Starting phenix.real_space_refine on Wed Sep 25 01:40:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rep_4853/09_2024/6rep_4853.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rep_4853/09_2024/6rep_4853.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rep_4853/09_2024/6rep_4853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rep_4853/09_2024/6rep_4853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rep_4853/09_2024/6rep_4853.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rep_4853/09_2024/6rep_4853.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= 0.001 sd= 1.061 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 13 5.49 5 Mg 5 5.21 5 S 149 5.16 5 C 34301 2.51 5 N 9113 2.21 5 O 10200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 402 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 53782 Number of models: 1 Model: "" Number of chains: 43 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "A" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "B" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "C" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain breaks: 1 Chain: "D" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "E" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "F" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "G" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "H" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "I" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 514 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1532 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "Q" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 561 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 5, 'TRANS': 66} Chain: "R" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1303 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain: "S" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2130 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 271} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3979 Classifications: {'peptide': 523} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "U" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 3980 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 497} Chain: "V" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3962 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 494} Chain: "X" Number of atoms: 4095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4095 Classifications: {'peptide': 539} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 514} Chain: "Y" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3957 Classifications: {'peptide': 521} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 498} Chain: "Z" Number of atoms: 4115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4115 Classifications: {'peptide': 542} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 517} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "T" 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: "U" 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: "V" 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: "X" 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: "Z" 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: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 24.05, per 1000 atoms: 0.45 Number of scatterers: 53782 At special positions: 0 Unit cell: (214.812, 133.731, 263.25, 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 149 16.00 P 13 15.00 Mg 5 11.99 O 10200 8.00 N 9113 7.00 C 34301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 9.85 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13088 Finding SS restraints... Secondary structure from input PDB file: 331 helices and 0 sheets defined 58.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain '0' and resid 3 through 8 removed outlier: 3.625A pdb=" N PHE 0 7 " --> pdb=" O TYR 0 3 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA 0 8 " --> pdb=" O SER 0 4 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 3 through 8' Processing helix chain '0' and resid 17 through 31 Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 removed outlier: 3.783A pdb=" N GLN 0 56 " --> pdb=" O ILE 0 52 " (cutoff:3.500A) Processing helix chain '1' and resid 45 through 70 removed outlier: 3.614A pdb=" N LYS 1 68 " --> pdb=" O LEU 1 64 " (cutoff:3.500A) Processing helix chain '1' and resid 96 through 100 removed outlier: 3.626A pdb=" N THR 1 99 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN 1 100 " --> pdb=" O PHE 1 97 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 96 through 100' Processing helix chain '1' and resid 106 through 142 removed outlier: 3.780A pdb=" N ALA 1 121 " --> pdb=" O THR 1 117 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA 1 122 " --> pdb=" O ARG 1 118 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE 1 129 " --> pdb=" O SER 1 125 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR 1 135 " --> pdb=" O ALA 1 131 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA 1 139 " --> pdb=" O THR 1 135 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA 1 140 " --> pdb=" O GLU 1 136 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA 1 142 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 3.868A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 205 removed outlier: 3.773A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP 1 199 " --> pdb=" O LYS 1 195 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE 1 200 " --> pdb=" O ALA 1 196 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL 1 204 " --> pdb=" O PHE 1 200 " (cutoff:3.500A) Processing helix chain '1' and resid 209 through 223 removed outlier: 3.582A pdb=" N LEU 1 216 " --> pdb=" O GLU 1 212 " (cutoff:3.500A) Processing helix chain '1' and resid 243 through 271 removed outlier: 3.687A pdb=" N ARG 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS 1 266 " --> pdb=" O LYS 1 262 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL 1 270 " --> pdb=" O LYS 1 266 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.549A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 282 through 286 Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 removed outlier: 3.654A pdb=" N ALA 1 303 " --> pdb=" O GLU 1 299 " (cutoff:3.500A) Processing helix chain '1' and resid 310 through 317 removed outlier: 3.773A pdb=" N SER 1 317 " --> pdb=" O GLN 1 313 " (cutoff:3.500A) Processing helix chain '1' and resid 318 through 322 Processing helix chain '1' and resid 323 through 327 removed outlier: 3.732A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 334 removed outlier: 3.562A pdb=" N GLU 1 334 " --> pdb=" O ALA 1 331 " (cutoff:3.500A) Processing helix chain '1' and resid 338 through 351 Processing helix chain '1' and resid 353 through 362 Processing helix chain '1' and resid 363 through 367 removed outlier: 3.977A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.849A pdb=" N ARG 1 381 " --> pdb=" O SER 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 418 removed outlier: 3.632A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU 1 415 " --> pdb=" O ALA 1 411 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.720A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 445 removed outlier: 3.713A pdb=" N PHE 1 441 " --> pdb=" O VAL 1 437 " (cutoff:3.500A) Processing helix chain '1' and resid 446 through 459 removed outlier: 3.500A pdb=" N ALA 1 459 " --> pdb=" O ALA 1 455 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 removed outlier: 3.659A pdb=" N THR 1 471 " --> pdb=" O ALA 1 467 " (cutoff:3.500A) Processing helix chain '1' and resid 479 through 483 removed outlier: 3.530A pdb=" N ILE 1 483 " --> pdb=" O PRO 1 480 " (cutoff:3.500A) Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 516 removed outlier: 3.592A pdb=" N GLU 1 495 " --> pdb=" O PRO 1 491 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU 1 496 " --> pdb=" O GLN 1 492 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER 1 503 " --> pdb=" O GLU 1 499 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP 1 508 " --> pdb=" O ASP 1 504 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU 1 512 " --> pdb=" O ASP 1 508 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU 1 516 " --> pdb=" O LEU 1 512 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.643A pdb=" N THR 1 526 " --> pdb=" O LEU 1 522 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 Processing helix chain '1' and resid 549 through 562 Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 576 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 removed outlier: 3.530A pdb=" N ALA 1 603 " --> pdb=" O ARG 1 599 " (cutoff:3.500A) Processing helix chain '2' and resid 7 through 17 removed outlier: 3.625A pdb=" N ILE 2 11 " --> pdb=" O ASP 2 7 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 removed outlier: 3.584A pdb=" N VAL 2 29 " --> pdb=" O SER 2 25 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 58 removed outlier: 3.647A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY 2 56 " --> pdb=" O LEU 2 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA 2 58 " --> pdb=" O LYS 2 54 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 76 removed outlier: 3.533A pdb=" N THR 2 67 " --> pdb=" O ALA 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 Processing helix chain '2' and resid 99 through 113 removed outlier: 3.504A pdb=" N SER 2 104 " --> pdb=" O PRO 2 100 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 129 removed outlier: 3.596A pdb=" N ALA 2 126 " --> pdb=" O ASN 2 122 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL 2 128 " --> pdb=" O ALA 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 150 removed outlier: 3.697A pdb=" N ARG 2 142 " --> pdb=" O ALA 2 138 " (cutoff:3.500A) Processing helix chain '2' and resid 154 through 168 removed outlier: 3.502A pdb=" N ALA 2 158 " --> pdb=" O ASP 2 154 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 removed outlier: 3.526A pdb=" N LYS 2 184 " --> pdb=" O TYR 2 180 " (cutoff:3.500A) Processing helix chain '2' and resid 189 through 198 removed outlier: 3.526A pdb=" N ASP 2 194 " --> pdb=" O LYS 2 190 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 207 through 220 Processing helix chain '2' and resid 227 through 232 Processing helix chain '2' and resid 240 through 254 removed outlier: 3.648A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.603A pdb=" N PHE 2 262 " --> pdb=" O ASP 2 258 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix Processing helix chain '2' and resid 281 through 295 removed outlier: 3.687A pdb=" N GLN 2 287 " --> pdb=" O SER 2 283 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 321 removed outlier: 3.539A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP 2 316 " --> pdb=" O GLY 2 312 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA 2 318 " --> pdb=" O ALA 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 341 Processing helix chain '2' and resid 345 through 354 removed outlier: 3.591A pdb=" N ALA 2 352 " --> pdb=" O GLU 2 348 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA 2 354 " --> pdb=" O ALA 2 350 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 409 removed outlier: 4.074A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG 2 406 " --> pdb=" O TYR 2 402 " (cutoff:3.500A) Processing helix chain '2' and resid 426 through 442 removed outlier: 3.594A pdb=" N VAL 2 441 " --> pdb=" O ALA 2 437 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 87 Processing helix chain '3' and resid 91 through 99 removed outlier: 3.620A pdb=" N ASN 3 97 " --> pdb=" O GLU 3 93 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA 3 