3.810A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) Processing helix chain 'c' and resid 233 through 261 removed outlier: 3.751A pdb=" N LYS c 239 " --> pdb=" O SER c 235 " (cutoff:3.500A) Processing helix chain 'c' and resid 280 through 309 Processing sheet with id=AA1, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'H' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'Y' and resid 345 through 348 removed outlier: 6.807A pdb=" N ARG Y 312 " --> pdb=" O THR Y 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'f' and resid 776 through 777 Processing sheet with id=AA5, first strand: chain 'f' and resid 781 through 782 Processing sheet with id=AA6, first strand: chain 'f' and resid 832 through 833 Processing sheet with id=AA7, first strand: chain 'f' and resid 863 through 869 removed outlier: 5.284A pdb=" N GLY f 864 " --> pdb=" O GLN f 848 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN f 848 " --> pdb=" O GLY f 864 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'U' and resid 744 through 746 Processing sheet with id=AA9, first strand: chain 'U' and resid 881 through 883 removed outlier: 5.488A pdb=" N CYS U 787 " --> pdb=" O GLY U 910 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE U 912 " --> pdb=" O CYS U 787 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE U 789 " --> pdb=" O ILE U 912 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'U' and resid 901 through 902 removed outlier: 3.667A pdb=" N GLN U 901 " --> pdb=" O LYS U 915 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 155 through 158 removed outlier: 3.880A pdb=" N ALA Z 137 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) removed outlier: 9.564A pdb=" N VAL Z 120 " --> pdb=" O ARG Z 90 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL Z 92 " --> pdb=" O VAL Z 120 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL Z 122 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TRP Z 94 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE Z 124 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N HIS Z 96 " --> pdb=" O ILE Z 124 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU Z 39 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N TRP Z 94 " --> pdb=" O GLY Z 37 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY Z 37 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N SER Z 42 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL Z 50 " --> pdb=" O SER Z 42 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Z' and resid 58 through 60 Processing sheet with id=AB4, first strand: chain 'a' and resid 324 through 325 removed outlier: 7.778A pdb=" N ILE a 324 " --> pdb=" O THR W 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'b' and resid 62 through 65 removed outlier: 5.518A pdb=" N THR b 63 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU b 51 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN b 48 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N SER b 5 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE b 110 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N MET b 7 " --> pdb=" O ILE b 110 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N PHE b 112 " --> pdb=" O MET b 7 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N CYS b 9 " --> pdb=" O PHE b 112 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ASP b 139 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE b 109 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE b 141 " --> pdb=" O ILE b 109 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ALA b 111 " --> pdb=" O ILE b 141 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL b 171 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE b 140 " --> pdb=" O VAL b 171 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 93 through 101 removed outlier: 5.836A pdb=" N CYS A 98 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ASN A 114 " --> pdb=" O CYS A 98 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 120 through 123 current: chain 'A' and resid 149 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 149 through 152 current: chain 'B' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 130 through 134 current: chain 'B' and resid 159 through 162 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 159 through 162 current: chain 'C' and resid 84 through 89 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 94 through 98 current: chain 'C' and resid 123 through 125 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 123 through 125 current: chain 'D' and resid 100 through 105 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 110 through 113 current: chain 'D' and resid 139 through 142 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 139 through 142 current: chain 'E' and resid 69 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 78 through 81 current: chain 'E' and resid 107 through 111 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 107 through 111 current: chain 'F' and resid 121 through 126 removed outlier: 3.821A pdb=" N GLN F 130 " --> pdb=" O THR F 126 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 130 through 134 current: chain 'F' and resid 160 through 163 Processing sheet with id=AB7, first strand: chain 'A' and resid 237 through 240 removed outlier: 6.436A pdb=" N ILE A 238 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASP A 275 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 240 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE A 272 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA A 320 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE A 274 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY A 211 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ILE A 341 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A 213 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 246 through 250 removed outlier: 6.499A pdb=" N THR B 246 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE B 283 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLY B 221 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE B 351 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE B 223 " --> pdb=" O ILE B 351 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 439 through 440 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 439 through 440 current: chain 'J' and resid 69 through 76 Processing sheet with id=AC1, first strand: chain 'C' and resid 213 through 214 removed outlier: 6.458A pdb=" N SER C 244 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE C 292 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE C 246 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ALA C 294 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N MET C 248 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLY C 185 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE C 315 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU C 187 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 337 through 338 removed outlier: 7.166A pdb=" N ASN C 337 " --> pdb=" O VAL C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AC4, first strand: chain 'D' and resid 226 through 230 removed outlier: 6.067A pdb=" N ALA D 226 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE D 263 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE D 228 " --> pdb=" O PHE D 263 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP D 265 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL D 230 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU D 266 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY D 201 " --> pdb=" O ARG D 329 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE D 331 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU D 203 " --> pdb=" O ILE D 331 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 170 through 171 removed outlier: 6.302A pdb=" N CYS E 170 " --> pdb=" O MET E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 247 through 252 removed outlier: 7.553A pdb=" N GLY F 222 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE F 352 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU F 224 " --> pdb=" O ILE F 352 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.616A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 69 through 73 removed outlier: 6.484A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 161 through 164 Processing sheet with id=AD1, first strand: chain 'I' and resid 72 through 74 removed outlier: 4.015A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY I 158 " --> pdb=" O ASP J 55 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 158 through 161 removed outlier: 3.584A pdb=" N VAL J 210 " --> pdb=" O LYS J 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 167 through 170 Processing sheet with id=AD4, first strand: chain 'K' and resid 67 through 69 Processing sheet with id=AD5, first strand: chain 'L' and resid 158 through 161 Processing sheet with id=AD6, first strand: chain 'L' and resid 63 through 67 removed outlier: 6.427A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP L 138 " --> pdb=" O GLY L 141 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 162 through 165 removed outlier: 3.937A pdb=" N GLY M 44 " --> pdb=" O CYS M 41 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 66 through 68 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 73 through 76 current: chain 'M' and resid 133 through 141 removed outlier: 3.647A pdb=" N MET M 150 " --> pdb=" O TYR M 158 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR M 158 " --> pdb=" O MET M 150 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 281 through 283 Processing sheet with id=AE1, first strand: chain 'g' and resid 98 through 104 Processing sheet with id=AE2, first strand: chain 'V' and resid 449 through 451 Processing sheet with id=AE3, first strand: chain 'c' and resid 30 through 34 removed outlier: 6.832A pdb=" N GLN c 30 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL c 69 " --> pdb=" O GLN c 30 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N TYR c 32 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASP c 71 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N SER c 34 " --> pdb=" O ASP c 71 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N PHE c 73 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LEU c 58 " --> pdb=" O ILE c 70 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL c 72 " --> pdb=" O LEU c 56 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU c 56 " --> pdb=" O VAL c 72 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ALA c 74 " --> pdb=" O MET c 54 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N MET c 54 " --> pdb=" O ALA c 74 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY c 110 " --> pdb=" O MET c 57 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY c 59 " --> pdb=" O VAL c 108 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL c 108 " --> pdb=" O GLY c 59 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL c 141 " --> pdb=" O MET c 107 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL c 109 " --> pdb=" O VAL c 141 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL c 143 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP c 111 " --> pdb=" O VAL c 143 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL c 145 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N HIS c 113 " --> pdb=" O VAL c 145 " (cutoff:3.500A) removed outlier: 10.283A pdb=" N ILE c 157 " --> pdb=" O ILE c 205 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE c 205 " --> pdb=" O ILE c 157 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL c 31 " --> pdb=" O ASN c 206 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG c 208 " --> pdb=" O VAL c 31 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ILE c 33 " --> pdb=" O ARG c 208 " (cutoff:3.500A) 3914 hydrogen bonds defined for protein. 11496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 26.84 Time building geometry restraints manager: 17.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23319 1.34 - 1.46: 14921 1.46 - 1.59: 32341 1.59 - 1.71: 19 1.71 - 1.83: 629 Bond restraints: 71229 Sorted by residual: bond pdb=" CB VAL Z 233 " pdb=" CG2 VAL Z 233 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.76e+00 bond pdb=" CA MET E 122 " pdb=" CB MET E 122 " ideal model delta sigma weight residual 1.531 1.579 -0.049 3.12e-02 1.03e+03 2.45e+00 bond pdb=" CA VAL M 53 " pdb=" CB VAL M 53 " ideal model delta sigma weight residual 1.530 1.546 -0.016 1.05e-02 9.07e+03 2.19e+00 bond pdb=" CB MET C 368 " pdb=" CG MET C 368 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.97e+00 bond pdb=" CD LYS B 258 " pdb=" CE LYS B 258 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.93e+00 ... (remaining 71224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 95794 3.52 - 7.03: 403 7.03 - 10.55: 45 10.55 - 14.07: 5 14.07 - 17.58: 1 Bond angle restraints: 96248 Sorted by residual: angle pdb=" CB MET Z 78 " pdb=" CG MET Z 78 " pdb=" SD MET Z 78 " ideal model delta sigma weight residual 112.70 130.28 -17.58 3.00e+00 1.11e-01 3.44e+01 angle pdb=" C LEU W 40 " pdb=" CA LEU W 40 " pdb=" CB LEU W 40 " ideal model delta sigma weight residual 117.23 110.15 7.08 1.36e+00 5.41e-01 2.71e+01 angle pdb=" N VAL F 335 " pdb=" CA VAL F 335 " pdb=" C VAL F 335 " ideal model delta sigma weight residual 112.96 108.68 4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" CB LYS B 258 " pdb=" CG LYS B 258 " pdb=" CD LYS B 258 " ideal model delta sigma weight residual 111.30 120.98 -9.68 2.30e+00 1.89e-01 1.77e+01 angle pdb=" CA LEU W 40 " pdb=" C LEU W 40 " pdb=" N GLN W 41 " ideal model delta sigma weight residual 119.98 116.57 3.41 8.50e-01 1.38e+00 1.61e+01 ... (remaining 96243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.24: 40146 26.24 - 52.47: 3240 52.47 - 78.71: 313 78.71 - 104.94: 64 104.94 - 131.18: 1 Dihedral angle restraints: 43764 sinusoidal: 17913 harmonic: 25851 Sorted by residual: dihedral pdb=" CB CYS G 115 " pdb=" SG CYS G 115 " pdb=" SG CYS G 154 " pdb=" CB CYS G 154 " ideal model delta sinusoidal sigma weight residual 93.00 160.00 -67.00 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 71.18 -131.18 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" CA PRO X 391 " pdb=" C PRO X 391 " pdb=" N PRO X 392 " pdb=" CA PRO X 392 " ideal model delta harmonic sigma weight residual -180.00 -157.83 -22.17 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 43761 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 9959 0.070 - 0.140: 1006 0.140 - 0.211: 26 0.211 - 0.281: 2 0.281 - 0.351: 2 Chirality restraints: 10995 Sorted by residual: chirality pdb=" CG LEU X 129 " pdb=" CB LEU X 129 " pdb=" CD1 LEU X 129 " pdb=" CD2 LEU X 129 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CB VAL E 374 " pdb=" CA VAL E 374 " pdb=" CG1 VAL E 374 " pdb=" CG2 VAL E 374 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CG LEU Y 84 " pdb=" CB LEU Y 84 " pdb=" CD1 LEU Y 84 " pdb=" CD2 LEU Y 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 10992 not shown) Planarity restraints: 12383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 322 " 0.014 2.00e-02 2.50e+03 2.83e-02 7.99e+00 pdb=" CG ASN A 322 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASN A 322 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 322 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE d 208 " -0.014 2.00e-02 2.50e+03 1.75e-02 5.38e+00 pdb=" CG PHE d 208 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 PHE d 208 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE d 208 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE d 208 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE d 208 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE d 208 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU b 22 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.78e+00 pdb=" N PRO b 23 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO b 23 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO b 23 " -0.031 5.00e-02 4.00e+02 ... (remaining 12380 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 687 2.55 - 3.14: 57500 3.14 - 3.72: 119473 3.72 - 4.31: 156845 4.31 - 4.90: 258688 Nonbonded interactions: 593193 Sorted by model distance: nonbonded pdb=" O2G ATP B 502 " pdb="MG MG B 503 " model vdw 1.962 2.170 nonbonded pdb=" OG1 THR B 233 " pdb="MG MG B 503 " model vdw 1.972 2.170 nonbonded pdb=" O3B ADP D 501 " pdb="MG MG D 502 " model vdw 1.996 2.170 nonbonded pdb=" O3B ATP F 501 " pdb="MG MG F 502 " model vdw 2.005 2.170 nonbonded pdb=" OG1 THR A 223 " pdb="MG MG A 501 " model vdw 2.012 2.170 ... (remaining 593188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 2.060 Check model and map are aligned: 0.400 Set scattering table: 0.490 Process input model: 131.750 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 71229 Z= 0.181 Angle : 0.628 17.583 96248 Z= 0.319 Chirality : 0.041 0.351 10995 Planarity : 0.004 0.055 12383 Dihedral : 17.617 131.175 27028 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.90 % Favored : 93.80 % Rotamer: Outliers : 3.45 % Allowed : 26.56 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.09), residues: 8774 helix: 1.41 (0.08), residues: 4894 sheet: -0.48 (0.19), residues: 793 loop : -0.82 (0.12), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP a 255 HIS 0.007 0.001 HIS a 69 PHE 0.041 0.001 PHE d 208 TYR 0.033 0.001 TYR B 295 ARG 0.009 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 999 time to evaluate : 6.