99 " --> pdb=" O LEU 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 113 removed outlier: 3.576A pdb=" N TYR 3 108 " --> pdb=" O PRO 3 104 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU 3 110 " --> pdb=" O TRP 3 106 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 125 removed outlier: 3.783A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 135 Processing helix chain '3' and resid 136 through 150 removed outlier: 3.629A pdb=" N VAL 3 145 " --> pdb=" O THR 3 141 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 168 removed outlier: 4.151A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 169 through 172 removed outlier: 3.664A pdb=" N PHE 3 172 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 169 through 172' Processing helix chain '3' and resid 173 through 187 removed outlier: 3.860A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 204 removed outlier: 3.574A pdb=" N LEU 3 195 " --> pdb=" O SER 3 191 " (cutoff:3.500A) Processing helix chain '3' and resid 215 through 230 removed outlier: 3.631A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 Processing helix chain '3' and resid 245 through 251 removed outlier: 3.530A pdb=" N LYS 3 251 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) Processing helix chain '3' and resid 253 through 271 removed outlier: 3.574A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 275 through 281 removed outlier: 3.605A pdb=" N GLU 3 279 " --> pdb=" O GLU 3 276 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA 3 280 " --> pdb=" O SER 3 277 " (cutoff:3.500A) Processing helix chain '3' and resid 288 through 292 removed outlier: 3.737A pdb=" N GLU 3 291 " --> pdb=" O SER 3 288 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 312 removed outlier: 3.753A pdb=" N LEU 3 297 " --> pdb=" O SER 3 293 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS 3 298 " --> pdb=" O ALA 3 294 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN 3 309 " --> pdb=" O VAL 3 305 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA 3 310 " --> pdb=" O ALA 3 306 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 14 removed outlier: 3.514A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 35 removed outlier: 3.522A pdb=" N TYR 4 34 " --> pdb=" O LEU 4 30 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA 4 35 " --> pdb=" O LYS 4 31 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 68 removed outlier: 4.064A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.712A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 96 Processing helix chain '4' and resid 100 through 113 Processing helix chain '4' and resid 118 through 124 Processing helix chain '4' and resid 131 through 138 removed outlier: 3.530A pdb=" N ALA 4 137 " --> pdb=" O ASP 4 133 " (cutoff:3.500A) Processing helix chain '4' and resid 138 through 150 removed outlier: 4.641A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 177 removed outlier: 3.687A pdb=" N PHE 4 165 " --> pdb=" O GLY 4 161 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 189 Processing helix chain '4' and resid 192 through 234 removed outlier: 3.597A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA 4 213 " --> pdb=" O SER 4 209 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA 4 217 " --> pdb=" O ALA 4 213 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 3.610A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 285 removed outlier: 3.583A pdb=" N GLU 4 266 " --> pdb=" O ALA 4 262 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA 4 285 " --> pdb=" O SER 4 281 " (cutoff:3.500A) Processing helix chain '5' and resid 7 through 29 removed outlier: 3.546A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 30 through 59 removed outlier: 3.716A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN 5 52 " --> pdb=" O ALA 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 67 Processing helix chain '5' and resid 72 through 81 Processing helix chain '5' and resid 89 through 106 removed outlier: 3.718A pdb=" N SER 5 97 " --> pdb=" O GLU 5 93 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL 5 102 " --> pdb=" O ALA 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 removed outlier: 3.740A pdb=" N LYS 5 119 " --> pdb=" O ILE 5 115 " (cutoff:3.500A) Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 47 through 49 No H-bonds generated for 'chain '6' and resid 47 through 49' Processing helix chain '6' and resid 50 through 58 Processing helix chain '6' and resid 72 through 95 removed outlier: 3.502A pdb=" N LEU 6 79 " --> pdb=" O ALA 6 75 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 104 Processing helix chain '6' and resid 104 through 120 removed outlier: 3.677A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU 6 113 " --> pdb=" O GLN 6 109 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE 6 120 " --> pdb=" O PHE 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 131 Processing helix chain '6' and resid 133 through 138 removed outlier: 3.847A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '7' and resid 83 through 102 removed outlier: 3.643A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) Processing helix chain '7' and resid 103 through 107 removed outlier: 3.957A pdb=" N TRP 7 107 " --> pdb=" O LEU 7 104 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 114 removed outlier: 3.519A pdb=" N THR 7 112 " --> pdb=" O ASP 7 109 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 120 Processing helix chain '7' and resid 123 through 145 removed outlier: 3.562A pdb=" N TYR 7 137 " --> pdb=" O ALA 7 133 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS 7 139 " --> pdb=" O ASP 7 135 " (cutoff:3.500A) Processing helix chain '7' and resid 146 through 148 No H-bonds generated for 'chain '7' and resid 146 through 148' Processing helix chain '7' and resid 149 through 163 removed outlier: 3.763A pdb=" N SER 7 155 " --> pdb=" O SER 7 151 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN 7 156 " --> pdb=" O ALA 7 152 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL 7 157 " --> pdb=" O LEU 7 153 " (cutoff:3.500A) Proline residue: 7 159 - end of helix Processing helix chain '7' and resid 174 through 187 removed outlier: 3.578A pdb=" N ASN 7 184 " --> pdb=" O GLY 7 180 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 removed outlier: 3.963A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 32 through 37 Processing helix chain '8' and resid 39 through 44 Processing helix chain '8' and resid 44 through 78 removed outlier: 3.824A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 17 removed outlier: 3.863A pdb=" N LYS 9 9 " --> pdb=" O SER 9 5 " (cutoff:3.500A) Processing helix chain '9' and resid 19 through 24 removed outlier: 3.541A pdb=" N PHE 9 24 " --> pdb=" O ALA 9 20 " (cutoff:3.500A) Processing helix chain '9' and resid 33 through 55 removed outlier: 3.516A pdb=" N ALA 9 38 " --> pdb=" O GLY 9 34 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN 9 50 " --> pdb=" O MET 9 46 " (cutoff:3.500A) Processing helix chain '9' and resid 76 through 80 removed outlier: 3.728A pdb=" N GLN 9 80 " --> pdb=" O TRP 9 77 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 95 removed outlier: 3.640A pdb=" N ALA 9 86 " --> pdb=" O ASP 9 82 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS 9 95 " --> pdb=" O LYS 9 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 68 removed outlier: 3.909A pdb=" N MET A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 92 removed outlier: 3.838A pdb=" N VAL A 74 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 86 " --> pdb=" O PHE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 3.671A pdb=" N GLY A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 120 " --> pdb=" O PHE A 116 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 68 removed outlier: 3.637A pdb=" N MET B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 92 removed outlier: 4.085A pdb=" N GLY B 73 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 86 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 119 removed outlier: 3.659A pdb=" N GLY B 101 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'C' and resid 55 through 68 removed outlier: 4.172A pdb=" N MET C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 92 removed outlier: 4.313A pdb=" N GLY C 73 " --> pdb=" O ILE C 69 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 125 removed outlier: 3.587A pdb=" N GLY C 101 " --> pdb=" O LYS C 97 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ILE C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 68 removed outlier: 3.944A pdb=" N MET D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 92 removed outlier: 4.243A pdb=" N GLY D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE D 86 " --> pdb=" O PHE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 3.564A pdb=" N ALA D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 68 removed outlier: 4.229A pdb=" N MET E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 92 removed outlier: 4.333A pdb=" N GLY E 73 " --> pdb=" O ILE E 69 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 86 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 126 removed outlier: 3.582A pdb=" N GLY E 101 " --> pdb=" O LYS E 97 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER E 112 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 114 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL E 120 " --> pdb=" O PHE E 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 68 removed outlier: 4.003A pdb=" N MET F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 92 removed outlier: 4.130A pdb=" N GLY F 73 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE F 86 " --> pdb=" O PHE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 125 removed outlier: 3.869A pdb=" N GLY F 101 " --> pdb=" O LYS F 97 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 105 " --> pdb=" O GLY F 101 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 114 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 120 " --> pdb=" O PHE F 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 68 removed outlier: 3.990A pdb=" N MET G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 92 removed outlier: 4.207A pdb=" N GLY G 73 " --> pdb=" O ILE G 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL G 74 " --> pdb=" O ALA G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 111 removed outlier: 3.707A pdb=" N GLY G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU G 105 " --> pdb=" O GLY G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 126 Processing helix chain 'H' and resid 55 through 68 removed outlier: 3.788A pdb=" N MET H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 92 removed outlier: 4.349A pdb=" N GLY H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL H 74 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN H 92 " --> pdb=" O GLY H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.508A pdb=" N VAL H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 109 " --> pdb=" O LEU H 105 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER H 112 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 66 removed outlier: 3.592A pdb=" N MET I 61 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY I 65 " --> pdb=" O MET I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 92 removed outlier: 4.133A pdb=" N GLY I 73 " --> pdb=" O ILE I 69 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL I 74 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE I 86 " --> pdb=" O PHE I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 127 removed outlier: 3.831A pdb=" N LEU I 105 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER I 112 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE I 113 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL I 120 " --> pdb=" O PHE I 116 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU I 125 " --> pdb=" O VAL I 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 68 removed outlier: 4.023A pdb=" N MET J 61 " --> pdb=" O ALA J 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL J 62 " --> pdb=" O ALA J 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 92 removed outlier: 4.104A pdb=" N GLY J 73 " --> pdb=" O ILE J 69 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 126 removed outlier: 3.567A pdb=" N GLY J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE J 113 " --> pdb=" O LEU J 109 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 119 Processing helix chain 'M' and resid 134 through 142 Processing helix chain 'M' and resid 147 through 164 removed outlier: 3.534A pdb=" N THR M 153 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 198 removed outlier: 3.655A pdb=" N SER M 187 " --> pdb=" O GLY M 183 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 264 removed outlier: 3.864A pdb=" N SER M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG M 232 " --> pdb=" O SER M 228 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA M 233 " --> pdb=" O TYR M 229 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL M 234 " --> pdb=" O THR M 230 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA M 260 " --> pdb=" O GLY M 256 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 270 through 308 removed outlier: 4.175A pdb=" N THR M 274 " --> pdb=" O MET M 270 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY M 276 " --> pdb=" O PRO M 272 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 311 No H-bonds generated for 'chain 'M' and resid 309 through 311' Processing helix chain 'P' and resid 50 through 64 removed outlier: 3.718A pdb=" N ALA P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 84 removed outlier: 4.046A pdb=" N ASP P 72 " --> pdb=" O ASP P 68 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU P 73 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU P 74 " --> pdb=" O VAL P 70 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 93 Processing helix chain 'P' and resid 97 through 109 removed outlier: 3.685A pdb=" N THR P 102 " --> pdb=" O THR P 98 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER P 107 " --> pdb=" O LYS P 103 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 128 removed outlier: 4.055A pdb=" N GLU P 123 " --> pdb=" O LYS P 119 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA P 124 " --> pdb=" O LYS P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 130 through 132 No H-bonds generated for 'chain 'P' and resid 130 through 132' Processing helix chain 'P' and resid 133 through 149 removed outlier: 3.951A pdb=" N VAL P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 165 through 175 removed outlier: 3.536A pdb=" N GLU P 169 " --> pdb=" O LEU P 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 229 removed outlier: 3.507A pdb=" N LYS P 224 " --> pdb=" O ASN P 220 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU P 227 " --> pdb=" O ASN P 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 13 removed outlier: 3.584A pdb=" N GLY Q 13 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 29 Processing helix chain 'Q' and resid 32 through 37 removed outlier: 3.511A pdb=" N ALA Q 37 " --> pdb=" O GLU Q 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 38 removed outlier: 3.799A pdb=" N THR R 34 " --> pdb=" O PRO R 30 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU R 35 " --> pdb=" O LYS R 31 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL R 36 " --> pdb=" O GLU R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 Processing helix chain 'R' and resid 153 through 155 No H-bonds generated for 'chain 'R' and resid 153 through 155' Processing helix chain 'R' and resid 156 through 168 removed outlier: 3.918A pdb=" N VAL R 160 " --> pdb=" O ASP R 156 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS R 161 " --> pdb=" O PRO R 157 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER R 162 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 196 removed outlier: 3.573A pdb=" N ALA R 190 " --> pdb=" O GLU R 186 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 71 removed outlier: 3.708A pdb=" N ASN S 52 " --> pdb=" O ARG S 48 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS S 58 " --> pdb=" O GLY S 54 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET S 62 " --> pdb=" O LYS S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 71 through 79 removed outlier: 3.690A pdb=" N VAL S 75 " --> pdb=" O ALA S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 89 removed outlier: 3.688A pdb=" N VAL S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 128 removed outlier: 3.681A pdb=" N THR S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG S 124 " --> pdb=" O THR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 171 through 185 removed outlier: 3.635A pdb=" N LEU S 182 " --> pdb=" O ILE S 178 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N HIS S 185 " --> pdb=" O GLU S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 216 through 221 removed outlier: 3.542A pdb=" N GLU S 221 " --> pdb=" O GLU S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 274 removed outlier: 3.898A pdb=" N ARG S 244 " --> pdb=" O SER S 240 " (cutoff:3.500A) Processing helix chain 'S' and resid 274 through 279 Processing helix chain 'S' and resid 279 through 313 removed outlier: 3.953A pdb=" N LEU S 285 " --> pdb=" O ALA S 281 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU S 290 " --> pdb=" O GLY S 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 65 Processing helix chain 'T' and resid 66 through 76 removed outlier: 3.592A pdb=" N LYS T 71 " --> pdb=" O ILE T 67 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 134 through 138 removed outlier: 3.913A pdb=" N VAL T 137 " --> pdb=" O ASN T 134 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 213 Processing helix chain 'T' and resid 230 through 247 removed outlier: 3.512A pdb=" N LYS T 243 " --> pdb=" O ILE T 239 " (cutoff:3.500A) Processing helix chain 'T' and resid 266 through 280 removed outlier: 3.529A pdb=" N ALA T 270 " --> pdb=" O ARG T 266 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU T 272 " --> pdb=" O THR T 268 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 283 No H-bonds generated for 'chain 'T' and resid 281 through 283' Processing helix chain 'T' and resid 295 through 316 Proline residue: T 303 - end of helix removed outlier: 4.343A pdb=" N PHE T 313 " --> pdb=" O MET T 309 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG T 314 " --> pdb=" O ALA T 310 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 removed outlier: 3.756A pdb=" N VAL T 332 " --> pdb=" O SER T 328 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA T 333 " --> pdb=" O LYS T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 350 Processing helix chain 'T' and resid 351 through 353 No H-bonds generated for 'chain 'T' and resid 351 through 353' Processing helix chain 'T' and resid 354 through 363 removed outlier: 3.509A pdb=" N HIS T 358 " --> pdb=" O VAL T 354 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU T 361 " --> pdb=" O LEU T 357 " (cutoff:3.500A) Processing helix chain 'T' and resid 392 through 402 Processing helix chain 'T' and resid 409 through 415 Processing helix chain 'T' and resid 430 through 435 removed outlier: 3.706A pdb=" N ALA T 433 " --> pdb=" O VAL T 430 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA T 434 " --> pdb=" O GLY T 431 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN T 435 " --> pdb=" O SER T 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 430 through 435' Processing helix chain 'T' and resid 436 through 441 removed outlier: 3.506A pdb=" N GLN T 441 " --> pdb=" O PRO T 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 442 through 456 removed outlier: 3.744A pdb=" N LEU T 448 " --> pdb=" O GLY T 444 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU T 455 " --> pdb=" O ALA T 451 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL T 456 " --> pdb=" O GLN T 452 " (cutoff:3.500A) Processing helix chain 'T' and resid 458 through 462 removed outlier: 3.517A pdb=" N GLN T 461 " --> pdb=" O ALA T 458 " (cutoff:3.500A) Processing helix chain 'T' and resid 470 through 481 Processing helix chain 'T' and resid 493 through 506 removed outlier: 3.808A pdb=" N ALA T 504 " --> pdb=" O ALA T 500 " (cutoff:3.500A) Processing helix chain 'T' and resid 516 through 521 removed outlier: 3.912A pdb=" N ALA T 520 " --> pdb=" O ASP T 516 " (cutoff:3.500A) Processing helix chain 'T' and resid 522 through 528 Processing helix chain 'T' and resid 530 through 540 Processing helix chain 'T' and resid 543 through 556 removed outlier: 4.078A pdb=" N ALA T 548 " --> pdb=" O PRO T 544 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS T 549 " --> pdb=" O ALA T 545 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG T 555 " --> pdb=" O LYS T 551 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS T 556 " --> pdb=" O ALA T 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 46 Processing helix chain 'U' and resid 47 through 50 Processing helix chain 'U' and resid 58 through 71 removed outlier: 3.724A pdb=" N SER U 63 " --> pdb=" O ILE U 59 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLN U 64 " --> pdb=" O GLN U 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE U 67 " --> pdb=" O SER U 63 " (cutoff:3.500A) Proline residue: U 68 - end of helix Processing helix chain 'U' and resid 72 through 74 No H-bonds generated for 'chain 'U' and resid 72 through 74' Processing helix chain 'U' and resid 156 through 160 Processing helix chain 'U' and resid 206 through 213 Processing helix chain 'U' and resid 230 through 247 removed outlier: 3.515A pdb=" N ALA U 235 " --> pdb=" O LYS U 231 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS U 243 " --> pdb=" O ILE U 239 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN U 244 " --> pdb=" O ILE U 240 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU U 247 " --> pdb=" O LYS U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 265 through 280 removed outlier: 3.659A pdb=" N LEU U 275 " --> pdb=" O GLN U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 281 through 284 Processing helix chain 'U' and resid 295 through 315 Proline residue: U 303 - end of helix removed outlier: 3.531A pdb=" N TYR U 312 " --> pdb=" O ALA U 308 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE U 313 " --> pdb=" O MET U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 329 through 341 Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 351 through 352 No H-bonds generated for 'chain 'U' and resid 351 through 352' Processing helix chain 'U' and resid 353 through 363 removed outlier: 3.772A pdb=" N HIS U 358 " --> pdb=" O VAL U 354 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU U 361 " --> pdb=" O LEU U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 369 through 373 Processing helix chain 'U' and resid 392 through 402 Processing helix chain 'U' and resid 409 through 415 removed outlier: 3.622A pdb=" N TYR U 414 " --> pdb=" O THR U 410 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 443 removed outlier: 3.557A pdb=" N GLN U 441 " --> pdb=" O PRO U 437 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL U 442 " --> pdb=" O GLY U 438 " (cutoff:3.500A) Processing helix chain 'U' and resid 443 