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.6913 (tmt170) REVERT: H 163 MET cc_start: 0.8855 (mtm) cc_final: 0.8639 (ptp) REVERT: H 175 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: H 179 ASN cc_start: 0.7962 (t0) cc_final: 0.7577 (t0) REVERT: H 181 ASP cc_start: 0.8012 (p0) cc_final: 0.7496 (p0) REVERT: Y 143 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.6950 (t80) REVERT: f 58 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7342 (tmm) REVERT: f 196 MET cc_start: 0.7909 (mmm) cc_final: 0.7579 (mmm) REVERT: f 306 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6348 (pp20) REVERT: f 403 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6312 (ptmm) REVERT: f 407 MET cc_start: 0.3375 (mmm) cc_final: 0.3156 (mmm) REVERT: f 477 MET cc_start: 0.1211 (mmp) cc_final: 0.0274 (mmt) REVERT: f 483 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6519 (t80) REVERT: f 524 MET cc_start: 0.7642 (ptt) cc_final: 0.7404 (ppp) REVERT: f 564 LEU cc_start: 0.6957 (OUTLIER) cc_final: 0.6648 (tp) REVERT: f 759 LEU cc_start: 0.8659 (mt) cc_final: 0.8452 (tt) REVERT: f 825 MET cc_start: 0.6035 (tpp) cc_final: 0.5450 (tpp) REVERT: f 848 GLN cc_start: 0.8446 (mp-120) cc_final: 0.8214 (mp-120) REVERT: f 861 THR cc_start: 0.7457 (m) cc_final: 0.6893 (p) REVERT: X 126 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8037 (tmm-80) REVERT: X 129 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8657 (mt) REVERT: X 155 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.8078 (mpt-90) REVERT: X 229 TYR cc_start: 0.8602 (t80) cc_final: 0.8263 (t80) REVERT: U 59 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7735 (t80) REVERT: U 253 TYR cc_start: 0.7741 (t80) cc_final: 0.7501 (t80) REVERT: U 497 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9194 (mm) REVERT: Z 189 GLN cc_start: 0.7894 (mt0) cc_final: 0.7565 (mt0) REVERT: Z 234 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.8116 (m-80) REVERT: Z 235 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.8277 (p0) REVERT: a 87 MET cc_start: 0.6504 (ppp) cc_final: 0.5876 (ppp) REVERT: a 212 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7192 (t0) REVERT: b 4 GLU cc_start: 0.6708 (pp20) cc_final: 0.6387 (pp20) REVERT: b 51 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6656 (pp) REVERT: b 57 ASP cc_start: 0.6054 (m-30) cc_final: 0.5772 (m-30) REVERT: A 66 LYS cc_start: 0.8885 (tptt) cc_final: 0.8507 (tptp) REVERT: A 429 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.6164 (t80) REVERT: B 101 ASP cc_start: 0.8470 (t0) cc_final: 0.8096 (t0) REVERT: B 107 MET cc_start: 0.8642 (mtt) cc_final: 0.8411 (mtp) REVERT: B 166 ASP cc_start: 0.7454 (t0) cc_final: 0.7061 (p0) REVERT: B 405 MET cc_start: 0.8857 (mmp) cc_final: 0.8654 (mmm) REVERT: C 51 GLU cc_start: 0.8076 (tp30) cc_final: 0.7729 (tp30) REVERT: C 134 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8723 (tt) REVERT: C 273 MET cc_start: 0.7826 (tpp) cc_final: 0.7428 (ttm) REVERT: D 185 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9206 (mm) REVERT: D 415 GLU cc_start: 0.8169 (pm20) cc_final: 0.7667 (pm20) REVERT: E 180 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7020 (mttm) REVERT: E 220 ASN cc_start: 0.8577 (t0) cc_final: 0.8160 (p0) REVERT: E 264 MET cc_start: 0.8313 (ppp) cc_final: 0.7243 (mmp) REVERT: E 275 MET cc_start: 0.7318 (tpp) cc_final: 0.6205 (ptp) REVERT: E 323 HIS cc_start: 0.5746 (t70) cc_final: 0.4986 (t-90) REVERT: E 339 ASN cc_start: 0.7143 (p0) cc_final: 0.6830 (p0) REVERT: F 96 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7917 (mt) REVERT: G 74 GLU cc_start: 0.8150 (tt0) cc_final: 0.7764 (tt0) REVERT: I 108 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: K 224 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7288 (tm-30) REVERT: L 143 HIS cc_start: 0.8116 (m90) cc_final: 0.7496 (m170) REVERT: L 146 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8641 (pt0) REVERT: M 19 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7587 (ptt90) REVERT: e 35 ASP cc_start: 0.7830 (m-30) cc_final: 0.7615 (m-30) REVERT: e 50 ASP cc_start: 0.8583 (p0) cc_final: 0.8365 (p0) REVERT: d 156 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8388 (tt) REVERT: d 166 ARG cc_start: 0.7100 (ptp-170) cc_final: 0.6531 (mtm-85) REVERT: d 289 ARG cc_start: 0.7360 (ttp80) cc_final: 0.6972 (tmt-80) REVERT: W 88 MET cc_start: 0.9065 (mmm) cc_final: 0.8864 (mmt) REVERT: W 168 GLU cc_start: 0.8202 (pp20) cc_final: 0.7658 (pp20) REVERT: W 190 MET cc_start: 0.8080 (mtt) cc_final: 0.7627 (mtt) REVERT: W 235 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7548 (mt0) REVERT: W 256 ILE cc_start: 0.8005 (mm) cc_final: 0.7758 (mm) REVERT: V 77 GLU cc_start: 0.8608 (tp30) cc_final: 0.8299 (tm-30) REVERT: V 201 ARG cc_start: 0.7992 (tpt170) cc_final: 0.7747 (tpt-90) REVERT: V 204 ASP cc_start: 0.8373 (m-30) cc_final: 0.7936 (m-30) REVERT: V 485 ASP cc_start: 0.7825 (t0) cc_final: 0.7535 (t0) REVERT: V 495 ARG cc_start: 0.7303 (mmp80) cc_final: 0.5650 (tpp-160) REVERT: c 98 MET cc_start: 0.7134 (ttt) cc_final: 0.6349 (ttt) REVERT: c 118 PHE cc_start: 0.8256 (m-10) cc_final: 0.7975 (m-10) outliers start: 262 outliers final: 202 residues processed: 1190 average time/residue: 0.6428 time to fit residues: 1328.5172 Evaluate side-chains 1153 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 925 time to evaluate : 6.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 4 ARG Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain Y residue 30 GLU Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 112 CYS Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 173 ASP Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain f residue 58 MET Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 182 GLU Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 266 LEU Chi-restraints excluded: chain f residue 306 GLU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 352 HIS Chi-restraints excluded: chain f residue 403 LYS Chi-restraints excluded: chain f residue 414 LEU Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 455 VAL Chi-restraints excluded: chain f residue 466 LEU Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 518 THR Chi-restraints excluded: chain f residue 564 LEU Chi-restraints excluded: chain f residue 646 MET Chi-restraints excluded: chain f residue 736 THR Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 865 PHE Chi-restraints excluded: chain f residue 878 GLU Chi-restraints excluded: chain f residue 900 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 126 ARG Chi-restraints excluded: chain X residue 129 LEU Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 153 LEU Chi-restraints excluded: chain X residue 262 ASN Chi-restraints excluded: chain X residue 266 ASP Chi-restraints excluded: chain X residue 356 LEU Chi-restraints excluded: chain X residue 377 ILE Chi-restraints excluded: chain U residue 25 HIS Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 167 ILE Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 390 LEU Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 422 LEU Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 492 ASP Chi-restraints excluded: chain U residue 497 LEU Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain U residue 586 VAL Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 693 LEU Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 776 SER Chi-restraints excluded: chain U residue 786 THR Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 794 ASP Chi-restraints excluded: chain U residue 828 VAL Chi-restraints excluded: chain U residue 875 PHE Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 188 SER Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 234 PHE Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 289 GLU Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 47 ASP Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 163 TYR Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 212 ASN Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain a residue 219 HIS Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 261 LEU Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 272 ILE Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 327 VAL Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain a residue 375 LEU Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 132 LYS Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 270 CYS Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 205 ASP Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 289 LEU Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 184 ASP Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 239 ARG Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 235 GLN Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 131 GLN Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 166 ASN Chi-restraints excluded: chain c residue 230 THR Chi-restraints excluded: chain c residue 263 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 738 optimal weight: 20.0000 chunk 663 optimal weight: 4.9990 chunk 368 optimal weight: 2.9990 chunk 226 optimal weight: 20.0000 chunk 447 optimal weight: 0.5980 chunk 354 optimal weight: 5.9990 chunk 685 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 chunk 417 optimal weight: 0.8980 chunk 510 optimal weight: 10.0000 chunk 794 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 302 HIS ** f 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 650 GLN U 58 GLN ** U 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 373 ASN U 377 HIS ** U 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 ASN ** a 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN B 195 GLN B 332 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN E 45 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS ** E 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 HIS F 325 GLN F 333 ASN G 75 ASN I 155 ASN ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 23 GLN L 65 HIS ** d 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 235 GLN ** V 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 118 GLN V 266 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.112347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.084081 restraints weight = 176104.807| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.29 r_work: 0.3185 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 71229 Z= 0.250 Angle : 0.604 11.383 96248 Z= 0.310 Chirality : 0.041 0.215 10995 Planarity : 0.004 0.060 12383 Dihedral : 7.989 133.694 10167 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.73 % Favored : 94.02 % Rotamer: Outliers : 4.41 % Allowed : 24.48 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.09), residues: 8774 helix: 1.48 (0.07), residues: 4981 sheet: -0.64 (0.18), residues: 846 loop : -0.74 (0.12), residues: 2947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP a 255 HIS 0.007 0.001 HIS a 69 PHE 0.022 0.001 PHE b 86 TYR 0.029 0.001 TYR C 23 ARG 0.008 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 335 poor density : 988 time to evaluate : 6.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 ARG cc_start: 0.7812 (ptm160) cc_final: 0.6905 (ttt-90) REVERT: H 79 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8247 (mtm) REVERT: H 163 MET cc_start: 0.9310 (mtm) cc_final: 0.9087 (ptp) REVERT: H 175 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: H 179 ASN cc_start: 0.8451 (t0) cc_final: 0.7956 (t0) REVERT: H 181 ASP cc_start: 0.8574 (p0) cc_final: 0.7835 (p0) REVERT: Y 138 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8484 (mm) REVERT: Y 143 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.7228 (t80) REVERT: f 407 MET cc_start: 0.4122 (mmm) cc_final: 0.3758 (mmm) REVERT: f 477 MET cc_start: 0.1386 (mmp) cc_final: 0.0241 (mmt) REVERT: f 483 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6664 (t80) REVERT: f 524 MET cc_start: 0.7710 (ptt) cc_final: 0.7297 (ppp) REVERT: f 560 LEU cc_start: 0.7842 (tt) cc_final: 0.7583 (tt) REVERT: f 564 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6520 (tp) REVERT: f 646 MET cc_start: 0.6331 (OUTLIER) cc_final: 0.5923 (mmm) REVERT: f 825 MET cc_start: 0.6153 (tpp) cc_final: 0.5334 (tpp) REVERT: f 848 GLN cc_start: 0.8705 (mp-120) cc_final: 0.8467 (mp-120) REVERT: f 861 THR cc_start: 0.7401 (m) cc_final: 0.6830 (p) REVERT: X 129 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8957 (mt) REVERT: X 155 ARG cc_start: 0.8920 (mtt-85) cc_final: 0.8392 (mpt-90) REVERT: X 229 TYR cc_start: 0.9026 (t80) cc_final: 0.8624 (t80) REVERT: U 59 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7447 (t80) REVERT: U 242 LEU cc_start: 0.8571 (mp) cc_final: 0.8179 (tt) REVERT: U 497 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9148 (mm) REVERT: U 757 MET cc_start: 0.8877 (tmm) cc_final: 0.8628 (tmm) REVERT: U 901 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8340 (pp30) REVERT: Z 189 GLN cc_start: 0.8606 (mt0) cc_final: 0.8235 (mt0) REVERT: Z 234 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: a 87 MET cc_start: 0.6763 (ppp) cc_final: 0.6019 (ppp) REVERT: a 212 ASN cc_start: 0.8157 (m-40) cc_final: 0.7480 (t0) REVERT: b 4 GLU cc_start: 0.8132 (pp20) cc_final: 0.7573 (pp20) REVERT: b 11 ASP cc_start: 0.7307 (t0) cc_final: 0.6899 (t0) REVERT: A 66 LYS cc_start: 0.8861 (tptt) cc_final: 0.8272 (tptp) REVERT: A 123 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8537 (p) REVERT: A 276 GLU cc_start: 0.8541 (tp30) cc_final: 0.8173 (tp30) REVERT: A 429 TYR cc_start: 0.6710 (OUTLIER) cc_final: 0.6234 (t80) REVERT: B 101 ASP cc_start: 0.8924 (t0) cc_final: 0.8527 (t0) REVERT: B 299 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.8027 (t) REVERT: B 405 MET cc_start: 0.9041 (mmp) cc_final: 0.8800 (mmm) REVERT: C 51 GLU cc_start: 0.8677 (tp30) cc_final: 0.8303 (tp30) REVERT: C 138 MET cc_start: 0.8978 (mtm) cc_final: 0.8365 (mtm) REVERT: C 368 MET cc_start: 0.9437 (mmt) cc_final: 0.9234 (mmt) REVERT: D 185 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9269 (mm) REVERT: D 415 GLU cc_start: 0.8593 (pm20) cc_final: 0.8048 (pm20) REVERT: E 47 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8197 (mm) REVERT: E 180 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.6987 (mttm) REVERT: E 217 GLU cc_start: 0.8288 (mp0) cc_final: 0.7968 (mp0) REVERT: E 220 ASN cc_start: 0.8721 (t0) cc_final: 0.8341 (p0) REVERT: E 264 MET cc_start: 0.7962 (ppp) cc_final: 0.7085 (mmt) REVERT: E 275 MET cc_start: 0.6928 (tpp) cc_final: 0.5605 (ptp) REVERT: E 277 MET cc_start: 0.6975 (ttp) cc_final: 0.6254 (tmm) REVERT: E 323 HIS cc_start: 0.7220 (t70) cc_final: 0.6347 (t-90) REVERT: E 339 ASN cc_start: 0.7560 (p0) cc_final: 0.7119 (p0) REVERT: F 149 ASP cc_start: 0.8924 (OUTLIER) cc_final: 0.8608 (m-30) REVERT: F 356 MET cc_start: 0.9358 (mmt) cc_final: 0.9015 (mmt) REVERT: G 74 GLU cc_start: 0.8301 (tt0) cc_final: 0.7975 (tt0) REVERT: G 83 MET cc_start: 0.8896 (mtm) cc_final: 0.8619 (mtm) REVERT: G 193 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: I 149 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7791 (tp40) REVERT: J 114 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9061 (tp) REVERT: K 224 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7538 (tm-30) REVERT: K 228 MET cc_start: 0.4603 (OUTLIER) cc_final: 0.3349 (tmm) REVERT: L 140 MET cc_start: 0.7623 (mtp) cc_final: 0.5096 (mpp) REVERT: L 143 HIS cc_start: 0.8564 (m90) cc_final: 0.8076 (m170) REVERT: M 22 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.7525 (mp-120) REVERT: M 212 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7864 (pt0) REVERT: e 35 ASP cc_start: 0.8135 (m-30) cc_final: 0.7848 (m-30) REVERT: e 50 ASP cc_start: 0.8804 (p0) cc_final: 0.8546 (p0) REVERT: d 146 ASP cc_start: 0.8444 (p0) cc_final: 0.8176 (p0) REVERT: d 156 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8845 (tt) REVERT: d 166 ARG cc_start: 0.7734 (ptp-170) cc_final: 0.7305 (mtm-85) REVERT: d 289 ARG cc_start: 0.7354 (ttp80) cc_final: 0.6923 (tmt-80) REVERT: W 21 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8653 (t) REVERT: W 73 MET cc_start: 0.8780 (mtt) cc_final: 0.8199 (mmm) REVERT: W 168 GLU cc_start: 0.8581 (pp20) cc_final: 0.8108 (pp20) REVERT: W 312 MET cc_start: 0.8573 (mmm) cc_final: 0.8080 (mmm) REVERT: V 77 GLU cc_start: 0.8834 (tp30) cc_final: 0.8472 (tm-30) REVERT: V 99 ARG cc_start: 0.6079 (tpt170) cc_final: 0.5829 (tpt170) REVERT: V 201 ARG cc_start: 0.7856 (tpt170) cc_final: 0.7394 (tpp80) REVERT: V 204 ASP cc_start: 0.8182 (m-30) cc_final: 0.7670 (m-30) REVERT: V 339 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8711 (mp) REVERT: V 485 ASP cc_start: 0.9031 (t0) cc_final: 0.8480 (t0) REVERT: V 495 ARG cc_start: 0.7614 (mmp80) cc_final: 0.6188 (tpp-160) REVERT: c 30 GLN cc_start: 0.8570 (pt0) cc_final: 0.8350 (pt0) REVERT: c 98 MET cc_start: 0.8405 (ttt) cc_final: 0.7570 (ttm) REVERT: c 101 GLN cc_start: 0.8514 (mt0) cc_final: 0.8301 (mp10) REVERT: c 118 PHE cc_start: 0.8537 (m-10) cc_final: 0.8285 (m-10) REVERT: c 139 ARG cc_start: 0.6922 (mtp180) cc_final: 0.6717 (ptm160) REVERT: c 190 GLN cc_start: 0.9061 (mt0) cc_final: 0.8632 (pm20) outliers start: 335 outliers final: 187 residues processed: 1246 average time/residue: 0.6316 time to fit residues: 1366.6399 Evaluate side-chains 1110 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 895 time to evaluate : 6.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 125 ILE Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain f residue 182 GLU Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 305 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 414 LEU Chi-restraints excluded: chain f residue 466 LEU Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 564 LEU Chi-restraints excluded: chain f residue 646 MET Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 692 LEU Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 762 VAL Chi-restraints excluded: chain f residue 778 LEU Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 865 PHE Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 129 LEU Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 224 ASP Chi-restraints excluded: chain X residue 357 SER Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 408 SER Chi-restraints excluded: chain U residue 25 HIS Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 390 LEU Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 422 LEU Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 497 LEU Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain U residue 573 ASP Chi-restraints excluded: chain U residue 586 VAL Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 639 LEU Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 715 LYS Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 737 LEU Chi-restraints excluded: chain U residue 828 VAL Chi-restraints excluded: chain U residue 875 PHE Chi-restraints excluded: chain U residue 901 GLN Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 91 ILE Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 183 THR Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 234 PHE Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 163 TYR Chi-restraints excluded: chain a residue 177 LEU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 195 GLU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain a residue 219 HIS Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 287 ASN Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 327 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 84 ILE Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 132 LYS Chi-restraints excluded: chain b residue 143 PHE Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 212 GLU Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 350 VAL Chi-restraints excluded: chain W residue 18 VAL Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 274 VAL Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 437 SER Chi-restraints excluded: chain W residue 438 LEU Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 152 LYS Chi-restraints excluded: chain V residue 67 LEU Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 103 SER Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 313 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 216 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 587 optimal weight: 10.0000 chunk 306 optimal weight: 1.9990 chunk 348 optimal weight: 20.0000 chunk 804 optimal weight: 8.9990 chunk 771 optimal weight: 9.9990 chunk 378 optimal weight: 4.9990 chunk 426 optimal weight: 2.9990 chunk 539 optimal weight: 20.0000 chunk 271 optimal weight: 7.9990 chunk 634 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 136 HIS Y 302 HIS Y 381 GLN f 195 ASN f 202 HIS ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 44 GLN ** U 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 377 HIS ** U 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 453 HIS ** U 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 611 ASN ** U 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN B 332 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS ** E 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 ASN F 64 HIS F 255 GLN F 333 ASN G 75 ASN K 23 GLN K 118 ASN ** d 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.111380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.083018 restraints weight = 177206.183| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.28 r_work: 0.3163 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 71229 Z= 0.278 Angle : 0.602 9.863 96248 Z= 0.307 Chirality : 0.042 0.239 10995 Planarity : 0.004 0.056 12383 Dihedral : 7.215 135.158 9942 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.81 % Favored : 93.93 % Rotamer: Outliers : 5.41 % Allowed : 23.85 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.09), residues: 8774 helix: 1.47 (0.07), residues: 4969 sheet: -0.68 (0.18), residues: 850 loop : -0.75 (0.12), residues: 2955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP a 255 HIS 0.007 0.001 HIS a 69 PHE 0.022 0.001 PHE b 86 TYR 0.046 0.001 TYR a 173 ARG 0.007 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1397 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 411 poor density : 986 time to evaluate : 6.