through 448 removed outlier: 3.704A pdb=" N LEU U 448 " --> pdb=" O GLY U 444 " (cutoff:3.500A) Processing helix chain 'U' and resid 450 through 455 Processing helix chain 'U' and resid 456 through 460 removed outlier: 3.836A pdb=" N ALA U 460 " --> pdb=" O ALA U 457 " (cutoff:3.500A) Processing helix chain 'U' and resid 465 through 469 removed outlier: 3.800A pdb=" N ALA U 468 " --> pdb=" O ASP U 465 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA U 469 " --> pdb=" O LEU U 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 465 through 469' Processing helix chain 'U' and resid 471 through 485 removed outlier: 3.575A pdb=" N ARG U 479 " --> pdb=" O GLU U 475 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU U 482 " --> pdb=" O ALA U 478 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET U 483 " --> pdb=" O ARG U 479 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS U 485 " --> pdb=" O THR U 481 " (cutoff:3.500A) Processing helix chain 'U' and resid 493 through 501 removed outlier: 3.520A pdb=" N ALA U 500 " --> pdb=" O ARG U 496 " (cutoff:3.500A) Processing helix chain 'U' and resid 501 through 506 Processing helix chain 'U' and resid 520 through 527 Processing helix chain 'U' and resid 530 through 540 removed outlier: 3.873A pdb=" N LYS U 534 " --> pdb=" O PRO U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 543 through 554 removed outlier: 3.563A pdb=" N ALA U 548 " --> pdb=" O PRO U 544 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS U 549 " --> pdb=" O ALA U 545 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 67 removed outlier: 3.855A pdb=" N HIS V 61 " --> pdb=" O TYR V 57 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 138 removed outlier: 3.748A pdb=" N VAL V 137 " --> pdb=" O ASN V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 160 removed outlier: 3.627A pdb=" N LEU V 160 " --> pdb=" O PRO V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 213 Processing helix chain 'V' and resid 230 through 247 removed outlier: 3.799A pdb=" N GLU V 247 " --> pdb=" O LYS V 243 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 253 Processing helix chain 'V' and resid 265 through 280 Processing helix chain 'V' and resid 281 through 283 No H-bonds generated for 'chain 'V' and resid 281 through 283' Processing helix chain 'V' and resid 295 through 315 Proline residue: V 303 - end of helix removed outlier: 4.502A pdb=" N PHE V 313 " --> pdb=" O MET V 309 " (cutoff:3.500A) Processing helix chain 'V' and resid 327 through 341 removed outlier: 3.558A pdb=" N ALA V 333 " --> pdb=" O LYS V 329 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 350 removed outlier: 3.677A pdb=" N ALA V 349 " --> pdb=" O GLY V 346 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 352 No H-bonds generated for 'chain 'V' and resid 351 through 352' Processing helix chain 'V' and resid 353 through 363 removed outlier: 3.694A pdb=" N HIS V 358 " --> pdb=" O VAL V 354 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU V 361 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 369 through 373 removed outlier: 3.793A pdb=" N GLY V 373 " --> pdb=" O LYS V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 400 Processing helix chain 'V' and resid 409 through 414 removed outlier: 3.548A pdb=" N TYR V 414 " --> pdb=" O THR V 410 " (cutoff:3.500A) Processing helix chain 'V' and resid 438 through 454 removed outlier: 3.634A pdb=" N GLY V 444 " --> pdb=" O LYS V 440 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR V 445 " --> pdb=" O GLN V 441 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN V 452 " --> pdb=" O LEU V 448 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 470 through 485 removed outlier: 3.505A pdb=" N LEU V 474 " --> pdb=" O THR V 470 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA V 478 " --> pdb=" O LEU V 474 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG V 479 " --> pdb=" O GLU V 475 " (cutoff:3.500A) Processing helix chain 'V' and resid 493 through 506 removed outlier: 3.831A pdb=" N VAL V 499 " --> pdb=" O GLU V 495 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA V 500 " --> pdb=" O ARG V 496 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA V 504 " --> pdb=" O ALA V 500 " (cutoff:3.500A) Processing helix chain 'V' and resid 513 through 515 No H-bonds generated for 'chain 'V' and resid 513 through 515' Processing helix chain 'V' and resid 516 through 528 removed outlier: 3.543A pdb=" N GLU V 522 " --> pdb=" O VAL V 518 " (cutoff:3.500A) Processing helix chain 'V' and resid 530 through 540 removed outlier: 3.899A pdb=" N LYS V 534 " --> pdb=" O PRO V 530 " (cutoff:3.500A) Processing helix chain 'V' and resid 545 through 555 removed outlier: 3.706A pdb=" N HIS V 549 " --> pdb=" O ALA V 545 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG V 555 " --> pdb=" O LYS V 551 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 118 Processing helix chain 'X' and resid 166 through 171 Processing helix chain 'X' and resid 188 through 200 Processing helix chain 'X' and resid 216 through 230 Processing helix chain 'X' and resid 235 through 242 removed outlier: 4.202A pdb=" N GLU X 238 " --> pdb=" O LEU X 235 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N GLY X 240 " --> pdb=" O ALA X 237 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 259 Processing helix chain 'X' and resid 260 through 275 Processing helix chain 'X' and resid 287 through 296 removed outlier: 3.700A pdb=" N THR X 291 " --> pdb=" O ILE X 287 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 302 Processing helix chain 'X' and resid 313 through 323 Processing helix chain 'X' and resid 342 through 345 Processing helix chain 'X' and resid 348 through 355 removed outlier: 3.707A pdb=" N THR X 354 " --> pdb=" O ALA X 350 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE X 355 " --> pdb=" O PRO X 351 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 365 through 370 Processing helix chain 'X' and resid 388 through 393 Processing helix chain 'X' and resid 393 through 421 removed outlier: 3.554A pdb=" N ASN X 398 " --> pdb=" O ALA X 394 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP X 415 " --> pdb=" O LYS X 411 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE X 416 " --> pdb=" O ASN X 412 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA X 418 " --> pdb=" O GLN X 414 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE X 419 " --> pdb=" O ASP X 415 " (cutoff:3.500A) Processing helix chain 'X' and resid 430 through 443 removed outlier: 3.589A pdb=" N ARG X 441 " --> pdb=" O ARG X 437 " (cutoff:3.500A) Processing helix chain 'X' and resid 447 through 449 No H-bonds generated for 'chain 'X' and resid 447 through 449' Processing helix chain 'X' and resid 450 through 455 Processing helix chain 'X' and resid 462 through 476 removed outlier: 3.682A pdb=" N GLY X 469 " --> pdb=" O ASP X 465 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL X 473 " --> pdb=" O GLY X 469 " (cutoff:3.500A) Processing helix chain 'X' and resid 482 through 487 removed outlier: 4.078A pdb=" N PHE X 486 " --> pdb=" O GLU X 483 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR X 487 " --> pdb=" O MET X 484 " (cutoff:3.500A) Processing helix chain 'X' and resid 491 through 505 removed outlier: 3.800A pdb=" N VAL X 495 " --> pdb=" O ASP X 491 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU X 497 " --> pdb=" O LYS X 493 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP X 500 " --> pdb=" O LYS X 496 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA X 503 " --> pdb=" O ALA X 499 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP X 505 " --> pdb=" O LYS X 501 " (cutoff:3.500A) Processing helix chain 'X' and resid 519 through 524 removed outlier: 4.316A pdb=" N ASP X 523 " --> pdb=" O GLU X 519 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 533 Processing helix chain 'Y' and resid 114 through 118 Processing helix chain 'Y' and resid 149 through 153 Processing helix chain 'Y' and resid 164 through 171 Processing helix chain 'Y' and resid 188 through 203 removed outlier: 3.568A pdb=" N MET Y 194 " --> pdb=" O THR Y 190 " (cutoff:3.500A) Processing helix chain 'Y' and resid 216 through 230 Processing helix chain 'Y' and resid 235 through 242 removed outlier: 3.850A pdb=" N GLU Y 238 " --> pdb=" O LEU Y 235 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG Y 239 " --> pdb=" O GLY Y 236 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLY Y 240 " --> pdb=" O ALA Y 237 " (cutoff:3.500A) Processing helix chain 'Y' and resid 254 through 275 removed outlier: 5.032A pdb=" N ALA Y 262 " --> pdb=" O ARG Y 258 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU Y 263 " --> pdb=" O ALA Y 259 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE Y 272 " --> pdb=" O VAL Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 301 Processing helix chain 'Y' and resid 313 through 323 removed outlier: 3.548A pdb=" N LEU Y 321 " --> pdb=" O ASP Y 317 " (cutoff:3.500A) Processing helix chain 'Y' and resid 341 through 345 Processing helix chain 'Y' and resid 348 through 355 Processing helix chain 'Y' and resid 365 through 371 Processing helix chain 'Y' and resid 388 through 412 removed outlier: 7.400A pdb=" N ALA Y 394 " --> pdb=" O ASN Y 390 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N GLU Y 395 " --> pdb=" O VAL Y 391 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N HIS Y 396 " --> pdb=" O ILE Y 392 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN Y 412 " --> pdb=" O GLN Y 408 " (cutoff:3.500A) Processing helix chain 'Y' and resid 413 through 420 removed outlier: 3.840A pdb=" N ILE Y 419 " --> pdb=" O ASP Y 415 " (cutoff:3.500A) Processing helix chain 'Y' and resid 426 through 440 removed outlier: 4.545A pdb=" N THR Y 432 " --> pdb=" O GLU Y 428 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL Y 433 " --> pdb=" O ASP Y 429 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing helix chain 'Y' and resid 447 through 451 Processing helix chain 'Y' and resid 462 through 476 removed outlier: 3.563A pdb=" N SER Y 468 " --> pdb=" O ALA Y 464 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N VAL Y 473 " --> pdb=" O GLY Y 469 " (cutoff:3.500A) Processing helix chain 'Y' and resid 491 through 504 removed outlier: 3.819A pdb=" N LYS Y 496 " --> pdb=" O ILE Y 492 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU Y 497 " --> pdb=" O LYS Y 493 " (cutoff:3.500A) Processing helix chain 'Y' and resid 505 through 508 Processing helix chain 'Y' and resid 526 through 531 Processing helix chain 'Y' and resid 544 through 554 removed outlier: 3.558A pdb=" N LYS Y 550 " --> pdb=" O GLU Y 546 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU Y 552 " --> pdb=" O ASP Y 548 " (cutoff:3.500A) Processing helix chain 'Z' and resid 114 through 118 Processing helix chain 'Z' and resid 149 through 153 removed outlier: 3.502A pdb=" N GLN Z 153 " --> pdb=" O PHE Z 150 " (cutoff:3.500A) Processing helix chain 'Z' and resid 164 through 171 Processing helix chain 'Z' and resid 190 through 201 Processing helix chain 'Z' and resid 216 through 230 Processing helix chain 'Z' and resid 235 through 242 removed outlier: 3.857A pdb=" N GLU Z 238 " --> pdb=" O LEU Z 235 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY Z 240 " --> pdb=" O ALA Z 237 " (cutoff:3.500A) Processing helix chain 'Z' and resid 254 through 275 removed outlier: 4.974A pdb=" N ALA Z 262 " --> pdb=" O ARG Z 258 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU Z 263 " --> pdb=" O ALA Z 259 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE Z 272 " --> pdb=" O VAL Z 268 " (cutoff:3.500A) Processing