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8138 (mtm) REVERT: H 163 MET cc_start: 0.9340 (mtm) cc_final: 0.9120 (ptp) REVERT: H 175 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: H 179 ASN cc_start: 0.8469 (t0) cc_final: 0.7963 (t0) REVERT: H 181 ASP cc_start: 0.8570 (p0) cc_final: 0.7810 (p0) REVERT: Y 138 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8499 (mm) REVERT: Y 143 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.7226 (t80) REVERT: f 162 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9178 (mm) REVERT: f 325 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8206 (pp30) REVERT: f 407 MET cc_start: 0.4157 (mmm) cc_final: 0.3780 (mmm) REVERT: f 477 MET cc_start: 0.1419 (mmp) cc_final: 0.0341 (mmt) REVERT: f 483 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6621 (t80) REVERT: f 505 MET cc_start: 0.4287 (mmm) cc_final: 0.3959 (mmm) REVERT: f 524 MET cc_start: 0.7729 (ptt) cc_final: 0.7324 (ppp) REVERT: f 564 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6496 (tp) REVERT: f 646 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6000 (mmm) REVERT: f 669 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8091 (tt0) REVERT: f 825 MET cc_start: 0.6240 (tpp) cc_final: 0.5400 (tpp) REVERT: f 848 GLN cc_start: 0.8685 (mp-120) cc_final: 0.8373 (mp-120) REVERT: f 861 THR cc_start: 0.7518 (m) cc_final: 0.7014 (p) REVERT: X 75 PRO cc_start: 0.8632 (Cg_exo) cc_final: 0.8426 (Cg_endo) REVERT: X 129 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9062 (mt) REVERT: X 344 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.8344 (mtm110) REVERT: U 59 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7435 (t80) REVERT: U 242 LEU cc_start: 0.8550 (mp) cc_final: 0.8127 (tt) REVERT: U 497 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9134 (mm) REVERT: U 503 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8496 (mm-40) REVERT: U 560 MET cc_start: 0.8996 (mmp) cc_final: 0.8781 (mmp) REVERT: U 666 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8366 (mtpp) REVERT: U 757 MET cc_start: 0.8947 (tmm) cc_final: 0.8694 (tmm) REVERT: U 901 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8275 (pp30) REVERT: Z 189 GLN cc_start: 0.8603 (mt0) cc_final: 0.8232 (mt0) REVERT: Z 234 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: a 87 MET cc_start: 0.6775 (ppp) cc_final: 0.6046 (ppp) REVERT: a 94 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8553 (tp) REVERT: a 212 ASN cc_start: 0.8142 (m-40) cc_final: 0.7453 (t0) REVERT: a 271 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8180 (tttp) REVERT: a 291 LEU cc_start: 0.9013 (mp) cc_final: 0.8804 (mp) REVERT: b 4 GLU cc_start: 0.8141 (pp20) cc_final: 0.7566 (pp20) REVERT: b 56 ASN cc_start: 0.7893 (t0) cc_final: 0.7641 (t0) REVERT: b 57 ASP cc_start: 0.7374 (m-30) cc_final: 0.6882 (m-30) REVERT: A 66 LYS cc_start: 0.8826 (tptt) cc_final: 0.8497 (tptp) REVERT: A 123 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8582 (p) REVERT: A 144 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8378 (mtm-85) REVERT: A 276 GLU cc_start: 0.8601 (tp30) cc_final: 0.8181 (tp30) REVERT: A 429 TYR cc_start: 0.6739 (OUTLIER) cc_final: 0.6298 (t80) REVERT: B 101 ASP cc_start: 0.8926 (t0) cc_final: 0.8658 (t0) REVERT: B 130 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8627 (mt-10) REVERT: B 299 SER cc_start: 0.8563 (OUTLIER) cc_final: 0.8065 (t) REVERT: B 405 MET cc_start: 0.9049 (mmp) cc_final: 0.8804 (mmm) REVERT: C 51 GLU cc_start: 0.8661 (tp30) cc_final: 0.8417 (tp30) REVERT: C 369 TYR cc_start: 0.9080 (m-10) cc_final: 0.8828 (m-10) REVERT: D 80 LYS cc_start: 0.9333 (tppp) cc_final: 0.9045 (tppp) REVERT: D 185 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9235 (mm) REVERT: D 239 TYR cc_start: 0.8045 (m-80) cc_final: 0.7720 (m-80) REVERT: E 124 HIS cc_start: 0.5614 (OUTLIER) cc_final: 0.5359 (m-70) REVERT: E 217 GLU cc_start: 0.8338 (mp0) cc_final: 0.7908 (pt0) REVERT: E 220 ASN cc_start: 0.8723 (t0) cc_final: 0.8240 (p0) REVERT: E 264 MET cc_start: 0.7945 (ppp) cc_final: 0.7604 (ppp) REVERT: E 275 MET cc_start: 0.7002 (tpp) cc_final: 0.5667 (ptp) REVERT: E 277 MET cc_start: 0.7098 (ttp) cc_final: 0.6461 (tmm) REVERT: E 323 HIS cc_start: 0.7209 (t70) cc_final: 0.6281 (t-90) REVERT: E 333 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8215 (mmmt) REVERT: E 339 ASN cc_start: 0.7662 (p0) cc_final: 0.7236 (p0) REVERT: F 149 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8634 (m-30) REVERT: F 295 ARG cc_start: 0.7646 (ptt90) cc_final: 0.7337 (ptm160) REVERT: F 356 MET cc_start: 0.9342 (mmt) cc_final: 0.9018 (mmt) REVERT: G 74 GLU cc_start: 0.8318 (tt0) cc_final: 0.7974 (tt0) REVERT: G 83 MET cc_start: 0.8850 (mtm) cc_final: 0.8585 (mtm) REVERT: G 193 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: I 89 GLU cc_start: 0.8328 (tp30) cc_final: 0.8053 (tt0) REVERT: I 149 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.7844 (tp40) REVERT: I 235 GLN cc_start: 0.9024 (pt0) cc_final: 0.8725 (tm-30) REVERT: I 241 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8599 (mt-10) REVERT: J 114 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9051 (tp) REVERT: K 224 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7552 (tm-30) REVERT: K 228 MET cc_start: 0.4721 (OUTLIER) cc_final: 0.3753 (ttp) REVERT: L 140 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.5011 (mpp) REVERT: L 143 HIS cc_start: 0.8541 (m90) cc_final: 0.8004 (m170) REVERT: L 146 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8970 (pt0) REVERT: M 22 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.7575 (mp-120) REVERT: M 66 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9108 (mm) REVERT: M 212 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7825 (pt0) REVERT: e 50 ASP cc_start: 0.8846 (p0) cc_final: 0.8619 (p0) REVERT: d 156 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8852 (tt) REVERT: d 166 ARG cc_start: 0.7768 (ptp-170) cc_final: 0.7315 (mtm-85) REVERT: d 192 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8451 (mm) REVERT: d 289 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7059 (tmt-80) REVERT: W 21 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8707 (t) REVERT: W 73 MET cc_start: 0.8795 (mtt) cc_final: 0.8196 (mmm) REVERT: W 451 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7710 (ttp) REVERT: V 77 GLU cc_start: 0.8836 (tp30) cc_final: 0.8460 (tm-30) REVERT: V 84 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8446 (mmtm) REVERT: V 99 ARG cc_start: 0.6104 (tpt170) cc_final: 0.5772 (tpt170) REVERT: V 201 ARG cc_start: 0.7880 (tpt170) cc_final: 0.7383 (tpp80) REVERT: V 204 ASP cc_start: 0.8283 (m-30) cc_final: 0.7701 (m-30) REVERT: V 339 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8758 (mp) REVERT: V 485 ASP cc_start: 0.9062 (t0) cc_final: 0.8497 (t0) REVERT: V 495 ARG cc_start: 0.7583 (mmp80) cc_final: 0.6210 (tpp-160) REVERT: c 98 MET cc_start: 0.8298 (ttt) cc_final: 0.7954 (ttm) REVERT: c 101 GLN cc_start: 0.8386 (mt0) cc_final: 0.7993 (mp10) REVERT: c 118 PHE cc_start: 0.8505 (m-10) cc_final: 0.8242 (m-10) REVERT: c 139 ARG cc_start: 0.7219 (mtp180) cc_final: 0.6836 (ptm160) REVERT: c 236 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8392 (tm-30) outliers start: 411 outliers final: 256 residues processed: 1303 average time/residue: 0.6715 time to fit residues: 1526.6931 Evaluate side-chains 1185 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 297 poor density : 888 time to evaluate : 6.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain f residue 182 GLU Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 305 LEU Chi-restraints excluded: chain f residue 325 GLN Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 414 LEU Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 466 LEU Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 564 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 646 MET Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 669 GLU Chi-restraints excluded: chain f residue 692 LEU Chi-restraints excluded: chain f residue 736 THR Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 762 VAL Chi-restraints excluded: chain f residue 778 LEU Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 832 THR Chi-restraints excluded: chain f residue 865 PHE Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 129 LEU Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 224 ASP Chi-restraints excluded: chain X residue 344 ARG Chi-restraints excluded: chain X residue 357 SER Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 408 SER Chi-restraints excluded: chain U residue 25 HIS Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 160 LEU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 390 LEU Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 422 LEU Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 492 ASP Chi-restraints excluded: chain U residue 497 LEU Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain U residue 573 ASP Chi-restraints excluded: chain U residue 586 VAL Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 639 LEU Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 666 LYS Chi-restraints excluded: chain U residue 693 LEU Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 715 LYS Chi-restraints excluded: chain U residue 724 VAL Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 737 LEU Chi-restraints excluded: chain U residue 828 VAL Chi-restraints excluded: chain U residue 875 PHE Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain U residue 901 GLN Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 91 ILE Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 183 THR Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 234 PHE Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 289 GLU Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 177 LEU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 195 GLU Chi-restraints excluded: chain a residue 205 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain a residue 219 HIS Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 261 LEU Chi-restraints excluded: chain a residue 271 LYS Chi-restraints excluded: chain a residue 272 ILE Chi-restraints excluded: chain a residue 287 ASN Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 327 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 358 THR Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 84 ILE Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 143 PHE Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 255 GLN Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 239 ARG Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 66 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 212 GLU Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain d residue 350 VAL Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 274 VAL Chi-restraints excluded: chain W residue 286 LEU Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 385 SER Chi-restraints excluded: chain W residue 437 SER Chi-restraints excluded: chain W residue 438 LEU Chi-restraints excluded: chain W residue 439 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 152 LYS Chi-restraints excluded: chain V residue 67 LEU Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 313 LEU Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 216 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 593 optimal weight: 0.0270 chunk 293 optimal weight: 9.9990 chunk 700 optimal weight: 1.9990 chunk 528 optimal weight: 3.9990 chunk 652 optimal weight: 6.9990 chunk 832 optimal weight: 5.9990 chunk 634 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 747 optimal weight: 5.9990 chunk 549 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 302 HIS f 202 HIS ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 44 GLN X 329 ASN ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 377 HIS ** U 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 537 GLN ** U 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN ** b 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 HIS J 18 GLN ** d 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.112846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.084493 restraints weight = 176365.032| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.33 r_work: 0.3192 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 71229 Z= 0.190 Angle : 0.586 13.360 96248 Z= 0.296 Chirality : 0.041 0.243 10995 Planarity : 0.004 0.056 12383 Dihedral : 7.052 132.793 9915 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.77 % Favored : 93.97 % Rotamer: Outliers : 4.83 % Allowed : 24.71 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.09), residues: 8774 helix: 1.53 (0.07), residues: 4971 sheet: -0.63 (0.18), residues: 840 loop : -0.75 (0.12), residues: 2963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP a 255 HIS 0.007 0.001 HIS a 69 PHE 0.024 0.001 PHE d 198 TYR 0.042 0.001 TYR a 173 ARG 0.007 0.000 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1389 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 367 poor density : 1022 time to evaluate : 6.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 ARG cc_start: 0.7974 (ptm-80) cc_final: 0.7610 (ptm-80) REVERT: H 79 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8065 (mtm) REVERT: H 163 MET cc_start: 0.9274 (mtm) cc_final: 0.9071 (ptp) REVERT: H 175 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: H 179 ASN cc_start: 0.8416 (t0) cc_final: 0.7837 (t0) REVERT: H 181 ASP cc_start: 0.8555 (p0) cc_final: 0.7742 (p0) REVERT: Y 138 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8412 (mm) REVERT: Y 143 TYR cc_start: 0.8790 (OUTLIER) cc_final: 0.7260 (t80) REVERT: Y 299 MET cc_start: 0.8565 (mmp) cc_final: 0.8077 (mmp) REVERT: f 58 MET cc_start: 0.8248 (ttm) cc_final: 0.7749 (tmm) REVERT: f 162 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9168 (mm) REVERT: f 325 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8195 (pp30) REVERT: f 407 MET cc_start: 0.4014 (mmm) cc_final: 0.3650 (mmm) REVERT: f 483 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6504 (t80) REVERT: f 505 MET cc_start: 0.4794 (mmm) cc_final: 0.4530 (mmm) REVERT: f 524 MET cc_start: 0.7656 (ptt) cc_final: 0.7286 (ppp) REVERT: f 564 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6517 (tp) REVERT: f 646 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.5918 (mmm) REVERT: f 669 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: f 681 TYR cc_start: 0.8129 (m-10) cc_final: 0.7429 (m-10) REVERT: f 825 MET cc_start: 0.6249 (tpp) cc_final: 0.5472 (tpp) REVERT: f 848 GLN cc_start: 0.8752 (mp-120) cc_final: 0.8450 (mp-120) REVERT: f 861 THR cc_start: 0.7480 (m) cc_final: 0.6966 (p) REVERT: X 75 PRO cc_start: 0.8677 (Cg_exo) cc_final: 0.8454 (Cg_endo) REVERT: X 129 LEU cc_start: 0.9304 (mp) cc_final: 0.9100 (mt) REVERT: U 59 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7407 (t80) REVERT: U 194 ARG cc_start: 0.8676 (tpp80) cc_final: 0.8331 (tpt-90) REVERT: U 242 LEU cc_start: 0.8530 (mp) cc_final: 0.8128 (tt) REVERT: U 351 MET cc_start: 0.7179 (tpp) cc_final: 0.6940 (tpp) REVERT: U 497 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9132 (mm) REVERT: U 503 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8501 (mm-40) REVERT: U 894 MET cc_start: 0.7516 (ttm) cc_final: 0.7144 (tpp) REVERT: U 901 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8303 (pp30) REVERT: Z 189 GLN cc_start: 0.8609 (mt0) cc_final: 0.8308 (mt0) REVERT: Z 234 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8209 (m-80) REVERT: a 87 MET cc_start: 0.6710 (ppp) cc_final: 0.5987 (ppp) REVERT: a 94 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8582 (tp) REVERT: a 177 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8858 (mm) REVERT: a 212 ASN cc_start: 0.8076 (m110) cc_final: 0.7424 (t0) REVERT: a 269 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8346 (pp) REVERT: a 271 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8143 (ttmm) REVERT: b 4 GLU cc_start: 0.8077 (pp20) cc_final: 0.7495 (pp20) REVERT: b 56 ASN cc_start: 0.7940 (t0) cc_final: 0.7635 (t0) REVERT: b 57 ASP cc_start: 0.7276 (m-30) cc_final: 0.6712 (m-30) REVERT: b 161 ASN cc_start: 0.5880 (OUTLIER) cc_final: 0.5673 (p0) REVERT: A 66 LYS cc_start: 0.8808 (tptt) cc_final: 0.8478 (tptp) REVERT: A 123 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8543 (p) REVERT: A 429 TYR cc_start: 0.6697 (OUTLIER) cc_final: 0.6230 (t80) REVERT: B 101 ASP cc_start: 0.8919 (t0) cc_final: 0.8651 (t0) REVERT: B 130 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8598 (mt-10) REVERT: B 299 SER cc_start: 0.8494 (OUTLIER) cc_final: 0.8006 (t) REVERT: B 405 MET cc_start: 0.9048 (mmp) cc_final: 0.8807 (mmm) REVERT: C 51 GLU cc_start: 0.8617 (tp30) cc_final: 0.8358 (tp30) REVERT: C 134 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9009 (tt) REVERT: D 77 GLU cc_start: 0.8975 (tp30) cc_final: 0.8706 (tp30) REVERT: D 80 LYS cc_start: 0.9301 (tppp) cc_final: 0.9069 (tptp) REVERT: D 185 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9221 (mm) REVERT: D 239 TYR cc_start: 0.8050 (m-80) cc_final: 0.7716 (m-80) REVERT: E 180 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7369 (mttm) REVERT: E 220 ASN cc_start: 0.8690 (t0) cc_final: 0.8236 (p0) REVERT: E 234 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: E 264 MET cc_start: 0.7955 (ppp) cc_final: 0.7456 (ppp) REVERT: E 275 MET cc_start: 0.7108 (tpp) cc_final: 0.5748 (ptp) REVERT: E 277 MET cc_start: 0.7064 (ttp) cc_final: 0.6395 (tmm) REVERT: E 323 HIS cc_start: 0.7228 (t70) cc_final: 0.6354 (t-90) REVERT: E 333 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8193 (mmmt) REVERT: E 339 ASN cc_start: 0.7654 (p0) cc_final: 0.7203 (p0) REVERT: F 149 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8634 (m-30) REVERT: F 208 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7738 (m-70) REVERT: F 295 ARG cc_start: 0.7751 (ptt90) cc_final: 0.7520 (ptm160) REVERT: F 356 MET cc_start: 0.9370 (mmt) cc_final: 0.9015 (mmt) REVERT: G 74 GLU cc_start: 0.8299 (tt0) cc_final: 0.7990 (tt0) REVERT: G 83 MET cc_start: 0.8863 (mtm) cc_final: 0.8622 (mtm) REVERT: G 130 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: G 193 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: I 89 GLU cc_start: 0.8288 (tp30) cc_final: 0.7846 (tp30) REVERT: I 149 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7849 (tp40) REVERT: I 232 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8439 (mp0) REVERT: I 235 GLN cc_start: 0.8996 (pt0) cc_final: 0.8721 (tm-30) REVERT: I 241 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8581 (mt-10) REVERT: J 114 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8979 (tp) REVERT: J 148 ASP cc_start: 0.9043 (t0) cc_final: 0.8841 (t0) REVERT: K 224 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7504 (tm-30) REVERT: L 140 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.5032 (mpp) REVERT: L 143 HIS cc_start: 0.8474 (m90) cc_final: 0.7918 (m170) REVERT: L 146 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8926 (pt0) REVERT: M 22 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.7748 (mp-120) REVERT: M 191 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8347 (ptpp) REVERT: M 212 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: e 35 ASP cc_start: 0.8179 (m-30) cc_final: 0.7847 (m-30) REVERT: e 50 ASP cc_start: 0.8870 (p0) cc_final: 0.8649 (p0) REVERT: d 156 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8837 (tt) REVERT: d 166 ARG cc_start: 0.7761 (ptp-170) cc_final: 0.7288 (mtm-85) REVERT: d 289 ARG cc_start: 0.7380 (ttp80) cc_final: 0.7061 (tmt-80) REVERT: W 21 SER cc_start: 0.9114 (OUTLIER) cc_final: 0.8776 (t) REVERT: W 213 PHE cc_start: 0.8628 (t80) cc_final: 0.8370 (t80) REVERT: W 451 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7669 (ttp) REVERT: V 77 GLU cc_start: 0.8788 (tp30) cc_final: 0.8430 (tm-30) REVERT: V 84 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8402 (mmtm) REVERT: V 99 ARG cc_start: 0.5901 (tpt170) cc_final: 0.5634 (tpt170) REVERT: V 201 ARG cc_start: 0.7848 (tpt170) cc_final: 0.7464 (tpt-90) REVERT: V 204 ASP cc_start: 0.8226 (m-30) cc_final: 0.7693 (m-30) REVERT: V 220 PHE cc_start: 0.8600 (m-80) cc_final: 0.8206 (m-80) REVERT: V 339 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8696 (mp) REVERT: V 485 ASP cc_start: 0.9008 (t0) cc_final: 0.8449 (t0) REVERT: V 495 ARG cc_start: 0.7469 (mmp80) cc_final: 0.6118 (tpp-160) REVERT: c 30 GLN cc_start: 0.8717 (pt0) cc_final: 0.8452 (pt0) REVERT: c 118 PHE cc_start: 0.8509 (m-10) cc_final: 0.8238 (m-10) REVERT: c 139 ARG cc_start: 0.7181 (mtp180) cc_final: 0.6979 (ptm160) REVERT: c 236 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8381 (tm-30) outliers start: 367 outliers final: 225 residues processed: 1306 average time/residue: 0.6319 time to fit residues: 1433.9420 Evaluate side-chains 1189 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 268 poor density : 921 time to evaluate : 6.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Y residue 112 CYS Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 210 SER Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain f residue 182 GLU Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 305 LEU Chi-restraints excluded: chain f residue 325 GLN Chi-restraints excluded: chain f residue 352 HIS Chi-restraints excluded: chain f residue 414 LEU Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 455 VAL Chi-restraints excluded: chain f residue 466 LEU Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 564 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 646 MET Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 669 GLU Chi-restraints excluded: chain f residue 692 LEU Chi-restraints excluded: chain f residue 736 THR Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 865 PHE Chi-restraints excluded: chain f residue 900 LEU Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 99 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 224 ASP Chi-restraints excluded: chain X residue 357 SER Chi-restraints excluded: chain X residue 377 ILE Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 408 SER Chi-restraints excluded: chain U residue 25 HIS Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 147 TYR Chi-restraints excluded: chain U residue 160 LEU Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 356 THR Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 497 LEU Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain U residue 586 VAL Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 639 LEU Chi-restraints excluded: chain U residue 693 LEU Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 715 LYS Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 737 LEU Chi-restraints excluded: chain U residue 806 CYS Chi-restraints excluded: chain U residue 828 VAL Chi-restraints excluded: chain U residue 875 PHE Chi-restraints excluded: chain U residue 901 GLN Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 234 PHE Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 289 GLU Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 163 TYR Chi-restraints excluded: chain a residue 177 LEU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 195 GLU Chi-restraints excluded: chain a residue 205 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain a residue 219 HIS Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 271 LYS Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 327 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 143 PHE Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 232 GLU Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 146 GLN Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 239 ARG Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain M residue 212 GLU Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 350 VAL Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 274 VAL Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 385 SER Chi-restraints excluded: chain W residue 438 LEU Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 152 LYS Chi-restraints excluded: chain V residue 67 LEU Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 216 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 28 optimal weight: 3.9990 chunk 608 optimal weight: 10.0000 chunk 320 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 760 optimal weight: 9.9990 chunk 432 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 422 optimal weight: 5.9990 chunk 479 optimal weight: 5.9990 chunk 503 optimal weight: 2.9990 chunk 605 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 140 ASN Y 302 HIS ** f 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 329 ASN ** U 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 99 HIS ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN B 207 HIS B 306 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS E 316 HIS F 64 HIS F 255 GLN G 75 ASN I 84 ASN I 240 HIS J 18 GLN ** d 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 215 GLN ** g 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.111112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082382 restraints weight = 177521.460| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.19 r_work: 0.3157 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 71229 Z= 0.302 Angle : 0.620 12.376 96248 Z= 0.313 Chirality : 0.042 0.248 10995 Planarity : 0.004 0.057 12383 Dihedral : 7.005 136.743 9898 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.12 % Favored : 93.63 % Rotamer: Outliers : 5.58 % Allowed : 24.46 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.09), residues: 8774 helix: 1.47 (0.07), residues: 4980 sheet: -0.70 (0.18), residues: 848 loop : -0.77 (0.12), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP a 255 HIS 0.007 0.001 HIS a 69 PHE 0.032 0.001 PHE W 309 TYR 0.039 0.001 TYR a 173 ARG 0.010 0.000 ARG E 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1381 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 424 poor density : 957 time to evaluate : 6.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 ARG cc_start: 0.8085 (ptm-80) cc_final: 0.7269 (ttt-90) REVERT: H 79 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8210 (mtm) REVERT: H 163 MET cc_start: 0.9335 (mtm) cc_final: 0.9116 (ptp) REVERT: H 175 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: H 179 ASN cc_start: 0.8478 (t0) cc_final: 0.7904 (t0) REVERT: H 181 ASP cc_start: 0.8571 (p0) cc_final: 0.7822 (p0) REVERT: Y 138 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8505 (mm) REVERT: Y 143 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.7250 (t80) REVERT: f 162 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9181 (mm) REVERT: f 275 MET cc_start: 0.8212 (pmm) cc_final: 0.7993 (pmm) REVERT: f 325 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8201 (pp30) REVERT: f 407 MET cc_start: 0.4132 (mmm) cc_final: 0.3745 (mmm) REVERT: f 477 MET cc_start: 0.1627 (mmp) cc_final: 0.0483 (mmt) REVERT: f 483 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6647 (t80) REVERT: f 524 MET cc_start: 0.7688 (ptt) cc_final: 0.7304 (ppp) REVERT: f 564 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6581 (tp) REVERT: f 646 MET cc_start: 0.6501 (OUTLIER) cc_final: 0.5976 (mmm) REVERT: f 669 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: f 825 MET cc_start: 0.6278 (tpp) cc_final: 0.5476 (tpp) REVERT: f 848 GLN cc_start: 0.8679 (mp-120) cc_final: 0.8383 (mp-120) REVERT: f 861 THR cc_start: 0.7558 (m) cc_final: 0.7052 (p) REVERT: X 66 LEU cc_start: 0.7331 (mt) cc_final: 0.7109 (mt) REVERT: X 75 PRO cc_start: 0.8657 (Cg_exo) cc_final: 0.8447 (Cg_endo) REVERT: X 344 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8315 (mtm110) REVERT: U 59 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7348 (t80) REVERT: U 242 LEU cc_start: 0.8520 (mp) cc_final: 0.8060 (tt) REVERT: U 492 ASP cc_start: 0.9168 (OUTLIER) cc_final: 0.8894 (p0) REVERT: U 497 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9150 (mm) REVERT: U 503 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8513 (mm-40) REVERT: U 666 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8396 (mtpp) REVERT: U 894 MET cc_start: 0.7443 (ttm) cc_final: 0.7048 (tpp) REVERT: U 901 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8272 (pp30) REVERT: Z 156 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7751 (tm-30) REVERT: Z 234 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8268 (m-80) REVERT: a 87 MET cc_start: 0.6501 (ppp) cc_final: 0.5692 (ppp) REVERT: a 94 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8596 (tp) REVERT: a 173 TYR cc_start: 0.8533 (t80) cc_final: 0.8177 (t80) REVERT: a 177 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8834 (mm) REVERT: a 212 ASN cc_start: 0.8095 (m110) cc_final: 0.7430 (t0) REVERT: a 271 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8068 (ttmt) REVERT: b 4 GLU cc_start: 0.8116 (pp20) cc_final: 0.7535 (pp20) REVERT: b 56 ASN cc_start: 0.7978 (t0) cc_final: 0.7625 (t0) REVERT: b 57 ASP cc_start: 0.7469 (m-30) cc_final: 0.7003 (m-30) REVERT: A 66 LYS cc_start: 0.8812 (tptt) cc_final: 0.8501 (tptp) REVERT: A 123 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8582 (p) REVERT: A 144 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8391 (mtm-85) REVERT: A 276 GLU cc_start: 0.8588 (tp30) cc_final: 0.8176 (tp30) REVERT: A 429 TYR cc_start: 0.6666 (OUTLIER) cc_final: 0.6282 (t80) REVERT: B 101 ASP cc_start: 0.8912 (t0) cc_final: 0.8664 (t0) REVERT: B 130 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8611 (mt-10) REVERT: B 255 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8593 (pp) REVERT: B 299 SER cc_start: 0.8541 (OUTLIER) cc_final: 0.8029 (t) REVERT: B 405 MET cc_start: 0.9045 (mmp) cc_final: 0.8828 (mmm) REVERT: C 51 GLU cc_start: 0.8644 (tp30) cc_final: 0.8404 (tp30) REVERT: C 134 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8940 (tt) REVERT: C 138 MET cc_start: 0.9090 (mtm) cc_final: 0.8886 (mtm) REVERT: D 77 GLU cc_start: 0.8976 (tp30) cc_final: 0.8730 (tp30) REVERT: D 80 LYS cc_start: 0.9306 (tppp) cc_final: 0.9082 (tppp) REVERT: D 185 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9250 (mm) REVERT: D 239 TYR cc_start: 0.8090 (m-80) cc_final: 0.7764 (m-80) REVERT: D 248 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7461 (ttp80) REVERT: E 180 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7476 (mttm) REVERT: E 196 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6840 (mm) REVERT: E 220 ASN cc_start: 0.8682 (t0) cc_final: 0.8223 (p0) REVERT: E 238 ILE cc_start: 0.4513 (OUTLIER) cc_final: 0.4128 (pt) REVERT: E 275 MET cc_start: 0.7078 (tpp) cc_final: 0.6767 (tpp) REVERT: E 277 MET cc_start: 0.6953 (ttp) cc_final: 0.6496 (tmm) REVERT: E 323 HIS cc_start: 0.6983 (t70) cc_final: 0.6115 (t-90) REVERT: E 333 LYS cc_start: 0.8576 (mmmt) cc_final: 0.8189 (mmmt) REVERT: E 339 ASN cc_start: 0.7785 (p0) cc_final: 0.7342 (p0) REVERT: F 69 MET cc_start: 0.6933 (tpp) cc_final: 0.6689 (tpp) REVERT: F 149 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8646 (m-30) REVERT: F 175 MET cc_start: 0.8147 (mtt) cc_final: 0.7898 (mtt) REVERT: F 208 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7828 (m-70) REVERT: F 295 ARG cc_start: 0.7670 (ptt90) cc_final: 0.7435 (ptm160) REVERT: G 74 GLU cc_start: 0.8319 (tt0) cc_final: 0.7993 (tt0) REVERT: G 83 MET cc_start: 0.8858 (mtm) cc_final: 0.8586 (mtm) REVERT: G 193 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: I 79 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8668 (mm) REVERT: I 89 GLU cc_start: 0.8363 (tp30) cc_final: 0.7878 (tp30) REVERT: I 149 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7839 (tp40) REVERT: I 151 ASP cc_start: 0.8520 (m-30) cc_final: 0.8254 (m-30) REVERT: I 226 ARG cc_start: 0.8605 (mtp85) cc_final: 0.8404 (mtp85) REVERT: I 235 GLN cc_start: 0.9012 (pt0) cc_final: 0.8783 (tm-30) REVERT: I 241 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8641 (mt-10) REVERT: J 182 GLU cc_start: 0.8923 (tp30) cc_final: 0.8548 (tp30) REVERT: K 224 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7538 (tm-30) REVERT: K 228 MET cc_start: 0.4739 (OUTLIER) cc_final: 0.3613 (ttp) REVERT: L 140 MET cc_start: 0.7372 (mtp) cc_final: 0.4849 (mpp) REVERT: L 143 HIS cc_start: 0.8519 (m90) cc_final: 0.8014 (m90) REVERT: M 22 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.7715 (mp-120) REVERT: M 108 LEU cc_start: 0.8989 (tp) cc_final: 0.8674 (tt) REVERT: M 191 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8387 (ptpp) REVERT: e 35 ASP cc_start: 0.8129 (m-30) cc_final: 0.7803 (m-30) REVERT: e 50 ASP cc_start: 0.8872 (p0) cc_final: 0.8638 (p0) REVERT: d 156 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8883 (tt) REVERT: d 166 ARG cc_start: 0.7895 (ptp-170) cc_final: 0.7387 (mtm-85) REVERT: d 289 ARG cc_start: 0.7463 (ttp80) cc_final: 0.7164 (tmt-80) REVERT: W 21 SER cc_start: 0.9095 (OUTLIER) cc_final: 0.8729 (t) REVERT: W 213 PHE cc_start: 0.8659 (t80) cc_final: 0.8428 (t80) REVERT: W 215 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8235 (pm20) REVERT: W 451 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7644 (ttp) REVERT: V 77 GLU cc_start: 0.8851 (tp30) cc_final: 0.8469 (tm-30) REVERT: V 84 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8409 (mmtm) REVERT: V 99 ARG cc_start: 0.5872 (tpt170) cc_final: 0.5565 (tpt170) REVERT: V 201 ARG cc_start: 0.7908 (tpt170) cc_final: 0.7521 (tpt-90) REVERT: V 204 ASP cc_start: 0.8315 (m-30) cc_final: 0.7758 (m-30) REVERT: V 220 PHE cc_start: 0.8661 (m-80) cc_final: 0.8303 (m-80) REVERT: V 485 ASP cc_start: 0.9051 (t0) cc_final: 0.8477 (t0) REVERT: V 495 ARG cc_start: 0.7501 (mmp80) cc_final: 0.6257 (tpp-160) REVERT: c 85 GLU cc_start: 0.8537 (mp0) cc_final: 0.8094 (tp30) REVERT: c 101 GLN cc_start: 0.8622 (mt0) cc_final: 0.8325 (mp10) REVERT: c 118 PHE cc_start: 0.8515 (m-10) cc_final: 0.8240 (m-10) REVERT: c 236 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8361 (tm-30) outliers start: 424 outliers final: 285 residues processed: 1295 average time/residue: 0.6270 time to fit residues: 1412.4069 Evaluate side-chains 1233 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 330 poor density : 903 time to evaluate : 6.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Y residue 112 CYS Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 305 LEU Chi-restraints excluded: chain f residue 325 GLN Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 352 HIS Chi-restraints excluded: chain f residue 414 LEU Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 455 VAL Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 564 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 646 MET Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 669 GLU Chi-restraints excluded: chain f residue 692 LEU Chi-restraints excluded: chain f residue 736 THR Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 762 VAL Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 832 THR Chi-restraints excluded: chain f residue 865 PHE Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 99 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 153 LEU Chi-restraints excluded: chain X residue 224 ASP Chi-restraints excluded: chain X residue 261 LEU Chi-restraints excluded: chain X residue 344 ARG Chi-restraints excluded: chain X residue 357 SER Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 408 SER Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 147 TYR Chi-restraints excluded: chain U residue 160 LEU Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 323 LEU Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 356 THR Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 390 LEU Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 492 ASP Chi-restraints excluded: chain U residue 497 LEU Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain U residue 573 ASP Chi-restraints excluded: chain U residue 586 VAL Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 666 LYS Chi-restraints excluded: chain U residue 694 ILE Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 715 LYS Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 737 LEU Chi-restraints excluded: chain U residue 795 LEU Chi-restraints excluded: chain U residue 806 CYS Chi-restraints excluded: chain U residue 828 VAL Chi-restraints excluded: chain U residue 875 PHE Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain U residue 901 GLN Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 91 ILE Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 129 LYS Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 156 GLU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 234 PHE Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 289 GLU Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 163 TYR Chi-restraints excluded: chain a residue 177 LEU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 195 GLU Chi-restraints excluded: chain a residue 205 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain a residue 219 HIS Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 261 LEU Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 271 LYS Chi-restraints excluded: chain a residue 272 ILE Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 327 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 358 THR Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 143 PHE Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 239 ARG Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 80 ASN Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain d residue 140 GLN Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 350 VAL Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 215 GLN Chi-restraints excluded: chain W residue 274 VAL Chi-restraints excluded: chain W residue 286 LEU Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 385 SER Chi-restraints excluded: chain W residue 437 SER Chi-restraints excluded: chain W residue 438 LEU Chi-restraints excluded: chain W residue 439 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 152 LYS Chi-restraints excluded: chain V residue 67 LEU Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 313 LEU Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 216 MET Chi-restraints excluded: chain c residue 226 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 82 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 584 optimal weight: 0.0370 chunk 161 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 190 optimal weight: 0.0170 chunk 470 optimal weight: 6.9990 chunk 834 optimal weight: 4.9990 chunk 828 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 325 optimal weight: 10.0000 overall best weight: 2.