helix chain 'Z' and resid 287 through 299 removed outlier: 3.780A pdb=" N THR Z 291 " --> pdb=" O ILE Z 287 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL Z 297 " --> pdb=" O ALA Z 293 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA Z 299 " --> pdb=" O SER Z 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 313 through 323 Processing helix chain 'Z' and resid 348 through 355 removed outlier: 3.555A pdb=" N THR Z 354 " --> pdb=" O ALA Z 350 " (cutoff:3.500A) Processing helix chain 'Z' and resid 356 through 358 No H-bonds generated for 'chain 'Z' and resid 356 through 358' Processing helix chain 'Z' and resid 365 through 371 removed outlier: 3.548A pdb=" N LEU Z 371 " --> pdb=" O SER Z 367 " (cutoff:3.500A) Processing helix chain 'Z' and resid 388 through 393 Processing helix chain 'Z' and resid 393 through 413 removed outlier: 3.548A pdb=" N VAL Z 399 " --> pdb=" O GLU Z 395 " (cutoff:3.500A) Processing helix chain 'Z' and resid 415 through 421 Processing helix chain 'Z' and resid 422 through 425 removed outlier: 3.644A pdb=" N LEU Z 425 " --> pdb=" O MET Z 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 422 through 425' Processing helix chain 'Z' and resid 429 through 443 removed outlier: 3.824A pdb=" N ARG Z 441 " --> pdb=" O ARG Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 450 through 455 Processing helix chain 'Z' and resid 462 through 476 removed outlier: 3.597A pdb=" N VAL Z 473 " --> pdb=" O GLY Z 469 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU Z 474 " --> pdb=" O PHE Z 470 " (cutoff:3.500A) Processing helix chain 'Z' and resid 491 through 500 removed outlier: 3.500A pdb=" N VAL Z 495 " --> pdb=" O ASP Z 491 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS Z 496 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) Processing helix chain 'Z' and resid 500 through 508 removed outlier: 3.803A pdb=" N ILE Z 506 " --> pdb=" O MET Z 502 " (cutoff:3.500A) Processing helix chain 'Z' and resid 509 through 511 No H-bonds generated for 'chain 'Z' and resid 509 through 511' Processing helix chain 'Z' and resid 527 through 533 removed outlier: 3.524A pdb=" N SER Z 532 " --> pdb=" O ASP Z 528 " (cutoff:3.500A) 2437 hydrogen bonds defined for protein. 7098 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: 17.24 Time building geometry restraints manager: 11.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14096 1.33 - 1.45: 9547 1.45 - 1.57: 30776 1.57 - 1.69: 21 1.69 - 1.81: 254 Bond restraints: 54694 Sorted by residual: bond pdb=" C4 ATP T1001 " pdb=" C5 ATP T1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.91e+01 bond pdb=" C4 ATP U1001 " pdb=" C5 ATP U1001 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.89e+01 bond pdb=" C4 ATP V1001 " pdb=" C5 ATP V1001 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C5 ATP U1001 " pdb=" C6 ATP U1001 " ideal model delta sigma weight residual 1.409 1.467 -0.058 1.00e-02 1.00e+04 3.39e+01 bond pdb=" C5 ATP V1001 " pdb=" N7 ATP V1001 " ideal model delta sigma weight residual 1.387 1.330 0.057 1.00e-02 1.00e+04 3.25e+01 ... (remaining 54689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 73103 3.21 - 6.42: 956 6.42 - 9.64: 94 9.64 - 12.85: 14 12.85 - 16.06: 5 Bond angle restraints: 74172 Sorted by residual: angle pdb=" PB ATP U1001 " pdb=" O3B ATP U1001 " pdb=" PG ATP U1001 " ideal model delta sigma weight residual 139.87 123.81 16.06 1.00e+00 1.00e+00 2.58e+02 angle pdb=" PB ATP T1001 " pdb=" O3B ATP T1001 " pdb=" PG ATP T1001 " ideal model delta sigma weight residual 139.87 124.81 15.06 1.00e+00 1.00e+00 2.27e+02 angle pdb=" PA ATP V1001 " pdb=" O3A ATP V1001 " pdb=" PB ATP V1001 " ideal model delta sigma weight residual 136.83 122.95 13.88 1.00e+00 1.00e+00 1.93e+02 angle pdb=" PB ATP V1001 " pdb=" O3B ATP V1001 " pdb=" PG ATP V1001 " ideal model delta sigma weight residual 139.87 126.96 12.91 1.00e+00 1.00e+00 1.67e+02 angle pdb=" PA ATP T1001 " pdb=" O3A ATP T1001 " pdb=" PB ATP T1001 " ideal model delta sigma weight residual 136.83 124.78 12.05 1.00e+00 1.00e+00 1.45e+02 ... (remaining 74167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 32457 35.96 - 71.91: 531 71.91 - 107.87: 38 107.87 - 143.83: 1 143.83 - 179.78: 3 Dihedral angle restraints: 33030 sinusoidal: 12669 harmonic: 20361 Sorted by residual: dihedral pdb=" CA ALA Y 307 " pdb=" C ALA Y 307 " pdb=" N VAL Y 308 " pdb=" CA VAL Y 308 " ideal model delta harmonic sigma weight residual -180.00 -124.45 -55.55 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA ALA Z 307 " pdb=" C ALA Z 307 " pdb=" N VAL Z 308 " pdb=" CA VAL Z 308 " ideal model delta harmonic sigma weight residual -180.00 -127.26 -52.74 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" CA ALA X 307 " pdb=" C ALA X 307 " pdb=" N VAL X 308 " pdb=" CA VAL X 308 " ideal model delta harmonic sigma weight residual -180.00 -129.04 -50.96 0 5.00e+00 4.00e-02 1.04e+02 ... (remaining 33027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 7182 0.078 - 0.155: 1363 0.155 - 0.233: 127 0.233 - 0.311: 14 0.311 - 0.388: 4 Chirality restraints: 8690 Sorted by residual: chirality pdb=" CB VAL V 180 " pdb=" CA VAL V 180 " pdb=" CG1 VAL V 180 " pdb=" CG2 VAL V 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CB ILE 3 90 " pdb=" CA ILE 3 90 " pdb=" CG1 ILE 3 90 " pdb=" CG2 ILE 3 90 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB VAL U 81 " pdb=" CA VAL U 81 " pdb=" CG1 VAL U 81 " pdb=" CG2 VAL U 81 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 8687 not shown) Planarity restraints: 9512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Z 503 " 0.032 2.00e-02 2.50e+03 6.33e-02 4.01e+01 pdb=" C ALA Z 503 " -0.110 2.00e-02 2.50e+03 pdb=" O ALA Z 503 " 0.041 2.00e-02 2.50e+03 pdb=" N LYS Z 504 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU M 261 " 0.064 5.00e-02 4.00e+02 9.68e-02 1.50e+01 pdb=" N PRO M 262 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO M 262 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO M 262 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR 1 92 " -0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO 1 93 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO 1 93 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO 1 93 " -0.047 5.00e-02 4.00e+02 ... (remaining 9509 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 15 2.13 - 2.82: 17582 2.82 - 3.51: 69894 3.51 - 4.21: 138761 4.21 - 4.90: 234634 Nonbonded interactions: 460886 Sorted by model distance: nonbonded pdb=" CD2 LEU P 37 " pdb=" NE1 TRP V 73 " model vdw 1.436 3.540 nonbonded pdb=" O ASP T 467 " pdb=" N ALA T 469 " model vdw 1.499 3.120 nonbonded pdb=" OE1 GLU M 288 " pdb=" O HOH M 701 " model vdw 1.660 3.040 nonbonded pdb=" O GLN Q 49 " pdb=" O SER Q 60 " model vdw 1.937 3.040 nonbonded pdb=" OG1 THR T 232 " pdb="MG MG T1002 " model vdw 2.038 2.170 ... (remaining 460881 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = (chain 'T' and (resid 43 through 562 or resid 1001 through 1002)) selection = (chain 'U' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) selection = (chain 'V' and (resid 43 through 561 or (resid 562 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1001 through 1002)) } ncs_group { reference = (chain 'X' and resid 36 through 556) selection = chain 'Y' selection = (chain 'Z' and resid 36 through 556) } 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=1.00 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: 4.520 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: 1.630 Check model and map are aligned: 0.330 Set scattering table: 0.400 Process input model: 102.400 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.360 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: 0.020 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.011 0.134 54694 Z= 0.691 Angle : 0.980 16.061 74172 Z= 0.559 Chirality : 0.061 0.388 8690 Planarity : 0.007 0.097 9512 Dihedral : 14.360 179.785 19942 Min Nonbonded Distance : 1.436 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.67 % Favored : 95.11 % Rotamer: Outliers : 0.48 % Allowed : 5.45 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -5.14 (0.07), residues: 7039 helix: -4.37 (0.04), residues: 3763 sheet: -1.41 (0.19), residues: 629 loop : -2.02 (0.10), residues: 2647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP Z 141 HIS 0.012 0.002 HIS 7 123 PHE 0.035 0.003 PHE S 249 TYR 0.025 0.003 TYR 7 119 ARG 0.014 0.001 ARG 3 242 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 883 time to evaluate : 4.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 109 LYS cc_start: 0.8624 (tptt) cc_final: 0.8355 (tppt) REVERT: 1 283 ASP cc_start: 0.8474 (m-30) cc_final: 0.8256 (m-30) REVERT: 1 604 ARG cc_start: 0.7649 (ttm-80) cc_final: 0.7357 (mtm-85) REVERT: 1 613 ASP cc_start: 0.8096 (m-30) cc_final: 0.7850 (m-30) REVERT: 2 131 LYS cc_start: 0.7744 (mppt) cc_final: 0.7335 (ptpt) REVERT: 2 154 ASP cc_start: 0.6538 (t0) cc_final: 0.5682 (p0) REVERT: 3 151 ASN cc_start: 0.7495 (t0) cc_final: 0.7192 (t0) REVERT: 4 133 ASP cc_start: 0.8248 (t0) cc_final: 0.7955 (t0) REVERT: 4 271 ASP cc_start: 0.7985 (m-30) cc_final: 0.7686 (m-30) REVERT: 5 54 LYS cc_start: 0.8965 (tttt) cc_final: 0.8736 (tttp) REVERT: 5 115 ILE cc_start: 0.9115 (tp) cc_final: 0.8660 (tp) REVERT: 6 37 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8118 (ttmt) REVERT: 7 24 GLN cc_start: 0.7760 (tm-30) cc_final: 0.7481 (tp40) REVERT: 7 129 LYS cc_start: 0.8414 (mttt) cc_final: 0.8128 (mtpt) REVERT: 8 39 LYS cc_start: 0.8818 (tttm) cc_final: 0.8609 (tttp) REVERT: 8 69 LYS cc_start: 0.8154 (mttt) cc_final: 0.5945 (tmtt) REVERT: B 81 MET cc_start: 0.8815 (ttp) cc_final: 0.8195 (tmm) REVERT: B 82 PHE cc_start: 0.8846 (m-80) cc_final: 0.8596 (m-80) REVERT: C 92 ASN cc_start: 0.8701 (t0) cc_final: 0.8414 (t0) REVERT: C 95 ILE cc_start: 0.9017 (pt) cc_final: 0.8483 (pt) REVERT: H 61 MET cc_start: 0.7608 (mmp) cc_final: 0.7333 (mmm) REVERT: J 81 MET cc_start: 0.7403 (ttp) cc_final: 0.7117 (ttp) REVERT: M 168 MET cc_start: 0.8156 (mmp) cc_final: 0.7887 (mmt) REVERT: M 230 THR cc_start: 0.9128 (t) cc_final: 0.8887 (m) REVERT: M 324 LYS cc_start: 0.6917 (tptt) cc_final: 0.6567 (tmtt) REVERT: P 73 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: P 136 GLU cc_start: 0.8245 (mp0) cc_final: 0.7661 (mp0) REVERT: Q 10 ARG cc_start: 0.8098 (tpp-160) cc_final: 0.7602 (mmt180) REVERT: Q 52 TYR cc_start: 0.7597 (m-80) cc_final: 0.7284 (m-80) REVERT: S 109 LYS cc_start: 0.8386 (pttt) cc_final: 0.8097 (pttp) REVERT: S 153 ILE cc_start: 0.7632 (tt) cc_final: 0.7171 (tt) REVERT: S 240 SER cc_start: 0.8936 (m) cc_final: 0.8477 (p) REVERT: S 244 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7480 (ttp80) REVERT: T 49 ARG cc_start: 0.8428 (mtp-110) cc_final: 0.7894 (mtp85) REVERT: T 447 LYS cc_start: 0.8498 (ptpt) cc_final: 0.8234 (ptpp) REVERT: T 448 LEU cc_start: 0.8772 (tp) cc_final: 0.8528 (tp) REVERT: T 479 ARG cc_start: 0.6691 (mmp-170) cc_final: 0.5157 (tpt170) REVERT: T 525 ILE cc_start: 0.8466 (pt) cc_final: 0.8242 (mm) REVERT: U 74 GLU cc_start: 0.8170 (pp20) cc_final: 0.7874 (pm20) REVERT: U 75 LYS cc_start: 0.8277 (mmpt) cc_final: 0.7506 (mttp) REVERT: U 496 ARG cc_start: 0.8675 (mtt180) cc_final: 0.8437 (mtt-85) REVERT: U 515 GLN cc_start: 0.8126 (mp10) cc_final: 0.7921 (mp10) REVERT: V 287 MET cc_start: 0.8547 (tpt) cc_final: 0.8223 (tpt) REVERT: V 471 GLN cc_start: 0.6782 (tp40) cc_final: 0.6432 (tp40) REVERT: X 168 ASP cc_start: 0.8455 (m-30) cc_final: 0.8016 (m-30) REVERT: X 386 MET cc_start: 0.8654 (mmm) cc_final: 0.8348 (mmm) REVERT: X 411 LYS cc_start: 0.8666 (tttt) cc_final: 0.8440 (mmmt) REVERT: Y 194 MET cc_start: 0.8981 (mtm) cc_final: 0.8778 (mtp) REVERT: Y 422 MET cc_start: 0.6434 (tpt) cc_final: 0.6214 (mmm) REVERT: Y 441 ARG cc_start: 0.8554 (mmt-90) cc_final: 0.8244 (mpt180) REVERT: Z 49 ASP cc_start: 0.8040 (m-30) cc_final: 0.7732 (m-30) REVERT: Z 82 ASP cc_start: 0.7676 (t0) cc_final: 0.7317 (t0) REVERT: Z 226 GLU cc_start: 0.7412 (tp30) cc_final: 0.7136 (tp30) REVERT: Z 502 MET cc_start: 0.8089 (mtp) cc_final: 0.7650 (mtp) outliers start: 27 outliers final: 14 residues processed: 908 average time/residue: 0.6013 time to fit residues: 888.1708 Evaluate side-chains 629 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 614 time to evaluate : 4.