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 140 ASN Y 302 HIS ** f 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 329 ASN U 25 HIS ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 754 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN ** b 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS ** E 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 HIS G 75 ASN J 18 GLN ** d 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 228 HIS ** g 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.111801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083274 restraints weight = 176640.015| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.23 r_work: 0.3175 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 71229 Z= 0.232 Angle : 0.605 11.222 96248 Z= 0.304 Chirality : 0.041 0.213 10995 Planarity : 0.004 0.059 12383 Dihedral : 6.945 134.899 9891 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.88 % Favored : 93.90 % Rotamer: Outliers : 5.46 % Allowed : 24.83 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.09), residues: 8774 helix: 1.47 (0.07), residues: 4985 sheet: -0.70 (0.18), residues: 843 loop : -0.76 (0.12), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP a 255 HIS 0.014 0.001 HIS E 316 PHE 0.026 0.001 PHE b 86 TYR 0.038 0.001 TYR B 295 ARG 0.010 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1385 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 415 poor density : 970 time to evaluate : 6.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8086 (mtm) REVERT: H 175 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: H 179 ASN cc_start: 0.8429 (t0) cc_final: 0.7862 (t0) REVERT: H 181 ASP cc_start: 0.8542 (p0) cc_final: 0.7790 (p0) REVERT: Y 138 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8487 (mm) REVERT: Y 143 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.7271 (t80) REVERT: Y 299 MET cc_start: 0.8672 (mmp) cc_final: 0.8067 (mmt) REVERT: f 162 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9173 (mm) REVERT: f 275 MET cc_start: 0.8207 (pmm) cc_final: 0.7988 (pmm) REVERT: f 325 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8194 (pp30) REVERT: f 407 MET cc_start: 0.4018 (mmm) cc_final: 0.3638 (mmm) REVERT: f 477 MET cc_start: 0.1593 (mmp) cc_final: 0.0493 (mmt) REVERT: f 483 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.6555 (t80) REVERT: f 524 MET cc_start: 0.7617 (ptt) cc_final: 0.7254 (ppp) REVERT: f 564 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6622 (tp) REVERT: f 646 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5923 (mmm) REVERT: f 669 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: f 681 TYR cc_start: 0.8018 (m-10) cc_final: 0.7671 (m-10) REVERT: f 729 MET cc_start: 0.8340 (mmm) cc_final: 0.8124 (mmm) REVERT: f 825 MET cc_start: 0.6312 (tpp) cc_final: 0.5532 (tpp) REVERT: f 848 GLN cc_start: 0.8724 (mp-120) cc_final: 0.8427 (mp-120) REVERT: f 861 THR cc_start: 0.7480 (m) cc_final: 0.6990 (p) REVERT: X 66 LEU cc_start: 0.7580 (mt) cc_final: 0.7237 (mt) REVERT: X 75 PRO cc_start: 0.8727 (Cg_exo) cc_final: 0.8526 (Cg_endo) REVERT: X 344 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8320 (mtm110) REVERT: U 59 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7358 (t80) REVERT: U 194 ARG cc_start: 0.8728 (tpp80) cc_final: 0.8433 (ttt180) REVERT: U 242 LEU cc_start: 0.8506 (mp) cc_final: 0.8068 (tt) REVERT: U 492 ASP cc_start: 0.9151 (OUTLIER) cc_final: 0.8884 (p0) REVERT: U 503 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8534 (mm-40) REVERT: U 556 MET cc_start: 0.7961 (mmm) cc_final: 0.7665 (mmt) REVERT: U 666 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8369 (mtpp) REVERT: U 725 MET cc_start: 0.7523 (mmt) cc_final: 0.7209 (mmt) REVERT: U 827 LYS cc_start: 0.5969 (OUTLIER) cc_final: 0.5485 (mtpt) REVERT: U 894 MET cc_start: 0.7538 (ttm) cc_final: 0.7146 (tpp) REVERT: U 901 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8311 (pp30) REVERT: Z 156 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7762 (tm-30) REVERT: Z 189 GLN cc_start: 0.8609 (mt0) cc_final: 0.8232 (mt0) REVERT: Z 234 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: a 87 MET cc_start: 0.6446 (ppp) cc_final: 0.5650 (ppp) REVERT: a 94 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8585 (tp) REVERT: a 173 TYR cc_start: 0.8625 (t80) cc_final: 0.8143 (t80) REVERT: a 177 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8839 (mm) REVERT: a 212 ASN cc_start: 0.8086 (m110) cc_final: 0.7429 (t0) REVERT: a 271 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8191 (ttmm) REVERT: a 278 MET cc_start: 0.7843 (tpp) cc_final: 0.7346 (tpp) REVERT: b 4 GLU cc_start: 0.8084 (pp20) cc_final: 0.7491 (pp20) REVERT: b 56 ASN cc_start: 0.7939 (t0) cc_final: 0.7645 (t0) REVERT: b 57 ASP cc_start: 0.7547 (m-30) cc_final: 0.7085 (m-30) REVERT: A 66 LYS cc_start: 0.8796 (tptt) cc_final: 0.8394 (tptp) REVERT: A 88 GLN cc_start: 0.8593 (pt0) cc_final: 0.8152 (pp30) REVERT: A 123 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8593 (p) REVERT: A 144 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8386 (mtm-85) REVERT: A 276 GLU cc_start: 0.8563 (tp30) cc_final: 0.8190 (tp30) REVERT: A 429 TYR cc_start: 0.6692 (OUTLIER) cc_final: 0.6293 (t80) REVERT: B 101 ASP cc_start: 0.8907 (t0) cc_final: 0.8663 (t0) REVERT: B 255 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8585 (pp) REVERT: B 299 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8015 (p) REVERT: B 405 MET cc_start: 0.9043 (mmp) cc_final: 0.8817 (mmm) REVERT: C 51 GLU cc_start: 0.8622 (tp30) cc_final: 0.8372 (tp30) REVERT: C 134 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8888 (tt) REVERT: C 138 MET cc_start: 0.9092 (mtm) cc_final: 0.8879 (mtm) REVERT: D 77 GLU cc_start: 0.8996 (tp30) cc_final: 0.8747 (tp30) REVERT: D 80 LYS cc_start: 0.9309 (tppp) cc_final: 0.9093 (tppp) REVERT: D 127 ASN cc_start: 0.9036 (m-40) cc_final: 0.8774 (t0) REVERT: D 185 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9249 (mm) REVERT: D 239 TYR cc_start: 0.8068 (m-80) cc_final: 0.7737 (m-80) REVERT: D 248 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7536 (ttp80) REVERT: E 180 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7463 (mttm) REVERT: E 196 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6895 (mm) REVERT: E 238 ILE cc_start: 0.4354 (OUTLIER) cc_final: 0.4015 (pt) REVERT: E 275 MET cc_start: 0.7174 (tpp) cc_final: 0.6848 (tpp) REVERT: E 277 MET cc_start: 0.6917 (ttp) cc_final: 0.6543 (tmm) REVERT: E 323 HIS cc_start: 0.7092 (t70) cc_final: 0.6219 (t-90) REVERT: E 333 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8222 (mmmt) REVERT: E 339 ASN cc_start: 0.7780 (p0) cc_final: 0.7330 (p0) REVERT: F 75 GLU cc_start: 0.8815 (tp30) cc_final: 0.8468 (tp30) REVERT: F 149 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8635 (m-30) REVERT: F 175 MET cc_start: 0.8249 (mtt) cc_final: 0.8002 (mtt) REVERT: F 208 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7865 (m-70) REVERT: F 295 ARG cc_start: 0.7707 (ptt90) cc_final: 0.7460 (ptm160) REVERT: G 74 GLU cc_start: 0.8304 (tt0) cc_final: 0.7975 (tt0) REVERT: G 83 MET cc_start: 0.8846 (mtm) cc_final: 0.8585 (mtm) REVERT: G 193 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: I 79 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8609 (mm) REVERT: I 89 GLU cc_start: 0.8360 (tp30) cc_final: 0.7863 (tp30) REVERT: I 149 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7871 (tp40) REVERT: I 235 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8778 (tm-30) REVERT: I 241 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8626 (mt-10) REVERT: J 114 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9021 (tp) REVERT: J 182 GLU cc_start: 0.8946 (tp30) cc_final: 0.8623 (tp30) REVERT: J 224 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8233 (tm-30) REVERT: K 224 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7513 (tm-30) REVERT: K 228 MET cc_start: 0.4672 (OUTLIER) cc_final: 0.3448 (tmm) REVERT: L 140 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.4850 (mpp) REVERT: L 143 HIS cc_start: 0.8479 (m90) cc_final: 0.7951 (m90) REVERT: M 22 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.7764 (mp-120) REVERT: M 108 LEU cc_start: 0.8988 (tp) cc_final: 0.8690 (tt) REVERT: M 191 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8344 (ptpp) REVERT: O 64 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8316 (tp30) REVERT: e 35 ASP cc_start: 0.8121 (m-30) cc_final: 0.7796 (m-30) REVERT: e 50 ASP cc_start: 0.8888 (p0) cc_final: 0.8660 (p0) REVERT: d 156 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8898 (tt) REVERT: d 166 ARG cc_start: 0.7882 (ptp-170) cc_final: 0.7360 (mtm-85) REVERT: d 289 ARG cc_start: 0.7275 (ttp80) cc_final: 0.6811 (tmt-80) REVERT: W 21 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8692 (t) REVERT: W 213 PHE cc_start: 0.8611 (t80) cc_final: 0.8301 (t80) REVERT: W 451 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7944 (mtt) REVERT: g 154 MET cc_start: 0.7289 (tpp) cc_final: 0.7075 (tpp) REVERT: V 77 GLU cc_start: 0.8820 (tp30) cc_final: 0.8454 (tm-30) REVERT: V 84 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8407 (mmtm) REVERT: V 99 ARG cc_start: 0.5856 (tpt170) cc_final: 0.5654 (tpt170) REVERT: V 201 ARG cc_start: 0.7824 (tpt170) cc_final: 0.7441 (tpt-90) REVERT: V 204 ASP cc_start: 0.8295 (m-30) cc_final: 0.7732 (m-30) REVERT: V 220 PHE cc_start: 0.8756 (m-80) cc_final: 0.8391 (m-80) REVERT: V 339 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8726 (mp) REVERT: V 485 ASP cc_start: 0.9048 (t0) cc_final: 0.8471 (t0) REVERT: V 495 ARG cc_start: 0.7356 (mmp80) cc_final: 0.6165 (tpp-160) REVERT: c 101 GLN cc_start: 0.8591 (mt0) cc_final: 0.8257 (mp10) REVERT: c 118 PHE cc_start: 0.8500 (m-10) cc_final: 0.8229 (m-10) REVERT: c 236 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8315 (tm-30) outliers start: 415 outliers final: 294 residues processed: 1291 average time/residue: 0.6284 time to fit residues: 1407.5313 Evaluate side-chains 1252 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 343 poor density : 909 time to evaluate : 6.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Y residue 112 CYS Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 245 ASN Chi-restraints excluded: chain f residue 266 LEU Chi-restraints excluded: chain f residue 296 PHE Chi-restraints excluded: chain f residue 305 LEU Chi-restraints excluded: chain f residue 325 GLN Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 352 HIS Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 455 VAL Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 562 LEU Chi-restraints excluded: chain f residue 564 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 646 MET Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 669 GLU Chi-restraints excluded: chain f residue 692 LEU Chi-restraints excluded: chain f residue 736 THR Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 762 VAL Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 865 PHE Chi-restraints excluded: chain f residue 900 LEU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 99 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 111 LEU Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 153 LEU Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 224 ASP Chi-restraints excluded: chain X residue 261 LEU Chi-restraints excluded: chain X residue 344 ARG Chi-restraints excluded: chain X residue 357 SER Chi-restraints excluded: chain X residue 377 ILE Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 408 SER Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 123 LYS Chi-restraints excluded: chain U residue 147 TYR Chi-restraints excluded: chain U residue 160 LEU Chi-restraints excluded: chain U residue 183 LEU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 356 THR Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 390 LEU Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 492 ASP Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain U residue 573 ASP Chi-restraints excluded: chain U residue 586 VAL Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 666 LYS Chi-restraints excluded: chain U residue 693 LEU Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 715 LYS Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 737 LEU Chi-restraints excluded: chain U residue 795 LEU Chi-restraints excluded: chain U residue 806 CYS Chi-restraints excluded: chain U residue 827 LYS Chi-restraints excluded: chain U residue 828 VAL Chi-restraints excluded: chain U residue 875 PHE Chi-restraints excluded: chain U residue 901 GLN Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 91 ILE Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 152 SER Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 156 GLU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 183 THR Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 234 PHE Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 289 GLU Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 177 LEU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 195 GLU Chi-restraints excluded: chain a residue 205 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain a residue 219 HIS Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 261 LEU Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 271 LYS Chi-restraints excluded: chain a residue 272 ILE Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 327 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 358 THR Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 143 PHE Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain b residue 169 HIS Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 235 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain L residue 239 ARG Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 80 ASN Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain d residue 140 GLN Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 350 VAL Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 250 ILE Chi-restraints excluded: chain W residue 274 VAL Chi-restraints excluded: chain W residue 286 LEU Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 385 SER Chi-restraints excluded: chain W residue 437 SER Chi-restraints excluded: chain W residue 438 LEU Chi-restraints excluded: chain W residue 439 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain g residue 130 VAL Chi-restraints excluded: chain g residue 152 LYS Chi-restraints excluded: chain V residue 67 LEU Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 313 LEU Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 216 MET Chi-restraints excluded: chain c residue 226 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 532 optimal weight: 6.9990 chunk 201 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 646 optimal weight: 20.0000 chunk 554 optimal weight: 3.9990 chunk 236 optimal weight: 0.8980 chunk 810 optimal weight: 20.0000 chunk 539 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 chunk 183 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 140 ASN Y 302 HIS ** f 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 329 ASN ** U 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 30 GLN b 101 GLN b 137 ASN b 161 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS E 316 HIS F 64 HIS ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN J 18 GLN ** K 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.110217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.082313 restraints weight = 177264.806| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.02 r_work: 0.3147 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 71229 Z= 0.330 Angle : 0.642 13.158 96248 Z= 0.323 Chirality : 0.043 0.220 10995 Planarity : 0.004 0.057 12383 Dihedral : 6.994 137.685 9885 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.26 % Favored : 93.54 % Rotamer: Outliers : 5.57 % Allowed : 24.93 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.09), residues: 8774 helix: 1.39 (0.07), residues: 4999 sheet: -0.75 (0.18), residues: 857 loop : -0.81 (0.12), residues: 2918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP a 255 HIS 0.007 0.001 HIS a 69 PHE 0.024 0.001 PHE b 86 TYR 0.039 0.002 TYR B 295 ARG 0.008 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1347 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 423 poor density : 924 time to evaluate : 6.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8270 (mtm) REVERT: H 175 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: H 179 ASN cc_start: 0.8471 (t0) cc_final: 0.7895 (t0) REVERT: H 181 ASP cc_start: 0.8558 (p0) cc_final: 0.7826 (p0) REVERT: Y 138 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8512 (mm) REVERT: Y 143 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.7291 (t80) REVERT: Y 299 MET cc_start: 0.8561 (mmp) cc_final: 0.8234 (mmt) REVERT: f 162 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9180 (mm) REVERT: f 196 MET cc_start: 0.8562 (mmm) cc_final: 0.8152 (mmm) REVERT: f 275 MET cc_start: 0.8246 (pmm) cc_final: 0.8037 (pmm) REVERT: f 325 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8223 (pp30) REVERT: f 390 LEU cc_start: 0.8546 (tp) cc_final: 0.8343 (tp) REVERT: f 407 MET cc_start: 0.4254 (mmm) cc_final: 0.3857 (mmm) REVERT: f 477 MET cc_start: 0.1673 (mmp) cc_final: 0.0545 (mmt) REVERT: f 483 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6619 (t80) REVERT: f 487 LEU cc_start: 0.8664 (mt) cc_final: 0.7854 (mt) REVERT: f 524 MET cc_start: 0.7630 (ptt) cc_final: 0.7292 (ppp) REVERT: f 543 MET cc_start: 0.7534 (mmp) cc_final: 0.7303 (mmp) REVERT: f 564 LEU cc_start: 0.6932 (tp) cc_final: 0.6535 (tp) REVERT: f 669 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: f 681 TYR cc_start: 0.8101 (m-10) cc_final: 0.7727 (m-10) REVERT: f 803 PHE cc_start: 0.8829 (m-80) cc_final: 0.8579 (m-80) REVERT: f 825 MET cc_start: 0.6420 (tpp) cc_final: 0.5637 (tpp) REVERT: f 848 GLN cc_start: 0.8682 (mp-120) cc_final: 0.8374 (mp-120) REVERT: f 861 THR cc_start: 0.7555 (m) cc_final: 0.7072 (p) REVERT: X 66 LEU cc_start: 0.7630 (mt) cc_final: 0.7309 (mt) REVERT: X 344 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8258 (mtm110) REVERT: U 59 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7403 (t80) REVERT: U 194 ARG cc_start: 0.8675 (tpp80) cc_final: 0.8344 (tpt-90) REVERT: U 374 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.8095 (p) REVERT: U 492 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8936 (p0) REVERT: U 503 GLN cc_start: 0.8896 (mm-40) cc_final: 0.8551 (mm-40) REVERT: U 666 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8439 (mtpp) REVERT: U 725 MET cc_start: 0.7544 (mmt) cc_final: 0.7218 (mmt) REVERT: U 894 MET cc_start: 0.7422 (ttm) cc_final: 0.6999 (tpp) REVERT: U 901 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8247 (pp30) REVERT: Z 90 ARG cc_start: 0.7973 (mmm160) cc_final: 0.7667 (mmm-85) REVERT: Z 121 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8308 (tp) REVERT: Z 156 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7752 (tm-30) REVERT: Z 189 GLN cc_start: 0.8642 (mt0) cc_final: 0.8256 (mt0) REVERT: Z 234 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8349 (m-80) REVERT: a 87 MET cc_start: 0.6503 (ppp) cc_final: 0.5596 (ppp) REVERT: a 92 VAL cc_start: 0.9011 (p) cc_final: 0.8793 (p) REVERT: a 173 TYR cc_start: 0.8709 (t80) cc_final: 0.8096 (t80) REVERT: a 177 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8867 (mm) REVERT: a 212 ASN cc_start: 0.8189 (m110) cc_final: 0.7525 (t0) REVERT: a 271 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8214 (ttmt) REVERT: a 291 LEU cc_start: 0.9146 (mp) cc_final: 0.8926 (mp) REVERT: a 335 TRP cc_start: 0.7563 (t-100) cc_final: 0.7312 (t-100) REVERT: b 4 GLU cc_start: 0.8097 (pp20) cc_final: 0.7472 (pp20) REVERT: b 56 ASN cc_start: 0.7962 (t0) cc_final: 0.7589 (t0) REVERT: b 57 ASP cc_start: 0.7538 (m-30) cc_final: 0.7150 (m-30) REVERT: A 66 LYS cc_start: 0.8832 (tptt) cc_final: 0.8426 (tptp) REVERT: A 88 GLN cc_start: 0.8631 (pt0) cc_final: 0.8176 (pp30) REVERT: A 144 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8327 (mtm-85) REVERT: A 276 GLU cc_start: 0.8477 (tp30) cc_final: 0.8117 (tp30) REVERT: A 429 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.6257 (t80) REVERT: B 55 HIS cc_start: 0.8874 (OUTLIER) cc_final: 0.8599 (p-80) REVERT: B 74 MET cc_start: 0.9313 (mmm) cc_final: 0.9049 (mtt) REVERT: B 255 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8651 (pp) REVERT: B 299 SER cc_start: 0.8590 (OUTLIER) cc_final: 0.8077 (p) REVERT: B 307 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8952 (mtm-85) REVERT: B 405 MET cc_start: 0.9043 (mmp) cc_final: 0.8829 (mmm) REVERT: C 51 GLU cc_start: 0.8635 (tp30) cc_final: 0.8299 (tp30) REVERT: C 134 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8885 (tt) REVERT: C 138 MET cc_start: 0.9113 (mtm) cc_final: 0.8888 (mtm) REVERT: C 375 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7006 (ptm-80) REVERT: D 80 LYS cc_start: 0.9304 (tppp) cc_final: 0.9094 (tppp) REVERT: D 185 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9244 (mm) REVERT: D 239 TYR cc_start: 0.8110 (m-80) cc_final: 0.7790 (m-80) REVERT: D 248 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7547 (ttp80) REVERT: E 180 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7462 (mttm) REVERT: E 196 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6823 (mm) REVERT: E 234 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.5966 (mm-30) REVERT: E 275 MET cc_start: 0.7075 (tpp) cc_final: 0.6787 (tpp) REVERT: E 277 MET cc_start: 0.6961 (ttp) cc_final: 0.6621 (tmm) REVERT: E 323 HIS cc_start: 0.6832 (OUTLIER) cc_final: 0.5952 (t-90) REVERT: E 339 ASN cc_start: 0.7882 (p0) cc_final: 0.7440 (p0) REVERT: F 75 GLU cc_start: 0.8813 (tp30) cc_final: 0.8525 (tp30) REVERT: F 96 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8229 (mt) REVERT: F 149 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8648 (m-30) REVERT: F 175 MET cc_start: 0.8288 (mtt) cc_final: 0.8064 (mtt) REVERT: F 208 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7793 (m-70) REVERT: F 295 ARG cc_start: 0.7712 (ptt90) cc_final: 0.7460 (ptm160) REVERT: F 356 MET cc_start: 0.9286 (mmt) cc_final: 0.8890 (mmt) REVERT: G 74 GLU cc_start: 0.8357 (tt0) cc_final: 0.8036 (tt0) REVERT: G 83 MET cc_start: 0.8881 (mtm) cc_final: 0.8627 (mtm) REVERT: G 193 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: I 79 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8682 (mm) REVERT: I 89 GLU cc_start: 0.8428 (tp30) cc_final: 0.7955 (tp30) REVERT: I 149 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7843 (tp40) REVERT: I 235 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8833 (tm-30) REVERT: I 241 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8603 (mt-10) REVERT: J 114 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9077 (tp) REVERT: J 182 GLU cc_start: 0.8950 (tp30) cc_final: 0.8520 (tp30) REVERT: K 168 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8252 (tpt90) REVERT: K 182 GLN cc_start: 0.8823 (mt0) cc_final: 0.8366 (mt0) REVERT: K 189 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8348 (mtm) REVERT: K 224 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7501 (tm-30) REVERT: K 228 MET cc_start: 0.4721 (OUTLIER) cc_final: 0.3563 (ttp) REVERT: L 55 GLU cc_start: 0.8126 (mp0) cc_final: 0.7660 (mp0) REVERT: L 140 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.4879 (mpp) REVERT: L 143 HIS cc_start: 0.8501 (m90) cc_final: 0.7931 (m170) REVERT: M 22 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7728 (mp-120) REVERT: M 191 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8396 (ptpp) REVERT: e 50 ASP cc_start: 0.8879 (p0) cc_final: 0.8662 (p0) REVERT: d 156 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8896 (tt) REVERT: d 166 ARG cc_start: 0.7915 (ptp-170) cc_final: 0.7395 (mtm-85) REVERT: d 289 ARG cc_start: 0.7487 (ttp80) cc_final: 0.7165 (tmt-80) REVERT: W 21 SER cc_start: 0.9070 (OUTLIER) cc_final: 0.8691 (t) REVERT: W 451 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7956 (mtt) REVERT: g 154 MET cc_start: 0.7458 (tpp) cc_final: 0.7161 (tpp) REVERT: V 77 GLU cc_start: 0.8856 (tp30) cc_final: 0.8463 (tm-30) REVERT: V 84 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8433 (mmtm) REVERT: V 201 ARG cc_start: 0.7882 (tpt170) cc_final: 0.7400 (tpp80) REVERT: V 204 ASP cc_start: 0.8323 (m-30) cc_final: 0.7732 (m-30) REVERT: V 220 PHE cc_start: 0.8730 (m-80) cc_final: 0.8375 (m-80) REVERT: V 339 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8783 (mp) REVERT: V 463 MET cc_start: 0.8020 (mmp) cc_final: 0.7213 (mpp) REVERT: V 485 ASP cc_start: 0.9046 (t0) cc_final: 0.8480 (t0) REVERT: V 495 ARG cc_start: 0.7460 (mmp80) cc_final: 0.6315 (tpp-160) REVERT: c 118 PHE cc_start: 0.8520 (m-10) cc_final: 0.8234 (m-10) REVERT: c 236 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8331 (tm-30) outliers start: 423 outliers final: 301 residues processed: 1254 average time/residue: 0.6331 time to fit residues: 1380.8635 Evaluate side-chains 1231 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 353 poor density : 878 time to evaluate : 6.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain H residue 186 ASP Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Y residue 112 CYS Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 245 ASN Chi-restraints excluded: chain f residue 266 LEU Chi-restraints excluded: chain f residue 296 PHE Chi-restraints excluded: chain f residue 305 LEU Chi-restraints excluded: chain f residue 325 GLN Chi-restraints excluded: chain f residue 337 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 352 HIS Chi-restraints excluded: chain f residue 414 LEU Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 455 VAL Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 562 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 669 GLU Chi-restraints excluded: chain f residue 692 LEU Chi-restraints excluded: chain f residue 736 THR Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 762 VAL Chi-restraints excluded: chain f residue 778 LEU Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 865 PHE Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 99 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 153 LEU Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 224 ASP Chi-restraints excluded: chain X residue 261 LEU Chi-restraints excluded: chain X residue 344 ARG Chi-restraints excluded: chain X residue 357 SER Chi-restraints excluded: chain X residue 377 ILE Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 408 SER Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 123 LYS Chi-restraints excluded: chain U residue 160 LEU Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 356 THR Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 390 LEU Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 492 ASP Chi-restraints excluded: chain U residue 545 LEU Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain U residue 573 ASP Chi-restraints excluded: chain U residue 586 VAL Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 666 LYS Chi-restraints excluded: chain U residue 694 ILE Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 737 LEU Chi-restraints excluded: chain U residue 795 LEU Chi-restraints excluded: chain U residue 806 CYS Chi-restraints excluded: chain U residue 827 LYS Chi-restraints excluded: chain U residue 828 VAL Chi-restraints excluded: chain U residue 875 PHE Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain U residue 901 GLN Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 129 LYS Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 152 SER Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 156 GLU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 183 THR Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 234 PHE Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 289 GLU Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 177 LEU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 195 GLU Chi-restraints excluded: chain a residue 205 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain a residue 219 HIS Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain a residue 233 LEU Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 261 LEU Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 271 LYS Chi-restraints excluded: chain a residue 272 ILE Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 327 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 358 THR Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 143 PHE Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 307 ARG Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 235 GLN Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 168 ARG Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 189 MET Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 80 ASN Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain d residue 140 GLN Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 350 VAL Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 250 ILE Chi-restraints excluded: chain W residue 274 VAL Chi-restraints excluded: chain W residue 286 LEU Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 385 SER Chi-restraints excluded: chain W residue 437 SER Chi-restraints excluded: chain W residue 438 LEU Chi-restraints excluded: chain W residue 439 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain V residue 67 LEU Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 313 LEU Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 107 MET Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 216 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 186 optimal weight: 9.9990 chunk 840 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 198 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 233 optimal weight: 7.9990 chunk 444 optimal weight: 1.9990 chunk 441 optimal weight: 6.9990 chunk 450 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 302 HIS ** f 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 329 ASN ** U 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 389 ASN ** U 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN B 195 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS F 64 HIS ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN J 18 GLN ** K 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 GLN M 97 ASN ** d 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.111223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083427 restraints weight = 176585.891| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.02 r_work: 0.3165 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 71229 Z= 0.253 Angle : 0.630 12.124 96248 Z= 0.315 Chirality : 0.042 0.251 10995 Planarity : 0.004 0.082 12383 Dihedral : 6.951 135.901 9878 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.92 % Favored : 93.88 % Rotamer: Outliers : 5.09 % Allowed : 25.52 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.09), residues: 8774 helix: 1.42 (0.07), residues: 4985 sheet: -0.74 (0.18), residues: 843 loop : -0.80 (0.12), residues: 2946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP a 255 HIS 0.007 0.001 HIS a 69 PHE 0.029 0.001 PHE d 198 TYR 0.037 0.001 TYR B 295 ARG 0.007 0.000 ARG M 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 387 poor density : 945 time to evaluate : 6.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8166 (mtm) REVERT: H 175 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8126 (mp0) REVERT: H 179 ASN cc_start: 0.8496 (t0) cc_final: 0.7932 (t0) REVERT: H 181 ASP cc_start: 0.8537 (p0) cc_final: 0.7792 (p0) REVERT: Y 138 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8492 (mm) REVERT: Y 143 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7256 (t80) REVERT: f 275 MET cc_start: 0.8222 (pmm) cc_final: 0.8014 (pmm) REVERT: f 325 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8209 (pp30) REVERT: f 390 LEU cc_start: 0.8471 (tp) cc_final: 0.8260 (tp) REVERT: f 407 MET cc_start: 0.4215 (mmm) cc_final: 0.3828 (mmm) REVERT: f 477 MET cc_start: 0.1608 (mmp) cc_final: 0.0478 (mmt) REVERT: f 483 PHE cc_start: 0.7186 (OUTLIER) cc_final: 0.6680 (t80) REVERT: f 524 MET cc_start: 0.7560 (ptt) cc_final: 0.7260 (ppp) REVERT: f 543 MET cc_start: 0.7536 (mmp) cc_final: 0.7310 (mmp) REVERT: f 564 LEU cc_start: 0.7020 (tp) cc_final: 0.6632 (tp) REVERT: f 646 MET cc_start: 0.5256 (pmm) cc_final: 0.4231 (mmm) REVERT: f 669 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: f 681 TYR cc_start: 0.8103 (m-10) cc_final: 0.7793 (m-10) REVERT: f 803 PHE cc_start: 0.8815 (m-80) cc_final: 0.8578 (m-80) REVERT: f 825 MET cc_start: 0.6363 (tpp) cc_final: 0.5586 (tpp) REVERT: f 848 GLN cc_start: 0.8718 (mp-120) cc_final: 0.8408 (mp-120) REVERT: f 861 THR cc_start: 0.7546 (m) cc_final: 0.7071 (p) REVERT: X 66 LEU cc_start: 0.7628 (mt) cc_final: 0.7313 (mt) REVERT: X 344 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8238 (mtm110) REVERT: X 379 ASP cc_start: 0.8753 (t0) cc_final: 0.8532 (t0) REVERT: U 25 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.8349 (p-80) REVERT: U 59 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7493 (t80) REVERT: U 194 ARG cc_start: 0.8683 (tpp80) cc_final: 0.7842 (tpt-90) REVERT: U 503 GLN cc_start: 0.8828 (mm-40) cc_final: 0.8547 (mm-40) REVERT: U 556 MET cc_start: 0.7904 (mmm) cc_final: 0.7606 (mmt) REVERT: U 666 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8406 (mtpp) REVERT: U 725 MET cc_start: 0.7544 (mmt) cc_final: 0.7222 (mmt) REVERT: U 894 MET cc_start: 0.7529 (ttm) cc_final: 0.7224 (tpp) REVERT: U 901 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8338 (pp30) REVERT: Z 121 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8324 (tp) REVERT: Z 156 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: Z 189 GLN cc_start: 0.8655 (mt0) cc_final: 0.8351 (mt0) REVERT: a 28 LEU cc_start: 0.8457 (mm) cc_final: 0.8078 (mp) REVERT: a 87 MET cc_start: 0.6477 (ppp) cc_final: 0.5585 (ppp) REVERT: a 92 VAL cc_start: 0.8962 (p) cc_final: 0.8738 (p) REVERT: a 173 TYR cc_start: 0.8755 (t80) cc_final: 0.8495 (t80) REVERT: a 177 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8894 (mm) REVERT: a 212 ASN cc_start: 0.8148 (m110) cc_final: 0.7500 (t0) REVERT: a 291 LEU cc_start: 0.9179 (mp) cc_final: 0.8942 (mp) REVERT: a 368 GLU cc_start: 0.8492 (pt0) cc_final: 0.8288 (pt0) REVERT: b 4 GLU cc_start: 0.8029 (pp20) cc_final: 0.7359 (pp20) REVERT: b 56 ASN cc_start: 0.8083 (t0) cc_final: 0.7705 (t0) REVERT: b 57 ASP cc_start: 0.7577 (m-30) cc_final: 0.7203 (m-30) REVERT: b 98 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8701 (ptpp) REVERT: A 66 LYS cc_start: 0.8839 (tptt) cc_final: 0.8422 (tptp) REVERT: A 88 GLN cc_start: 0.8588 (pt0) cc_final: 0.8161 (pp30) REVERT: A 123 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8593 (p) REVERT: A 144 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8346 (mtm-85) REVERT: A 276 GLU cc_start: 0.8456 (tp30) cc_final: 0.8123 (tp30) REVERT: A 429 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.6255 (t80) REVERT: B 55 HIS cc_start: 0.8850 (OUTLIER) cc_final: 0.8619 (p-80) REVERT: B 101 ASP cc_start: 0.8906 (t0) cc_final: 0.8556 (t0) REVERT: B 130 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8629 (mt-10) REVERT: B 255 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8688 (pp) REVERT: B 299 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8029 (p) REVERT: B 405 MET cc_start: 0.9051 (mmp) cc_final: 0.8827 (mmm) REVERT: C 51 GLU cc_start: 0.8625 (tp30) cc_final: 0.8290 (tp30) REVERT: C 134 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8839 (tt) REVERT: C 138 MET cc_start: 0.9082 (mtm) cc_final: 0.8838 (mtm) REVERT: C 273 MET cc_start: 0.8263 (tpp) cc_final: 0.7988 (ttm) REVERT: C 375 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.6965 (ptm-80) REVERT: D 80 LYS cc_start: 0.9314 (tppp) cc_final: 0.9101 (tppp) REVERT: D 127 ASN cc_start: 0.9005 (m-40) cc_final: 0.8722 (t0) REVERT: D 185 LEU cc_start: 0.9572 (OUTLIER) cc_final: 0.9244 (mm) REVERT: D 239 TYR cc_start: 0.8080 (m-80) cc_final: 0.7744 (m-80) REVERT: D 248 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7594 (ttp80) REVERT: D 332 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8704 (tt0) REVERT: E 180 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7489 (mttm) REVERT: E 196 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6790 (mm) REVERT: E 234 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5951 (mm-30) REVERT: E 275 MET cc_start: 0.7098 (tpp) cc_final: 0.5730 (ptp) REVERT: E 323 HIS cc_start: 0.6775 (OUTLIER) cc_final: 0.5913 (t-90) REVERT: E 339 ASN cc_start: 0.7944 (p0) cc_final: 0.7504 (p0) REVERT: F 75 GLU cc_start: 0.8833 (tp30) cc_final: 0.8564 (tp30) REVERT: F 96 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8192 (mp) REVERT: F 149 ASP cc_start: 0.8947 (OUTLIER) cc_final: 0.8632 (m-30) REVERT: F 208 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7788 (m-70) REVERT: F 295 ARG cc_start: 0.7847 (ptt90) cc_final: 0.7577 (ptm160) REVERT: G 74 GLU cc_start: 0.8359 (tt0) cc_final: 0.8031 (tt0) REVERT: G 83 MET cc_start: 0.8881 (mtm) cc_final: 0.8628 (mtm) REVERT: G 193 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: I 79 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8634 (mm) REVERT: I 89 GLU cc_start: 0.8436 (tp30) cc_final: 0.7956 (tp30) REVERT: I 149 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7879 (tp40) REVERT: I 241 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8648 (mt-10) REVERT: J 114 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9043 (tp) REVERT: J 182 GLU cc_start: 0.8953 (tp30) cc_final: 0.8507 (tp30) REVERT: K 20 ARG cc_start: 0.8834 (mtp180) cc_final: 0.8597 (mtp180) REVERT: K 182 GLN cc_start: 0.8803 (mt0) cc_final: 0.8395 (mt0) REVERT: K 224 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7480 (tm-30) REVERT: K 228 MET cc_start: 0.4619 (OUTLIER) cc_final: 0.3347 (tmm) REVERT: L 55 GLU cc_start: 0.8049 (mp0) cc_final: 0.7594 (mp0) REVERT: L 140 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.4874 (mpp) REVERT: L 143 HIS cc_start: 0.8460 (m90) cc_final: 0.7878 (m170) REVERT: M 22 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.7760 (mp-120) REVERT: M 108 LEU cc_start: 0.9000 (tp) cc_final: 0.8721 (tt) REVERT: M 191 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8363 (ptpp) REVERT: e 50 ASP cc_start: 0.8881 (p0) cc_final: 0.8655 (p0) REVERT: d 156 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8895 (tt) REVERT: d 166 ARG cc_start: 0.7964 (ptp-170) cc_final: 0.7429 (mtm-85) REVERT: d 289 ARG cc_start: 0.7544 (ttp80) cc_final: 0.7242 (tmt-80) REVERT: W 21 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8688 (t) REVERT: W 203 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8422 (tp40) REVERT: W 451 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7918 (mtt) REVERT: g 149 HIS cc_start: 0.5973 (m-70) cc_final: 0.5725 (m-70) REVERT: g 154 MET cc_start: 0.7467 (tpp) cc_final: 0.7256 (tpp) REVERT: V 77 GLU cc_start: 0.8829 (tp30) cc_final: 0.8455 (tm-30) REVERT: V 201 ARG cc_start: 0.7910 (tpt170) cc_final: 0.7432 (tpp80) REVERT: V 204 ASP cc_start: 0.8330 (m-30) cc_final: 0.7736 (m-30) REVERT: V 220 PHE cc_start: 0.8746 (m-80) cc_final: 0.8462 (m-80) REVERT: V 339 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8758 (mp) REVERT: V 463 MET cc_start: 0.8159 (mmp) cc_final: 0.7130 (mpp) REVERT: V 485 ASP cc_start: 0.9053 (t0) cc_final: 0.8479 (t0) REVERT: V 495 ARG cc_start: 0.7263 (mmp80) cc_final: 0.6120 (tpp-160) REVERT: c 118 PHE cc_start: 0.8513 (m-10) cc_final: 0.8208 (m-10) REVERT: c 236 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8290 (tm-30) outliers start: 387 outliers final: 290 residues processed: 1253 average time/residue: 0.6300 time to fit residues: 1371.0157 Evaluate side-chains 1233 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 336 poor density : 897 time to evaluate : 7.