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain P residue 73 GLU Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain V residue 180 VAL Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain Z residue 399 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 589 optimal weight: 3.9990 chunk 529 optimal weight: 0.8980 chunk 293 optimal weight: 0.6980 chunk 180 optimal weight: 0.9980 chunk 356 optimal weight: 2.9990 chunk 282 optimal weight: 0.6980 chunk 547 optimal weight: 0.8980 chunk 211 optimal weight: 0.6980 chunk 332 optimal weight: 0.9990 chunk 407 optimal weight: 0.7980 chunk 633 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 0 60 GLN 0 61 HIS 1 48 ASN 1 257 HIS 1 285 GLN 1 316 ASN 1 482 ASN 1 531 HIS 1 587 ASN 1 590 HIS ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 74 ASN 2 243 GLN 2 289 HIS 3 206 ASN 4 135 ASN 4 240 GLN 5 107 ASN 6 40 ASN 6 74 GLN 7 86 HIS 7 123 HIS 7 170 HIS 7 184 ASN 8 26 HIS 8 78 HIS 9 35 GLN 9 56 ASN F 92 ASN F 98 GLN G 92 ASN H 98 GLN J 94 ASN M 108 ASN M 163 ASN P 52 GLN P 66 GLN P 223 ASN R 73 ASN R 85 GLN R 104 HIS R 137 HIS ** S 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 257 ASN S 262 ASN T 64 GLN T 134 ASN ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 386 GLN T 435 GLN U 60 GLN U 78 GLN U 179 ASN U 242 GLN U 319 HIS U 497 GLN U 539 ASN V 64 GLN V 123 GLN V 139 HIS V 152 ASN V 196 GLN V 242 GLN V 386 GLN V 435 GLN V 461 GLN V 486 GLN V 497 GLN X 204 HIS Y 199 ASN Y 252 ASN Y 278 GLN Y 286 ASN Z 42 GLN Z 199 ASN Z 337 GLN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 54694 Z= 0.197 Angle : 0.615 12.858 74172 Z= 0.324 Chirality : 0.043 0.174 8690 Planarity : 0.005 0.070 9512 Dihedral : 7.412 177.537 7690 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.27 % Favored : 96.59 % Rotamer: Outliers : 1.42 % Allowed : 8.75 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.94 (0.09), residues: 7039 helix: -2.14 (0.07), residues: 3842 sheet: -1.31 (0.20), residues: 617 loop : -1.46 (0.11), residues: 2580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP V 73 HIS 0.005 0.001 HIS V 61 PHE 0.022 0.001 PHE P 221 TYR 0.026 0.001 TYR 4 211 ARG 0.005 0.000 ARG Y 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 713 time to evaluate : 4.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 109 LYS cc_start: 0.8360 (tptt) cc_final: 0.8096 (tppt) REVERT: 1 486 ASP cc_start: 0.7687 (m-30) cc_final: 0.7427 (m-30) REVERT: 1 613 ASP cc_start: 0.7865 (m-30) cc_final: 0.7544 (m-30) REVERT: 2 74 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.7985 (m-40) REVERT: 2 131 LYS cc_start: 0.7649 (mppt) cc_final: 0.7177 (ptpt) REVERT: 2 154 ASP cc_start: 0.6642 (t0) cc_final: 0.5725 (p0) REVERT: 2 358 LYS cc_start: 0.8565 (mttp) cc_final: 0.8316 (mttt) REVERT: 3 151 ASN cc_start: 0.7522 (t0) cc_final: 0.7278 (t0) REVERT: 4 133 ASP cc_start: 0.8192 (t0) cc_final: 0.7964 (t0) REVERT: 4 271 ASP cc_start: 0.7998 (m-30) cc_final: 0.7600 (m-30) REVERT: 5 115 ILE cc_start: 0.9030 (tp) cc_final: 0.8588 (tp) REVERT: 6 30 ASN cc_start: 0.8372 (p0) cc_final: 0.8124 (p0) REVERT: 8 3 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8251 (tt) REVERT: 8 69 LYS cc_start: 0.8126 (mttt) cc_final: 0.6015 (tmtt) REVERT: 9 56 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8446 (p0) REVERT: A 81 MET cc_start: 0.8131 (ttp) cc_final: 0.7771 (ttp) REVERT: B 81 MET cc_start: 0.8668 (ttp) cc_final: 0.8419 (ttp) REVERT: E 102 TYR cc_start: 0.8524 (m-80) cc_final: 0.8230 (m-10) REVERT: H 61 MET cc_start: 0.7597 (mmp) cc_final: 0.7379 (mmm) REVERT: M 168 MET cc_start: 0.8076 (mmp) cc_final: 0.7809 (mmt) REVERT: M 230 THR cc_start: 0.9235 (t) cc_final: 0.8916 (m) REVERT: M 254 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8175 (mp) REVERT: M 324 LYS cc_start: 0.7020 (tptt) cc_final: 0.6514 (tmtt) REVERT: P 49 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7827 (t) REVERT: P 127 ASP cc_start: 0.8385 (t70) cc_final: 0.8034 (t70) REVERT: P 136 GLU cc_start: 0.7912 (mp0) cc_final: 0.7365 (mp0) REVERT: P 191 ASP cc_start: 0.7821 (t0) cc_final: 0.7518 (t0) REVERT: Q 10 ARG cc_start: 0.8442 (tpp-160) cc_final: 0.7964 (mmt180) REVERT: Q 52 TYR cc_start: 0.7728 (m-80) cc_final: 0.7479 (m-80) REVERT: S 109 LYS cc_start: 0.8369 (pttt) cc_final: 0.8005 (pttp) REVERT: S 158 TYR cc_start: 0.7974 (t80) cc_final: 0.7686 (t80) REVERT: S 240 SER cc_start: 0.8932 (m) cc_final: 0.8595 (p) REVERT: S 244 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7448 (ttp80) REVERT: T 49 ARG cc_start: 0.8374 (mtp-110) cc_final: 0.7786 (mtp85) REVERT: T 447 LYS cc_start: 0.8438 (ptpt) cc_final: 0.8079 (ptpp) REVERT: T 479 ARG cc_start: 0.6747 (mmp-170) cc_final: 0.5167 (tpt170) REVERT: U 46 ASP cc_start: 0.7342 (m-30) cc_final: 0.7009 (m-30) REVERT: U 49 ARG cc_start: 0.6666 (mtp180) cc_final: 0.6262 (mtt-85) REVERT: U 74 GLU cc_start: 0.8152 (pp20) cc_final: 0.7764 (pm20) REVERT: U 474 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7339 (mp) REVERT: U 476 ARG cc_start: 0.7013 (tpp80) cc_final: 0.6786 (tpp80) REVERT: U 539 ASN cc_start: 0.8152 (m-40) cc_final: 0.7560 (m110) REVERT: V 236 ILE cc_start: 0.9166 (pt) cc_final: 0.8963 (pt) REVERT: V 287 MET cc_start: 0.8501 (tpt) cc_final: 0.8138 (tpt) REVERT: V 452 GLN cc_start: 0.7597 (pt0) cc_final: 0.7077 (pt0) REVERT: V 471 GLN cc_start: 0.6562 (tp40) cc_final: 0.6306 (tp40) REVERT: V 549 HIS cc_start: 0.7102 (m90) cc_final: 0.6868 (m-70) REVERT: Y 430 LYS cc_start: 0.6390 (ptmt) cc_final: 0.5778 (mtmm) REVERT: Z 49 ASP cc_start: 0.8060 (m-30) cc_final: 0.7741 (m-30) REVERT: Z 82 ASP cc_start: 0.7767 (t0) cc_final: 0.7303 (t0) REVERT: Z 198 ASN cc_start: 0.8582 (t0) cc_final: 0.8254 (t0) REVERT: Z 266 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8380 (tt) outliers start: 80 outliers final: 42 residues processed: 764 average time/residue: 0.5427 time to fit residues: 684.5548 Evaluate side-chains 662 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 613 time to evaluate : 4.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 261 LEU Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 2 residue 74 ASN Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 268 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 56 ASN Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 199 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 475 GLU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 352 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 527 optimal weight: 0.3980 chunk 431 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 635 optimal weight: 6.9990 chunk 685 optimal weight: 1.9990 chunk 565 optimal weight: 0.0030 chunk 629 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 509 optimal weight: 0.0970 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 1 298 GLN ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 74 ASN 2 177 GLN 4 111 GLN 7 24 GLN 9 27 ASN 9 35 GLN F 92 ASN F 98 GLN H 98 GLN S 41 GLN T 126 HIS ** T 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 497 GLN U 386 GLN ** U 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 515 GLN V 121 ASN V 126 HIS V 241 HIS Y 286 ASN Y 440 GLN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 54694 Z= 0.172 Angle : 0.545 11.010 74172 Z= 0.284 Chirality : 0.042 0.187 8690 Planarity : 0.004 0.062 9512 Dihedral : 6.832 168.381 7680 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.41 % Rotamer: Outliers : 1.94 % Allowed : 10.12 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.60 (0.10), residues: 7039 helix: -0.83 (0.08), residues: 3838 sheet: -1.18 (0.20), residues: 622 loop : -1.12 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 9 73 HIS 0.007 0.001 HIS V 83 PHE 0.021 0.001 PHE A 107 TYR 0.025 0.001 TYR 4 211 ARG 0.004 0.000 ARG T 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 698 time to evaluate : 4.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 109 LYS cc_start: 0.8282 (tptt) cc_final: 0.7994 (tppt) REVERT: 1 486 ASP cc_start: 0.7735 (m-30) cc_final: 0.7488 (m-30) REVERT: 1 613 ASP cc_start: 0.7672 (m-30) cc_final: 0.7312 (m-30) REVERT: 2 74 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7936 (m-40) REVERT: 2 131 LYS cc_start: 0.7626 (mppt) cc_final: 0.7179 (ptpt) REVERT: 2 154 ASP cc_start: 0.6597 (t0) cc_final: 0.5709 (p0) REVERT: 2 358 LYS cc_start: 0.8570 (mttp) cc_final: 0.8325 (mttt) REVERT: 3 151 ASN cc_start: 0.7483 (t0) cc_final: 0.7250 (t0) REVERT: 5 108 LEU cc_start: 0.8487 (mt) cc_final: 0.8260 (mt) REVERT: 5 115 ILE cc_start: 0.9043 (tp) cc_final: 0.8604 (tp) REVERT: 7 101 TYR cc_start: 0.8632 (t80) cc_final: 0.8425 (t80) REVERT: 8 39 LYS cc_start: 0.8775 (tttm) cc_final: 0.8403 (tppt) REVERT: 8 69 LYS cc_start: 0.8047 (mttt) cc_final: 0.6006 (tmtt) REVERT: 9 56 ASN cc_start: 0.8650 (p0) cc_final: 0.8097 (p0) REVERT: 9 80 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7587 (mm110) REVERT: A 81 MET cc_start: 0.8065 (ttp) cc_final: 0.7728 (ttp) REVERT: B 81 MET cc_start: 0.8688 (ttp) cc_final: 0.8462 (ttp) REVERT: B 92 ASN cc_start: 0.9105 (p0) cc_final: 0.8776 (p0) REVERT: B 102 TYR cc_start: 0.8156 (m-10) cc_final: 0.7912 (m-80) REVERT: I 61 MET cc_start: 0.7215 (ttm) cc_final: 0.6971 (ttt) REVERT: J 119 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.6702 (mt) REVERT: M 168 MET cc_start: 0.7963 (mmp) cc_final: 0.7694 (mmt) REVERT: M 187 SER cc_start: 0.8583 (m) cc_final: 0.8339 (m) REVERT: M 230 THR cc_start: 0.9226 (t) cc_final: 0.8902 (m) REVERT: M 254 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8126 (mp) REVERT: M 324 LYS cc_start: 0.7039 (tptt) cc_final: 0.6531 (tmtt) REVERT: P 49 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7726 (t) REVERT: P 127 ASP cc_start: 0.8342 (t70) cc_final: 0.8067 (t70) REVERT: P 136 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: P 227 LEU cc_start: 0.8630 (mt) cc_final: 0.8390 (mt) REVERT: Q 10 ARG cc_start: 0.8442 (tpp-160) cc_final: 0.7859 (mmt180) REVERT: Q 52 TYR cc_start: 0.7612 (m-80) cc_final: 0.7367 (m-80) REVERT: S 48 ARG cc_start: 0.7082 (ttt-90) cc_final: 0.6785 (ttt-90) REVERT: S 240 SER cc_start: 0.8959 (m) cc_final: 0.8636 (p) REVERT: S 244 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7461 (ttp80) REVERT: T 49 ARG cc_start: 0.8364 (mtp-110) cc_final: 0.7803 (mtp85) REVERT: T 447 LYS cc_start: 0.8423 (ptpt) cc_final: 0.8096 (ptpp) REVERT: T 475 GLU cc_start: 0.5729 (tm-30) cc_final: 0.5157 (mm-30) REVERT: T 479 ARG cc_start: 0.6828 (mmp-170) cc_final: 0.5117 (tpt170) REVERT: U 46 ASP cc_start: 0.7351 (m-30) cc_final: 0.7039 (m-30) REVERT: U 49 ARG cc_start: 0.6531 (mtp180) cc_final: 0.6236 (mtt-85) REVERT: U 74 GLU cc_start: 0.8189 (pp20) cc_final: 0.7683 (pm20) REVERT: U 474 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7250 (mp) REVERT: U 539 ASN cc_start: 0.8182 (m-40) cc_final: 0.7606 (m110) REVERT: V 287 MET cc_start: 0.8531 (tpt) cc_final: 0.8214 (tpt) REVERT: V 471 GLN cc_start: 0.6569 (tp40) cc_final: 0.6336 (tp40) REVERT: X 480 ASP cc_start: 0.6420 (OUTLIER) cc_final: 0.6073 (m-30) REVERT: Y 430 LYS cc_start: 0.6177 (ptmt) cc_final: 0.5908 (mtmm) REVERT: Y 437 ARG cc_start: 0.8278 (mtp180) cc_final: 0.7809 (mtp85) REVERT: Z 49 ASP cc_start: 0.8043 (m-30) cc_final: 0.7506 (m-30) REVERT: Z 82 ASP cc_start: 0.7765 (t0) cc_final: 0.7283 (t0) REVERT: Z 198 ASN cc_start: 0.8502 (t0) cc_final: 0.8220 (t0) REVERT: Z 226 GLU cc_start: 0.7494 (tp30) cc_final: 0.6940 (tp30) REVERT: Z 229 GLU cc_start: 0.7526 (pp20) cc_final: 0.7210 (pp20) REVERT: Z 266 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8363 (tt) REVERT: Z 359 ASP cc_start: 0.8600 (m-30) cc_final: 0.8243 (m-30) outliers start: 109 outliers final: 62 residues processed: 767 average time/residue: 0.5482 time to fit residues: 699.6596 Evaluate side-chains 684 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 614 time to evaluate : 4.