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Y residue 112 CYS Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain Y residue 186 LEU Chi-restraints excluded: chain Y residue 220 VAL Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 245 ASN Chi-restraints excluded: chain f residue 296 PHE Chi-restraints excluded: chain f residue 305 LEU Chi-restraints excluded: chain f residue 325 GLN Chi-restraints excluded: chain f residue 337 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 352 HIS Chi-restraints excluded: chain f residue 414 LEU Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 455 VAL Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 562 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 669 GLU Chi-restraints excluded: chain f residue 692 LEU Chi-restraints excluded: chain f residue 736 THR Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 762 VAL Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 865 PHE Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 99 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 153 LEU Chi-restraints excluded: chain X residue 157 LEU Chi-restraints excluded: chain X residue 224 ASP Chi-restraints excluded: chain X residue 270 LEU Chi-restraints excluded: chain X residue 344 ARG Chi-restraints excluded: chain X residue 357 SER Chi-restraints excluded: chain X residue 377 ILE Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 408 SER Chi-restraints excluded: chain U residue 25 HIS Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 123 LYS Chi-restraints excluded: chain U residue 160 LEU Chi-restraints excluded: chain U residue 179 TYR Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 356 THR Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 554 LEU Chi-restraints excluded: chain U residue 573 ASP Chi-restraints excluded: chain U residue 586 VAL Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 639 LEU Chi-restraints excluded: chain U residue 666 LYS Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 715 LYS Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 737 LEU Chi-restraints excluded: chain U residue 795 LEU Chi-restraints excluded: chain U residue 806 CYS Chi-restraints excluded: chain U residue 827 LYS Chi-restraints excluded: chain U residue 828 VAL Chi-restraints excluded: chain U residue 875 PHE Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain U residue 901 GLN Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 91 ILE Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 129 LYS Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 152 SER Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 156 GLU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 183 THR Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 289 GLU Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 177 LEU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 195 GLU Chi-restraints excluded: chain a residue 205 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain a residue 219 HIS Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain a residue 233 LEU Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 261 LEU Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 272 ILE Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 327 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 358 THR Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 98 LYS Chi-restraints excluded: chain b residue 143 PHE Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 157 SER Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 80 ASN Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain d residue 140 GLN Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 350 VAL Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 274 VAL Chi-restraints excluded: chain W residue 286 LEU Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 385 SER Chi-restraints excluded: chain W residue 437 SER Chi-restraints excluded: chain W residue 439 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain V residue 67 LEU Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 230 PHE Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 313 LEU Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 107 MET Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 216 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 369 optimal weight: 0.9980 chunk 332 optimal weight: 0.6980 chunk 342 optimal weight: 2.9990 chunk 450 optimal weight: 10.0000 chunk 337 optimal weight: 10.0000 chunk 819 optimal weight: 5.9990 chunk 392 optimal weight: 0.5980 chunk 799 optimal weight: 9.9990 chunk 806 optimal weight: 7.9990 chunk 847 optimal weight: 6.9990 chunk 873 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 302 HIS ** f 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 329 ASN ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 389 ASN ** U 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 101 GLN b 161 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS F 64 HIS G 75 ASN I 155 ASN J 18 GLN J 159 ASN ** d 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.112576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.084480 restraints weight = 177345.217| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.12 r_work: 0.3198 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 71229 Z= 0.196 Angle : 0.625 12.474 96248 Z= 0.312 Chirality : 0.042 0.258 10995 Planarity : 0.004 0.059 12383 Dihedral : 6.873 133.821 9872 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.72 % Favored : 94.07 % Rotamer: Outliers : 4.45 % Allowed : 26.30 % Favored : 69.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 8774 helix: 1.48 (0.07), residues: 4979 sheet: -0.65 (0.18), residues: 846 loop : -0.78 (0.12), residues: 2949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP a 255 HIS 0.008 0.001 HIS a 69 PHE 0.027 0.001 PHE b 156 TYR 0.038 0.001 TYR d 95 ARG 0.007 0.000 ARG Y 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 338 poor density : 981 time to evaluate : 6.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8140 (mtm) REVERT: H 175 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: H 179 ASN cc_start: 0.8476 (t0) cc_final: 0.7910 (t0) REVERT: H 181 ASP cc_start: 0.8554 (p0) cc_final: 0.7819 (p0) REVERT: Y 138 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8485 (mm) REVERT: Y 143 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7283 (t80) REVERT: f 196 MET cc_start: 0.8433 (mmm) cc_final: 0.8008 (mmm) REVERT: f 275 MET cc_start: 0.8225 (pmm) cc_final: 0.8014 (pmm) REVERT: f 321 MET cc_start: 0.5755 (ttm) cc_final: 0.5372 (ptm) REVERT: f 407 MET cc_start: 0.4055 (mmm) cc_final: 0.3681 (mmm) REVERT: f 477 MET cc_start: 0.1532 (mmp) cc_final: 0.0414 (mmt) REVERT: f 524 MET cc_start: 0.7560 (ptt) cc_final: 0.7261 (ppp) REVERT: f 543 MET cc_start: 0.7593 (mmp) cc_final: 0.7386 (mmp) REVERT: f 551 LYS cc_start: 0.7553 (tttt) cc_final: 0.7310 (mttm) REVERT: f 564 LEU cc_start: 0.6965 (tp) cc_final: 0.6591 (tp) REVERT: f 646 MET cc_start: 0.5430 (pmm) cc_final: 0.4232 (mmm) REVERT: f 669 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: f 825 MET cc_start: 0.6351 (tpp) cc_final: 0.5594 (tpp) REVERT: f 848 GLN cc_start: 0.8732 (mp-120) cc_final: 0.8423 (mp-120) REVERT: f 861 THR cc_start: 0.7474 (m) cc_final: 0.6939 (p) REVERT: X 66 LEU cc_start: 0.7588 (mt) cc_final: 0.7279 (mt) REVERT: X 344 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8227 (mtm110) REVERT: X 379 ASP cc_start: 0.8599 (t0) cc_final: 0.8388 (t0) REVERT: U 25 HIS cc_start: 0.8732 (OUTLIER) cc_final: 0.8368 (p-80) REVERT: U 59 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7435 (t80) REVERT: U 194 ARG cc_start: 0.8663 (tpp80) cc_final: 0.7832 (tpt-90) REVERT: U 503 GLN cc_start: 0.8793 (mm-40) cc_final: 0.8530 (mm-40) REVERT: U 556 MET cc_start: 0.7862 (mmm) cc_final: 0.7584 (mmt) REVERT: U 666 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8356 (mtpp) REVERT: U 725 MET cc_start: 0.7528 (mmt) cc_final: 0.7208 (mmt) REVERT: U 797 MET cc_start: 0.5598 (mpp) cc_final: 0.4972 (mpp) REVERT: U 827 LYS cc_start: 0.5892 (OUTLIER) cc_final: 0.5560 (mtpp) REVERT: U 894 MET cc_start: 0.7488 (ttm) cc_final: 0.7215 (tpp) REVERT: Z 121 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8303 (tp) REVERT: Z 156 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: Z 189 GLN cc_start: 0.8595 (mt0) cc_final: 0.8283 (mt0) REVERT: a 28 LEU cc_start: 0.8443 (mm) cc_final: 0.8057 (mp) REVERT: a 87 MET cc_start: 0.6450 (ppp) cc_final: 0.5547 (ppp) REVERT: a 92 VAL cc_start: 0.8920 (p) cc_final: 0.8681 (p) REVERT: a 173 TYR cc_start: 0.8761 (t80) cc_final: 0.8506 (t80) REVERT: a 177 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8841 (mm) REVERT: a 212 ASN cc_start: 0.8102 (m110) cc_final: 0.7504 (t0) REVERT: a 291 LEU cc_start: 0.9089 (mp) cc_final: 0.8851 (mp) REVERT: a 368 GLU cc_start: 0.8467 (pt0) cc_final: 0.8263 (pt0) REVERT: b 4 GLU cc_start: 0.7855 (pp20) cc_final: 0.7264 (pp20) REVERT: b 56 ASN cc_start: 0.8081 (t0) cc_final: 0.7708 (t0) REVERT: b 57 ASP cc_start: 0.7544 (m-30) cc_final: 0.7160 (m-30) REVERT: b 98 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8694 (ptpp) REVERT: A 66 LYS cc_start: 0.8812 (tptt) cc_final: 0.8412 (tptp) REVERT: A 88 GLN cc_start: 0.8558 (pt0) cc_final: 0.8160 (pp30) REVERT: A 123 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8559 (p) REVERT: A 144 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8483 (mtm-85) REVERT: A 276 GLU cc_start: 0.8468 (tp30) cc_final: 0.8155 (tp30) REVERT: A 429 TYR cc_start: 0.6656 (OUTLIER) cc_final: 0.6237 (t80) REVERT: B 101 ASP cc_start: 0.8914 (t0) cc_final: 0.8592 (t0) REVERT: B 255 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8508 (pp) REVERT: B 299 SER cc_start: 0.8431 (OUTLIER) cc_final: 0.7972 (p) REVERT: B 405 MET cc_start: 0.9038 (mmp) cc_final: 0.8805 (mmm) REVERT: C 51 GLU cc_start: 0.8634 (tp30) cc_final: 0.8264 (tp30) REVERT: C 134 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8960 (tt) REVERT: C 273 MET cc_start: 0.8253 (tpp) cc_final: 0.8003 (ttm) REVERT: C 375 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.6948 (ptm-80) REVERT: D 77 GLU cc_start: 0.8902 (tp30) cc_final: 0.8636 (tp30) REVERT: D 80 LYS cc_start: 0.9314 (tppp) cc_final: 0.9111 (tppp) REVERT: D 127 ASN cc_start: 0.8948 (m-40) cc_final: 0.8684 (t0) REVERT: D 185 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9216 (mm) REVERT: D 239 TYR cc_start: 0.8071 (m-80) cc_final: 0.7735 (m-80) REVERT: D 248 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7628 (ttp80) REVERT: D 332 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8716 (tt0) REVERT: D 415 GLU cc_start: 0.8696 (pm20) cc_final: 0.8133 (pm20) REVERT: E 44 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7784 (tm-30) REVERT: E 180 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7361 (mttm) REVERT: E 196 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6787 (mm) REVERT: E 217 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7955 (pt0) REVERT: E 234 GLU cc_start: 0.6364 (OUTLIER) cc_final: 0.6082 (mp0) REVERT: E 264 MET cc_start: 0.8033 (ppp) cc_final: 0.7091 (mpp) REVERT: E 275 MET cc_start: 0.7064 (tpp) cc_final: 0.5586 (ptp) REVERT: E 277 MET cc_start: 0.6918 (ttp) cc_final: 0.6430 (tmm) REVERT: E 323 HIS cc_start: 0.6957 (OUTLIER) cc_final: 0.6074 (t-90) REVERT: E 339 ASN cc_start: 0.7930 (p0) cc_final: 0.7474 (p0) REVERT: F 149 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8639 (m-30) REVERT: F 206 MET cc_start: 0.7299 (ttm) cc_final: 0.7035 (tpp) REVERT: F 208 HIS cc_start: 0.8186 (OUTLIER) cc_final: 0.7739 (m-70) REVERT: F 295 ARG cc_start: 0.7836 (ptt90) cc_final: 0.7562 (ptm160) REVERT: G 74 GLU cc_start: 0.8366 (tt0) cc_final: 0.8046 (tt0) REVERT: G 83 MET cc_start: 0.8836 (mtm) cc_final: 0.8605 (mtm) REVERT: G 193 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: I 79 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8555 (mm) REVERT: I 149 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7863 (tp40) REVERT: I 241 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8631 (mt-10) REVERT: J 114 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8962 (tp) REVERT: J 182 GLU cc_start: 0.8924 (tp30) cc_final: 0.8531 (tp30) REVERT: K 20 ARG cc_start: 0.8817 (mtp180) cc_final: 0.8585 (mtp180) REVERT: K 182 GLN cc_start: 0.8769 (mt0) cc_final: 0.8409 (mt0) REVERT: K 224 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7493 (tm-30) REVERT: L 55 GLU cc_start: 0.7956 (mp0) cc_final: 0.7705 (mp0) REVERT: L 140 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.4771 (mpp) REVERT: L 143 HIS cc_start: 0.8443 (m90) cc_final: 0.7825 (m170) REVERT: M 22 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.7776 (mp-120) REVERT: M 108 LEU cc_start: 0.8995 (tp) cc_final: 0.8752 (tt) REVERT: M 191 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8294 (ptpp) REVERT: e 50 ASP cc_start: 0.8897 (p0) cc_final: 0.8679 (p0) REVERT: d 156 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8900 (tt) REVERT: d 166 ARG cc_start: 0.8025 (ptp-170) cc_final: 0.7502 (mtm-85) REVERT: d 289 ARG cc_start: 0.7438 (ttp80) cc_final: 0.7137 (tmt-80) REVERT: W 21 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8701 (t) REVERT: W 203 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8417 (tp40) REVERT: W 213 PHE cc_start: 0.8729 (t80) cc_final: 0.8203 (t80) REVERT: W 451 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7779 (mtt) REVERT: g 149 HIS cc_start: 0.6046 (m-70) cc_final: 0.5796 (m-70) REVERT: V 77 GLU cc_start: 0.8805 (tp30) cc_final: 0.8423 (tm-30) REVERT: V 84 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8388 (mmtm) REVERT: V 201 ARG cc_start: 0.7839 (tpt170) cc_final: 0.7442 (tpp80) REVERT: V 204 ASP cc_start: 0.8306 (m-30) cc_final: 0.7724 (m-30) REVERT: V 213 TYR cc_start: 0.8279 (m-80) cc_final: 0.7903 (m-80) REVERT: V 220 PHE cc_start: 0.8769 (m-80) cc_final: 0.8461 (m-80) REVERT: V 339 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8735 (mp) REVERT: V 463 MET cc_start: 0.8168 (mmp) cc_final: 0.7118 (mpp) REVERT: V 485 ASP cc_start: 0.8999 (t0) cc_final: 0.8471 (t0) REVERT: V 495 ARG cc_start: 0.7246 (mmp80) cc_final: 0.6109 (tpp-160) REVERT: c 118 PHE cc_start: 0.8455 (m-10) cc_final: 0.8166 (m-10) REVERT: c 158 ASP cc_start: 0.7948 (t0) cc_final: 0.7731 (t70) REVERT: c 236 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8258 (tm-30) outliers start: 338 outliers final: 258 residues processed: 1246 average time/residue: 0.6404 time to fit residues: 1383.8805 Evaluate side-chains 1230 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 301 poor density : 929 time to evaluate : 6.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Y residue 112 CYS Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 162 LEU Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 266 LEU Chi-restraints excluded: chain f residue 296 PHE Chi-restraints excluded: chain f residue 337 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 352 HIS Chi-restraints excluded: chain f residue 414 LEU Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 455 VAL Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 562 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 669 GLU Chi-restraints excluded: chain f residue 692 LEU Chi-restraints excluded: chain f residue 736 THR Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 762 VAL Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 865 PHE Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 99 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 153 LEU Chi-restraints excluded: chain X residue 224 ASP Chi-restraints excluded: chain X residue 270 LEU Chi-restraints excluded: chain X residue 344 ARG Chi-restraints excluded: chain X residue 357 SER Chi-restraints excluded: chain X residue 377 ILE Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 408 SER Chi-restraints excluded: chain U residue 25 HIS Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 123 LYS Chi-restraints excluded: chain U residue 160 LEU Chi-restraints excluded: chain U residue 179 TYR Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 356 THR Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 545 LEU Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 573 ASP Chi-restraints excluded: chain U residue 578 LEU Chi-restraints excluded: chain U residue 586 VAL Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 666 LYS Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 715 LYS Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 795 LEU Chi-restraints excluded: chain U residue 827 LYS Chi-restraints excluded: chain U residue 828 VAL Chi-restraints excluded: chain U residue 875 PHE Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 91 ILE Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 156 GLU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 289 GLU Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 83 VAL Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 177 LEU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 195 GLU Chi-restraints excluded: chain a residue 205 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 219 HIS Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain a residue 233 LEU Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 261 LEU Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 272 ILE Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 327 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 98 LYS Chi-restraints excluded: chain b residue 143 PHE Chi-restraints excluded: chain b residue 161 ASN Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 159 ASN Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 80 ASN Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain d residue 140 GLN Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 350 VAL Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 286 LEU Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 385 SER Chi-restraints excluded: chain W residue 437 SER Chi-restraints excluded: chain W residue 438 LEU Chi-restraints excluded: chain W residue 439 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain W residue 451 MET Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 230 PHE Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 313 LEU Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 216 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 176 optimal weight: 7.9990 chunk 164 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 818 optimal weight: 7.9990 chunk 238 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 chunk 596 optimal weight: 10.0000 chunk 518 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 606 optimal weight: 5.9990 chunk 633 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 302 HIS ** f 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 329 ASN ** U 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 389 ASN ** U 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 264 ASN b 101 GLN ** b 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS F 64 HIS ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN J 18 GLN ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.109869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081141 restraints weight = 177969.534| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.21 r_work: 0.3135 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 71229 Z= 0.383 Angle : 0.690 12.984 96248 Z= 0.346 Chirality : 0.044 0.269 10995 Planarity : 0.004 0.080 12383 Dihedral : 6.933 138.757 9865 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.37 % Favored : 93.42 % Rotamer: Outliers : 4.55 % Allowed : 26.18 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 8774 helix: 1.36 (0.07), residues: 4998 sheet: -0.84 (0.18), residues: 883 loop : -0.82 (0.12), residues: 2893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP a 255 HIS 0.007 0.001 HIS a 69 PHE 0.033 0.002 PHE d 198 TYR 0.037 0.002 TYR B 295 ARG 0.008 0.000 ARG b 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17548 Ramachandran restraints generated. 8774 Oldfield, 0 Emsley, 8774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 346 poor density : 914 time to evaluate : 7.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 79 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8317 (mtm) REVERT: H 175 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: H 179 ASN cc_start: 0.8534 (t0) cc_final: 0.7954 (t0) REVERT: H 181 ASP cc_start: 0.8575 (p0) cc_final: 0.7857 (p0) REVERT: Y 138 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8514 (mm) REVERT: Y 143 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.7298 (t80) REVERT: f 196 MET cc_start: 0.8540 (mmm) cc_final: 0.8113 (mmm) REVERT: f 477 MET cc_start: 0.1731 (mmp) cc_final: 0.0646 (mmt) REVERT: f 483 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6815 (t80) REVERT: f 524 MET cc_start: 0.7553 (ptt) cc_final: 0.7242 (ppp) REVERT: f 551 LYS cc_start: 0.7554 (tttt) cc_final: 0.7307 (mttm) REVERT: f 564 LEU cc_start: 0.6986 (tp) cc_final: 0.6581 (tp) REVERT: f 646 MET cc_start: 0.5480 (pmm) cc_final: 0.4314 (mmm) REVERT: f 669 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: f 803 PHE cc_start: 0.8862 (m-80) cc_final: 0.8632 (m-80) REVERT: f 825 MET cc_start: 0.6442 (tpp) cc_final: 0.5633 (tpp) REVERT: f 848 GLN cc_start: 0.8663 (mp-120) cc_final: 0.8352 (mp-120) REVERT: f 861 THR cc_start: 0.7636 (m) cc_final: 0.7143 (p) REVERT: X 66 LEU cc_start: 0.7534 (mt) cc_final: 0.7218 (mt) REVERT: X 344 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8255 (mtm110) REVERT: U 25 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8340 (p-80) REVERT: U 59 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7486 (t80) REVERT: U 194 ARG cc_start: 0.8614 (tpp80) cc_final: 0.7750 (tpt-90) REVERT: U 556 MET cc_start: 0.7951 (mmm) cc_final: 0.7671 (mmt) REVERT: U 666 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8427 (mtpp) REVERT: U 725 MET cc_start: 0.7559 (mmt) cc_final: 0.7216 (mmt) REVERT: U 827 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.5480 (mtpp) REVERT: U 894 MET cc_start: 0.7532 (ttm) cc_final: 0.7230 (tpp) REVERT: Z 121 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8329 (tp) REVERT: Z 156 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7744 (tm-30) REVERT: Z 189 GLN cc_start: 0.8653 (mt0) cc_final: 0.8266 (mt0) REVERT: a 28 LEU cc_start: 0.8494 (mm) cc_final: 0.8108 (mp) REVERT: a 161 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8199 (mmtm) REVERT: a 173 TYR cc_start: 0.8791 (t80) cc_final: 0.8569 (t80) REVERT: a 177 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8854 (mm) REVERT: a 212 ASN cc_start: 0.8227 (m110) cc_final: 0.7578 (t0) REVERT: a 269 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8304 (pp) REVERT: a 291 LEU cc_start: 0.9218 (mp) cc_final: 0.8976 (mp) REVERT: b 4 GLU cc_start: 0.8085 (pp20) cc_final: 0.7511 (pp20) REVERT: b 56 ASN cc_start: 0.7996 (t0) cc_final: 0.7602 (t0) REVERT: b 57 ASP cc_start: 0.7470 (m-30) cc_final: 0.7097 (m-30) REVERT: b 98 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8740 (ptpp) REVERT: A 66 LYS cc_start: 0.8847 (tptt) cc_final: 0.8453 (tptp) REVERT: A 88 GLN cc_start: 0.8634 (pt0) cc_final: 0.8205 (pp30) REVERT: A 144 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8318 (mtm-85) REVERT: A 276 GLU cc_start: 0.8448 (tp30) cc_final: 0.8007 (tp30) REVERT: A 429 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.6355 (t80) REVERT: B 55 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.8639 (p-80) REVERT: B 74 MET cc_start: 0.9299 (mmm) cc_final: 0.9088 (mtt) REVERT: B 255 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8618 (pp) REVERT: B 299 SER cc_start: 0.8598 (OUTLIER) cc_final: 0.8076 (p) REVERT: B 405 MET cc_start: 0.9043 (mmp) cc_final: 0.8843 (mmm) REVERT: C 51 GLU cc_start: 0.8663 (tp30) cc_final: 0.8370 (tp30) REVERT: C 134 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8673 (tt) REVERT: C 138 MET cc_start: 0.8828 (mtm) cc_final: 0.8327 (mtm) REVERT: C 375 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7028 (ptm-80) REVERT: D 80 LYS cc_start: 0.9325 (tppp) cc_final: 0.9122 (tppp) REVERT: D 185 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9246 (mm) REVERT: D 204 MET cc_start: 0.9087 (mtm) cc_final: 0.8877 (mtm) REVERT: D 239 TYR cc_start: 0.8082 (m-80) cc_final: 0.7753 (m-80) REVERT: D 248 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7442 (ttp80) REVERT: D 332 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8759 (tt0) REVERT: E 44 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7859 (tm-30) REVERT: E 180 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7435 (mtpp) REVERT: E 196 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6655 (mm) REVERT: E 217 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: E 232 MET cc_start: 0.5255 (ppp) cc_final: 0.4935 (ppp) REVERT: E 234 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5932 (mm-30) REVERT: E 275 MET cc_start: 0.7118 (tpp) cc_final: 0.6811 (tpp) REVERT: E 277 MET cc_start: 0.6985 (ttp) cc_final: 0.6620 (tmm) REVERT: E 323 HIS cc_start: 0.6855 (OUTLIER) cc_final: 0.5939 (t-90) REVERT: E 339 ASN cc_start: 0.7940 (p0) cc_final: 0.7501 (p0) REVERT: F 96 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8239 (mp) REVERT: F 149 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8651 (m-30) REVERT: F 206 MET cc_start: 0.7379 (ttm) cc_final: 0.7022 (tpp) REVERT: F 208 HIS cc_start: 0.8184 (OUTLIER) cc_final: 0.7685 (m-70) REVERT: F 295 ARG cc_start: 0.7775 (ptt90) cc_final: 0.7521 (ptm160) REVERT: F 356 MET cc_start: 0.9297 (mmt) cc_final: 0.8944 (mmt) REVERT: G 74 GLU cc_start: 0.8387 (tt0) cc_final: 0.8086 (tt0) REVERT: G 83 MET cc_start: 0.8899 (mtm) cc_final: 0.8608 (mtm) REVERT: G 193 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: I 79 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8749 (mm) REVERT: I 149 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7844 (tp40) REVERT: I 241 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8610 (mt-10) REVERT: J 114 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9087 (tp) REVERT: J 159 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8436 (m-40) REVERT: J 182 GLU cc_start: 0.8957 (tp30) cc_final: 0.8567 (tp30) REVERT: K 182 GLN cc_start: 0.8860 (mt0) cc_final: 0.8471 (mt0) REVERT: K 224 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7513 (tm-30) REVERT: K 228 MET cc_start: 0.4649 (OUTLIER) cc_final: 0.3821 (ttp) REVERT: L 55 GLU cc_start: 0.7987 (mp0) cc_final: 0.7644 (mp0) REVERT: L 140 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.4919 (mpp) REVERT: L 143 HIS cc_start: 0.8514 (m90) cc_final: 0.7945 (m170) REVERT: M 22 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.7705 (mp-120) REVERT: M 191 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8415 (ptpp) REVERT: e 50 ASP cc_start: 0.8897 (p0) cc_final: 0.8685 (p0) REVERT: d 156 ILE cc_start: 0.9205 (OUTLIER) cc_final: 0.8951 (tt) REVERT: d 166 ARG cc_start: 0.7886 (ptp-170) cc_final: 0.7473 (mtm-85) REVERT: d 289 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7264 (tmt-80) REVERT: W 21 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8698 (t) REVERT: g 149 HIS cc_start: 0.6117 (m-70) cc_final: 0.5879 (m-70) REVERT: V 77 GLU cc_start: 0.8836 (tp30) cc_final: 0.8458 (tm-30) REVERT: V 84 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8427 (mmtm) REVERT: V 99 ARG cc_start: 0.6061 (tpt170) cc_final: 0.5778 (tpt170) REVERT: V 201 ARG cc_start: 0.7888 (tpt170) cc_final: 0.7398 (tpp80) REVERT: V 204 ASP cc_start: 0.8349 (m-30) cc_final: 0.7747 (m-30) REVERT: V 220 PHE cc_start: 0.8736 (m-80) cc_final: 0.8408 (m-80) REVERT: V 339 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8818 (mp) REVERT: V 463 MET cc_start: 0.8179 (mmp) cc_final: 0.7062 (mpp) REVERT: V 485 ASP cc_start: 0.9071 (t0) cc_final: 0.8502 (t0) REVERT: V 495 ARG cc_start: 0.7413 (mmp80) cc_final: 0.6334 (tpp-160) REVERT: c 118 PHE cc_start: 0.8532 (m-10) cc_final: 0.8222 (m-10) REVERT: c 131 GLN cc_start: 0.8853 (mt0) cc_final: 0.8512 (mp10) REVERT: c 158 ASP cc_start: 0.8042 (t0) cc_final: 0.7726 (t0) REVERT: c 236 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8321 (tm-30) outliers start: 346 outliers final: 270 residues processed: 1191 average time/residue: 0.6379 time to fit residues: 1321.1108 Evaluate side-chains 1209 residues out of total 7678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 317 poor density : 892 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 175 GLU Chi-restraints excluded: chain Y residue 84 LEU Chi-restraints excluded: chain Y residue 95 LEU Chi-restraints excluded: chain Y residue 112 CYS Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 143 TYR Chi-restraints excluded: chain f residue 82 ILE Chi-restraints excluded: chain f residue 216 MET Chi-restraints excluded: chain f residue 245 ASN Chi-restraints excluded: chain f residue 266 LEU Chi-restraints excluded: chain f residue 296 PHE Chi-restraints excluded: chain f residue 337 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 352 HIS Chi-restraints excluded: chain f residue 414 LEU Chi-restraints excluded: chain f residue 440 ILE Chi-restraints excluded: chain f residue 455 VAL Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 562 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 669 GLU Chi-restraints excluded: chain f residue 692 LEU Chi-restraints excluded: chain f residue 736 THR Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 762 VAL Chi-restraints excluded: chain f residue 791 VAL Chi-restraints excluded: chain f residue 865 PHE Chi-restraints excluded: chain f residue 900 LEU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 99 MET Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 210 LEU Chi-restraints excluded: chain X residue 270 LEU Chi-restraints excluded: chain X residue 344 ARG Chi-restraints excluded: chain X residue 357 SER Chi-restraints excluded: chain X residue 377 ILE Chi-restraints excluded: chain X residue 385 LEU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 408 SER Chi-restraints excluded: chain X residue 411 VAL Chi-restraints excluded: chain U residue 25 HIS Chi-restraints excluded: chain U residue 56 SER Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 123 LYS Chi-restraints excluded: chain U residue 160 LEU Chi-restraints excluded: chain U residue 179 TYR Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 356 THR Chi-restraints excluded: chain U residue 360 VAL Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 408 LEU Chi-restraints excluded: chain U residue 415 HIS Chi-restraints excluded: chain U residue 486 MET Chi-restraints excluded: chain U residue 545 LEU Chi-restraints excluded: chain U residue 552 ILE Chi-restraints excluded: chain U residue 573 ASP Chi-restraints excluded: chain U residue 578 LEU Chi-restraints excluded: chain U residue 586 VAL Chi-restraints excluded: chain U residue 629 THR Chi-restraints excluded: chain U residue 663 THR Chi-restraints excluded: chain U residue 666 LYS Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 715 LYS Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 795 LEU Chi-restraints excluded: chain U residue 806 CYS Chi-restraints excluded: chain U residue 827 LYS Chi-restraints excluded: chain U residue 828 VAL Chi-restraints excluded: chain U residue 875 PHE Chi-restraints excluded: chain U residue 884 VAL Chi-restraints excluded: chain Z residue 25 ARG Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 62 ASP Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 154 THR Chi-restraints excluded: chain Z residue 156 GLU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 227 ILE Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 235 ASN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 289 GLU Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 118 ILE Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 136 GLU Chi-restraints excluded: chain a residue 148 VAL Chi-restraints excluded: chain a residue 151 VAL Chi-restraints excluded: chain a residue 177 LEU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 195 GLU Chi-restraints excluded: chain a residue 205 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 219 HIS Chi-restraints excluded: chain a residue 222 LEU Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 261 LEU Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 272 ILE Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 280 MET Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 307 VAL Chi-restraints excluded: chain a residue 327 VAL Chi-restraints excluded: chain a residue 349 MET Chi-restraints excluded: chain a residue 358 THR Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain a residue 374 ILE Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 51 LEU Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 98 LYS Chi-restraints excluded: chain b residue 143 PHE Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 144 ARG Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 429 TYR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 300 ILE Chi-restraints excluded: chain C residue 351 MET Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 383 PHE Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 83 CYS Chi-restraints excluded: chain E residue 120 TYR Chi-restraints excluded: chain E residue 180 LYS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 217 GLU Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 323 HIS Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 435 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain G residue 190 THR Chi-restraints excluded: chain G residue 193 GLN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 51 ASN Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 224 VAL Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 159 ASN Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 188 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 54 LEU Chi-restraints excluded: chain M residue 158 TYR Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 80 ASN Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain d residue 156 ILE Chi-restraints excluded: chain d residue 350 VAL Chi-restraints excluded: chain W residue 21 SER Chi-restraints excluded: chain W residue 63 THR Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 159 VAL Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 274 VAL Chi-restraints excluded: chain W residue 286 LEU Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 338 THR Chi-restraints excluded: chain W residue 385 SER Chi-restraints excluded: chain W residue 437 SER Chi-restraints excluded: chain W residue 438 LEU Chi-restraints excluded: chain W residue 439 VAL Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 122 LEU Chi-restraints excluded: chain V residue 67 LEU Chi-restraints excluded: chain V residue 84 LYS Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 230 PHE Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 313 LEU Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 339 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 54 MET Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 96 LEU Chi-restraints excluded: chain c residue 102 THR Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 216 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 9 optimal weight: 0.9980 chunk 788 optimal weight: 10.0000 chunk 432 optimal weight: 0.9980 chunk 667 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 632 optimal weight: 4.9990 chunk 673 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 266 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 866 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 389 ASN ** U 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 101 GLN b 161 ASN ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS F 64 HIS G 75 ASN J 18 GLN ** J 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 HIS ** d 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.110075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082457 restraints weight = 177005.061| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.01 r_work: 0.3141 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.215 71229 Z= 0.324 Angle : 0.729 59.191 96248 Z= 0.381 Chirality : 0.043 0.487 10995 Planarity : 0.004 0.100 12383 Dihedral : 6.943 138.314 9865 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.35 % Favored : 93.45 % Rotamer: Outliers : 4.64 % Allowed : 26.23 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.47 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.09), residues: 8774 helix: 1.37 (0.07), residues: 4999 sheet: -0.86 (0.18), residues: 883 loop : -0.82 (0.12), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.002 TRP f 398 HIS 0.018 0.001 HIS b 38 PHE 0.026 0.002 PHE b 86 TYR 0.034 0.002 TYR B 295 ARG 0.027 0.000 ARG F 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39417.55 seconds wall clock time: 677 minutes 3.94 seconds (40623.94 seconds total)