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 608 ASP Chi-restraints excluded: chain 2 residue 74 ASN Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 268 VAL Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 7 residue 24 GLN Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 216 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 159 GLN Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 300 PHE Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 383 THR Chi-restraints excluded: chain X residue 480 ASP Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 530 LEU Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 627 optimal weight: 0.0010 chunk 477 optimal weight: 0.0040 chunk 329 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 303 optimal weight: 0.0870 chunk 426 optimal weight: 4.9990 chunk 637 optimal weight: 5.9990 chunk 674 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 603 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 74 ASN 7 24 GLN 8 78 HIS 9 35 GLN F 98 GLN P 52 GLN R 181 ASN S 41 GLN S 195 ASN T 134 ASN T 497 GLN T 549 HIS U 515 GLN V 121 ASN Y 286 ASN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 471 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 54694 Z= 0.160 Angle : 0.521 10.501 74172 Z= 0.270 Chirality : 0.041 0.195 8690 Planarity : 0.004 0.058 9512 Dihedral : 6.459 157.240 7678 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.41 % Favored : 96.49 % Rotamer: Outliers : 2.06 % Allowed : 11.13 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.84 (0.10), residues: 7039 helix: -0.12 (0.08), residues: 3845 sheet: -0.99 (0.21), residues: 595 loop : -0.90 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 9 73 HIS 0.009 0.001 HIS U 549 PHE 0.025 0.001 PHE I 107 TYR 0.024 0.001 TYR 4 211 ARG 0.005 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 697 time to evaluate : 4.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 276 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8961 (pt) REVERT: 1 486 ASP cc_start: 0.7718 (m-30) cc_final: 0.7466 (m-30) REVERT: 1 613 ASP cc_start: 0.7631 (m-30) cc_final: 0.7296 (m-30) REVERT: 2 74 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7840 (m-40) REVERT: 2 131 LYS cc_start: 0.7632 (mppt) cc_final: 0.7219 (ptpt) REVERT: 2 154 ASP cc_start: 0.6774 (t0) cc_final: 0.5750 (p0) REVERT: 2 358 LYS cc_start: 0.8524 (mttp) cc_final: 0.8272 (mttt) REVERT: 3 151 ASN cc_start: 0.7474 (t0) cc_final: 0.7257 (t0) REVERT: 3 269 GLN cc_start: 0.8389 (tt0) cc_final: 0.8186 (tp40) REVERT: 4 54 GLU cc_start: 0.8131 (pt0) cc_final: 0.7905 (pt0) REVERT: 5 108 LEU cc_start: 0.8309 (mt) cc_final: 0.8032 (mt) REVERT: 8 3 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8406 (tt) REVERT: 8 39 LYS cc_start: 0.8825 (tttm) cc_final: 0.8412 (tppt) REVERT: 8 69 LYS cc_start: 0.8002 (mttt) cc_final: 0.5996 (tmtt) REVERT: 9 56 ASN cc_start: 0.8673 (p0) cc_final: 0.8453 (p0) REVERT: 9 80 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7609 (mm110) REVERT: A 81 MET cc_start: 0.8010 (ttp) cc_final: 0.7721 (ttp) REVERT: B 81 MET cc_start: 0.8700 (ttp) cc_final: 0.8461 (ttp) REVERT: B 92 ASN cc_start: 0.9104 (p0) cc_final: 0.8672 (p0) REVERT: H 107 PHE cc_start: 0.8407 (t80) cc_final: 0.8095 (t80) REVERT: J 119 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.6645 (mt) REVERT: M 168 MET cc_start: 0.7989 (mmt) cc_final: 0.7745 (mmt) REVERT: M 187 SER cc_start: 0.8586 (m) cc_final: 0.8334 (m) REVERT: M 230 THR cc_start: 0.9175 (t) cc_final: 0.8883 (m) REVERT: M 324 LYS cc_start: 0.7082 (tptt) cc_final: 0.6517 (tmtt) REVERT: P 127 ASP cc_start: 0.8410 (t70) cc_final: 0.8187 (t70) REVERT: P 136 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: P 186 MET cc_start: 0.4470 (mmm) cc_final: 0.4120 (mmm) REVERT: P 227 LEU cc_start: 0.8631 (mt) cc_final: 0.8398 (mt) REVERT: Q 10 ARG cc_start: 0.8494 (tpp-160) cc_final: 0.8083 (mmt180) REVERT: S 48 ARG cc_start: 0.7171 (ttt-90) cc_final: 0.6855 (ttt-90) REVERT: S 220 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8081 (mm) REVERT: S 240 SER cc_start: 0.8972 (m) cc_final: 0.8640 (p) REVERT: S 244 ARG cc_start: 0.7871 (ttm-80) cc_final: 0.7438 (ttp80) REVERT: T 49 ARG cc_start: 0.8371 (mtp-110) cc_final: 0.7875 (mtp85) REVERT: T 447 LYS cc_start: 0.8424 (ptpt) cc_final: 0.8090 (ptpp) REVERT: T 475 GLU cc_start: 0.5852 (tm-30) cc_final: 0.5342 (mm-30) REVERT: T 479 ARG cc_start: 0.6801 (mmp-170) cc_final: 0.5075 (tpt170) REVERT: U 46 ASP cc_start: 0.7416 (m-30) cc_final: 0.7110 (m-30) REVERT: U 49 ARG cc_start: 0.6546 (mtp180) cc_final: 0.6242 (mtt-85) REVERT: U 74 GLU cc_start: 0.8133 (pp20) cc_final: 0.7610 (pm20) REVERT: U 474 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7411 (mp) REVERT: U 496 ARG cc_start: 0.8538 (mtt-85) cc_final: 0.8254 (mtt-85) REVERT: U 539 ASN cc_start: 0.8202 (m-40) cc_final: 0.7625 (m110) REVERT: V 61 HIS cc_start: 0.7812 (t-170) cc_final: 0.7526 (t-170) REVERT: V 287 MET cc_start: 0.8553 (tpt) cc_final: 0.8236 (tpt) REVERT: V 471 GLN cc_start: 0.6509 (tp40) cc_final: 0.6288 (tp40) REVERT: X 538 VAL cc_start: 0.6979 (OUTLIER) cc_final: 0.6631 (m) REVERT: Y 430 LYS cc_start: 0.6316 (ptmt) cc_final: 0.5872 (mtmm) REVERT: Y 437 ARG cc_start: 0.8249 (mtp180) cc_final: 0.7800 (mtp85) REVERT: Y 530 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8168 (tt) REVERT: Z 49 ASP cc_start: 0.8002 (m-30) cc_final: 0.7512 (m-30) REVERT: Z 82 ASP cc_start: 0.7710 (t0) cc_final: 0.7209 (t0) REVERT: Z 226 GLU cc_start: 0.7391 (tp30) cc_final: 0.7124 (tp30) REVERT: Z 266 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8355 (tt) REVERT: Z 359 ASP cc_start: 0.8540 (m-30) cc_final: 0.8139 (m-30) outliers start: 116 outliers final: 71 residues processed: 776 average time/residue: 0.5476 time to fit residues: 708.0041 Evaluate side-chains 708 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 627 time to evaluate : 4.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 437 VAL Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 74 ASN Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 24 GLN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 216 GLU Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Y residue 530 LEU Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 561 optimal weight: 0.5980 chunk 382 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 502 optimal weight: 0.2980 chunk 278 optimal weight: 9.9990 chunk 575 optimal weight: 0.8980 chunk 466 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 344 optimal weight: 2.9990 chunk 605 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 48 ASN 2 44 ASN ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 229 ASN 7 24 GLN 8 78 HIS F 98 GLN P 59 GLN P 187 GLN R 181 ASN S 41 GLN T 134 ASN T 461 GLN T 497 GLN T 549 HIS U 515 GLN V 121 ASN Y 241 ASN Y 286 ASN ** Z 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54694 Z= 0.194 Angle : 0.527 11.431 74172 Z= 0.271 Chirality : 0.042 0.172 8690 Planarity : 0.004 0.057 9512 Dihedral : 6.334 162.881 7675 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.47 % Favored : 96.45 % Rotamer: Outliers : 2.36 % Allowed : 11.97 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.44 (0.10), residues: 7039 helix: 0.25 (0.09), residues: 3833 sheet: -0.93 (0.21), residues: 605 loop : -0.78 (0.12), residues: 2601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.006 0.001 HIS U 549 PHE 0.025 0.001 PHE I 107 TYR 0.023 0.001 TYR 4 211 ARG 0.011 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 661 time to evaluate : 4.613 Fit side-chains revert: symmetry clash REVERT: 1 39 LYS cc_start: 0.8371 (tppt) cc_final: 0.8111 (tptp) REVERT: 1 216 LEU cc_start: 0.8842 (mt) cc_final: 0.8362 (tt) REVERT: 1 276 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8963 (pt) REVERT: 1 486 ASP cc_start: 0.7664 (m-30) cc_final: 0.7445 (m-30) REVERT: 1 572 ASP cc_start: 0.7865 (m-30) cc_final: 0.7517 (m-30) REVERT: 1 613 ASP cc_start: 0.7681 (m-30) cc_final: 0.7314 (m-30) REVERT: 2 74 ASN cc_start: 0.8238 (t0) cc_final: 0.7801 (m-40) REVERT: 2 131 LYS cc_start: 0.7649 (mppt) cc_final: 0.7232 (ptpt) REVERT: 2 154 ASP cc_start: 0.6719 (t0) cc_final: 0.5743 (p0) REVERT: 2 358 LYS cc_start: 0.8580 (mttp) cc_final: 0.8281 (mttt) REVERT: 3 151 ASN cc_start: 0.7437 (t0) cc_final: 0.7236 (t0) REVERT: 4 54 GLU cc_start: 0.8061 (pt0) cc_final: 0.7844 (pt0) REVERT: 5 108 LEU cc_start: 0.8285 (mt) cc_final: 0.7986 (mt) REVERT: 6 71 TYR cc_start: 0.7013 (m-10) cc_final: 0.6740 (m-80) REVERT: 8 39 LYS cc_start: 0.8822 (tttm) cc_final: 0.8425 (tppt) REVERT: 8 69 LYS cc_start: 0.8003 (mttt) cc_final: 0.6005 (tmtt) REVERT: 9 1 MET cc_start: 0.2106 (ptt) cc_final: -0.0877 (mpp) REVERT: 9 50 ASN cc_start: 0.7872 (m-40) cc_final: 0.7670 (m110) REVERT: 9 56 ASN cc_start: 0.8765 (p0) cc_final: 0.8015 (p0) REVERT: 9 80 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7631 (mm110) REVERT: A 81 MET cc_start: 0.8001 (ttp) cc_final: 0.7712 (ttp) REVERT: B 81 MET cc_start: 0.8720 (ttp) cc_final: 0.8481 (ttp) REVERT: B 92 ASN cc_start: 0.9094 (p0) cc_final: 0.8651 (p0) REVERT: H 107 PHE cc_start: 0.8446 (t80) cc_final: 0.8088 (t80) REVERT: J 119 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.6607 (mt) REVERT: M 168 MET cc_start: 0.7994 (mmt) cc_final: 0.7763 (mmt) REVERT: M 187 SER cc_start: 0.8586 (m) cc_final: 0.8326 (m) REVERT: M 230 THR cc_start: 0.9163 (t) cc_final: 0.8865 (m) REVERT: M 324 LYS cc_start: 0.7207 (tptt) cc_final: 0.6539 (tmtt) REVERT: P 66 GLN cc_start: 0.8423 (mt0) cc_final: 0.7983 (mt0) REVERT: P 127 ASP cc_start: 0.8438 (t70) cc_final: 0.8212 (t70) REVERT: P 136 GLU cc_start: 0.7870 (mp0) cc_final: 0.7290 (mp0) REVERT: P 227 LEU cc_start: 0.8632 (mt) cc_final: 0.8412 (mt) REVERT: Q 10 ARG cc_start: 0.8496 (tpp-160) cc_final: 0.8053 (mmt180) REVERT: S 48 ARG cc_start: 0.7190 (ttt-90) cc_final: 0.6851 (ttt-90) REVERT: S 220 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7861 (mm) REVERT: S 240 SER cc_start: 0.8966 (m) cc_final: 0.8638 (p) REVERT: S 244 ARG cc_start: 0.7881 (ttm-80) cc_final: 0.7440 (ttp80) REVERT: T 49 ARG cc_start: 0.8380 (mtp-110) cc_final: 0.7882 (mtp85) REVERT: T 447 LYS cc_start: 0.8425 (ptpt) cc_final: 0.8196 (ptpp) REVERT: T 475 GLU cc_start: 0.6085 (tm-30) cc_final: 0.5527 (mm-30) REVERT: T 479 ARG cc_start: 0.6846 (mmp-170) cc_final: 0.5150 (tpt170) REVERT: U 72 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7732 (tm-30) REVERT: U 74 GLU cc_start: 0.8124 (pp20) cc_final: 0.7589 (pm20) REVERT: U 474 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7382 (mp) REVERT: U 539 ASN cc_start: 0.8212 (m-40) cc_final: 0.7672 (m110) REVERT: V 61 HIS cc_start: 0.7774 (t-170) cc_final: 0.7449 (t-170) REVERT: V 287 MET cc_start: 0.8533 (tpt) cc_final: 0.8217 (tpt) REVERT: V 471 GLN cc_start: 0.6510 (tp40) cc_final: 0.6287 (tp40) REVERT: V 515 GLN cc_start: 0.7862 (mt0) cc_final: 0.7558 (pm20) REVERT: X 538 VAL cc_start: 0.6977 (OUTLIER) cc_final: 0.6633 (m) REVERT: Y 371 LEU cc_start: 0.8271 (mp) cc_final: 0.8028 (mp) REVERT: Y 430 LYS cc_start: 0.6491 (ptmt) cc_final: 0.6086 (mtmm) REVERT: Z 49 ASP cc_start: 0.8010 (m-30) cc_final: 0.7500 (m-30) REVERT: Z 82 ASP cc_start: 0.7720 (t0) cc_final: 0.7219 (t0) REVERT: Z 266 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8387 (tt) REVERT: Z 359 ASP cc_start: 0.8556 (m-30) cc_final: 0.8141 (m-30) REVERT: Z 395 GLU cc_start: 0.8159 (tp30) cc_final: 0.7950 (tp30) outliers start: 133 outliers final: 87 residues processed: 761 average time/residue: 0.5373 time to fit residues: 680.4718 Evaluate side-chains 714 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 621 time to evaluate : 4.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 437 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 497 LEU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 24 GLN Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 216 GLU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 93 THR Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 266 LEU Chi-restraints excluded: chain Z residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 226 optimal weight: 5.9990 chunk 607 optimal weight: 0.2980 chunk 133 optimal weight: 7.9990 chunk 396 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 675 optimal weight: 0.7980 chunk 560 optimal weight: 4.9990 chunk 312 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 chunk 354 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 111 GLN 5 82 HIS 8 78 HIS F 98 GLN R 181 ASN S 41 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 461 GLN T 497 GLN U 515 GLN V 121 ASN Y 286 ASN Z 388 ASN Z 440 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54694 Z= 0.225 Angle : 0.539 11.981 74172 Z= 0.276 Chirality : 0.043 0.165 8690 Planarity : 0.004 0.056 9512 Dihedral : 6.317 171.787 7675 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 2.47 % Allowed : 12.25 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.22 (0.10), residues: 7039 helix: 0.44 (0.09), residues: 3837 sheet: -0.85 (0.21), residues: 615 loop : -0.70 (0.13), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.005 0.001 HIS V 83 PHE 0.027 0.001 PHE I 107 TYR 0.023 0.001 TYR 4 211 ARG 0.011 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 650 time to evaluate : 4.600 Fit side-chains revert: symmetry clash REVERT: 1 39 LYS cc_start: 0.8388 (tppt) cc_final: 0.8173 (tptp) REVERT: 1 216 LEU cc_start: 0.8822 (mt) cc_final: 0.8342 (tt) REVERT: 1 276 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8970 (pt) REVERT: 1 486 ASP cc_start: 0.7689 (m-30) cc_final: 0.7484 (m-30) REVERT: 1 572 ASP cc_start: 0.7876 (m-30) cc_final: 0.7408 (m-30) REVERT: 1 613 ASP cc_start: 0.7711 (m-30) cc_final: 0.7354 (m-30) REVERT: 2 74 ASN cc_start: 0.8262 (t0) cc_final: 0.7816 (t0) REVERT: 2 131 LYS cc_start: 0.7689 (mppt) cc_final: 0.7250 (ptpt) REVERT: 2 154 ASP cc_start: 0.6779 (t0) cc_final: 0.5785 (p0) REVERT: 2 358 LYS cc_start: 0.8582 (mttp) cc_final: 0.8266 (mttt) REVERT: 3 151 ASN cc_start: 0.7443 (t0) cc_final: 0.7217 (t0) REVERT: 4 54 GLU cc_start: 0.8002 (pt0) cc_final: 0.7777 (pt0) REVERT: 5 108 LEU cc_start: 0.8285 (mt) cc_final: 0.7982 (mt) REVERT: 6 71 TYR cc_start: 0.6959 (m-10) cc_final: 0.6736 (m-80) REVERT: 8 3 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8387 (tt) REVERT: 8 39 LYS cc_start: 0.8875 (tttm) cc_final: 0.8470 (tppt) REVERT: 8 69 LYS cc_start: 0.7973 (mttt) cc_final: 0.5957 (tmtt) REVERT: 9 1 MET cc_start: 0.2140 (ptt) cc_final: -0.0604 (mpp) REVERT: 9 56 ASN cc_start: 0.8761 (p0) cc_final: 0.8500 (p0) REVERT: 9 80 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7620 (mm110) REVERT: A 81 MET cc_start: 0.8023 (ttp) cc_final: 0.7718 (ttp) REVERT: B 81 MET cc_start: 0.8733 (ttp) cc_final: 0.8484 (ttp) REVERT: B 92 ASN cc_start: 0.9099 (p0) cc_final: 0.8660 (p0) REVERT: H 107 PHE cc_start: 0.8448 (t80) cc_final: 0.8073 (t80) REVERT: I 60 LYS cc_start: 0.7888 (mttm) cc_final: 0.7599 (ttmm) REVERT: J 119 LEU cc_start: 0.7975 (tt) cc_final: 0.6615 (mt) REVERT: M 168 MET cc_start: 0.8022 (mmt) cc_final: 0.7796 (mmt) REVERT: M 187 SER cc_start: 0.8593 (m) cc_final: 0.8333 (m) REVERT: M 294 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8754 (mp) REVERT: M 324 LYS cc_start: 0.7124 (tptt) cc_final: 0.6565 (tmtt) REVERT: P 66 GLN cc_start: 0.8472 (mt0) cc_final: 0.8028 (mt0) REVERT: P 127 ASP cc_start: 0.8444 (t70) cc_final: 0.8186 (t70) REVERT: P 136 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: P 186 MET cc_start: 0.3351 (mmm) cc_final: 0.2941 (mmm) REVERT: P 227 LEU cc_start: 0.8633 (mt) cc_final: 0.8417 (mt) REVERT: Q 10 ARG cc_start: 0.8520 (tpp-160) cc_final: 0.8158 (mmt180) REVERT: S 48 ARG cc_start: 0.7198 (ttt-90) cc_final: 0.6888 (ttt-90) REVERT: S 158 TYR cc_start: 0.8135 (t80) cc_final: 0.7789 (t80) REVERT: S 220 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7883 (mm) REVERT: S 240 SER cc_start: 0.8966 (m) cc_final: 0.8612 (p) REVERT: S 244 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7454 (ttp80) REVERT: T 49 ARG cc_start: 0.8395 (mtp-110) cc_final: 0.7894 (mtp85) REVERT: T 447 LYS cc_start: 0.8438 (ptpt) cc_final: 0.8083 (ptpp) REVERT: T 475 GLU cc_start: 0.6138 (tm-30) cc_final: 0.5559 (mm-30) REVERT: T 479 ARG cc_start: 0.6945 (mmp-170) cc_final: 0.5171 (tpt170) REVERT: U 72 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8121 (tm-30) REVERT: U 74 GLU cc_start: 0.8159 (pp20) cc_final: 0.7551 (pm20) REVERT: U 474 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7341 (mp) REVERT: V 61 HIS cc_start: 0.7811 (t-170) cc_final: 0.7451 (t-170) REVERT: V 471 GLN cc_start: 0.6526 (tp40) cc_final: 0.6304 (tp40) REVERT: V 515 GLN cc_start: 0.7877 (mt0) cc_final: 0.7527 (pm20) REVERT: X 538 VAL cc_start: 0.6975 (OUTLIER) cc_final: 0.6640 (m) REVERT: Y 371 LEU cc_start: 0.8269 (mp) cc_final: 0.8011 (mp) REVERT: Y 430 LYS cc_start: 0.6442 (ptmt) cc_final: 0.6032 (mtmm) REVERT: Z 49 ASP cc_start: 0.8057 (m-30) cc_final: 0.7529 (m-30) REVERT: Z 82 ASP cc_start: 0.7758 (t0) cc_final: 0.7255 (t0) REVERT: Z 359 ASP cc_start: 0.8582 (m-30) cc_final: 0.8187 (m-30) outliers start: 139 outliers final: 109 residues processed: 752 average time/residue: 0.5245 time to fit residues: 660.2624 Evaluate side-chains 738 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 622 time to evaluate : 4.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 437 VAL Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 493 LEU Chi-restraints excluded: chain 1 residue 497 LEU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 4 residue 255 ARG Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 73 TRP Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 294 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 192 LYS Chi-restraints excluded: chain P residue 216 GLU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 93 THR Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 286 ASN Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 440 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 651 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 384 optimal weight: 5.9990 chunk 493 optimal weight: 3.9990 chunk 382 optimal weight: 3.9990 chunk 568 optimal weight: 0.8980 chunk 377 optimal weight: 0.9980 chunk 672 optimal weight: 0.6980 chunk 421 optimal weight: 1.9990 chunk 410 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 189 HIS 8 78 HIS F 98 GLN R 181 ASN S 41 GLN S 77 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 461 GLN T 539 ASN U 515 GLN V 121 ASN V 244 ASN V 358 HIS ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54694 Z= 0.214 Angle : 0.534 11.614 74172 Z= 0.273 Chirality : 0.042 0.161 8690 Planarity : 0.004 0.055 9512 Dihedral : 6.255 178.353 7675 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.29 % Rotamer: Outliers : 2.45 % Allowed : 12.52 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.05 (0.10), residues: 7039 helix: 0.59 (0.09), residues: 3841 sheet: -0.79 (0.21), residues: 607 loop : -0.64 (0.13), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 PHE 0.026 0.001 PHE J 107 TYR 0.022 0.001 TYR 4 211 ARG 0.012 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 647 time to evaluate : 4.604 Fit side-chains revert: symmetry clash REVERT: 1 216 LEU cc_start: 0.8827 (mt) cc_final: 0.8350 (tt) REVERT: 1 276 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8955 (pt) REVERT: 1 399 MET cc_start: 0.8680 (mmt) cc_final: 0.8397 (mmt) REVERT: 1 486 ASP cc_start: 0.7683 (m-30) cc_final: 0.7483 (m-30) REVERT: 1 572 ASP cc_start: 0.7948 (m-30) cc_final: 0.7660 (m-30) REVERT: 1 613 ASP cc_start: 0.7717 (m-30) cc_final: 0.7369 (m-30) REVERT: 2 74 ASN cc_start: 0.8213 (t0) cc_final: 0.7827 (t0) REVERT: 2 131 LYS cc_start: 0.7699 (mppt) cc_final: 0.7233 (ptpt) REVERT: 2 154 ASP cc_start: 0.6811 (t0) cc_final: 0.5834 (p0) REVERT: 2 358 LYS cc_start: 0.8575 (mttp) cc_final: 0.8251 (mttt) REVERT: 3 151 ASN cc_start: 0.7406 (t0) cc_final: 0.7182 (t0) REVERT: 4 54 GLU cc_start: 0.7989 (pt0) cc_final: 0.7765 (pt0) REVERT: 8 3 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8379 (tt) REVERT: 8 39 LYS cc_start: 0.8914 (tttm) cc_final: 0.8540 (tppt) REVERT: 8 69 LYS cc_start: 0.7999 (mttt) cc_final: 0.6024 (tmtt) REVERT: 9 1 MET cc_start: 0.2084 (ptt) cc_final: -0.0506 (mpp) REVERT: 9 80 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7653 (mm110) REVERT: A 81 MET cc_start: 0.8016 (ttp) cc_final: 0.7711 (ttp) REVERT: B 81 MET cc_start: 0.8729 (ttp) cc_final: 0.8487 (ttp) REVERT: B 92 ASN cc_start: 0.9094 (p0) cc_final: 0.8622 (p0) REVERT: H 107 PHE cc_start: 0.8439 (t80) cc_final: 0.8070 (t80) REVERT: J 119 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.6511 (mt) REVERT: M 168 MET cc_start: 0.8014 (mmt) cc_final: 0.7756 (mmt) REVERT: M 187 SER cc_start: 0.8591 (m) cc_final: 0.8328 (m) REVERT: M 275 PHE cc_start: 0.7543 (t80) cc_final: 0.7281 (t80) REVERT: M 294 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8751 (mp) REVERT: M 324 LYS cc_start: 0.7201 (tptt) cc_final: 0.6587 (tmtt) REVERT: P 66 GLN cc_start: 0.8438 (mt0) cc_final: 0.7868 (mt0) REVERT: P 136 GLU cc_start: 0.7973 (mp0) cc_final: 0.7446 (mp0) REVERT: P 185 VAL cc_start: 0.4392 (OUTLIER) cc_final: 0.3864 (m) REVERT: P 227 LEU cc_start: 0.8625 (mt) cc_final: 0.8411 (mt) REVERT: Q 10 ARG cc_start: 0.8521 (tpp-160) cc_final: 0.8131 (mmt180) REVERT: S 48 ARG cc_start: 0.7208 (ttt-90) cc_final: 0.6884 (ttt-90) REVERT: S 158 TYR cc_start: 0.8159 (t80) cc_final: 0.7779 (t80) REVERT: S 220 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7895 (mm) REVERT: S 244 ARG cc_start: 0.7883 (ttm-80) cc_final: 0.7450 (ttp80) REVERT: T 49 ARG cc_start: 0.8389 (mtp-110) cc_final: 0.7890 (mtp85) REVERT: T 447 LYS cc_start: 0.8432 (ptpt) cc_final: 0.8086 (ptpp) REVERT: T 475 GLU cc_start: 0.6127 (tm-30) cc_final: 0.5548 (mm-30) REVERT: T 479 ARG cc_start: 0.6937 (mmp-170) cc_final: 0.5175 (tpt170) REVERT: U 72 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8115 (tm-30) REVERT: U 74 GLU cc_start: 0.8233 (pp20) cc_final: 0.7590 (pm20) REVERT: U 474 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7312 (mp) REVERT: U 476 ARG cc_start: 0.7391 (tpt-90) cc_final: 0.7055 (ttt90) REVERT: V 61 HIS cc_start: 0.7803 (t-170) cc_final: 0.7549 (t-170) REVERT: V 515 GLN cc_start: 0.7747 (mt0) cc_final: 0.7396 (pm20) REVERT: X 538 VAL cc_start: 0.6953 (OUTLIER) cc_final: 0.6621 (m) REVERT: Y 371 LEU cc_start: 0.8353 (mp) cc_final: 0.8102 (mp) REVERT: Y 430 LYS cc_start: 0.6458 (ptmt) cc_final: 0.6055 (mtmm) REVERT: Z 49 ASP cc_start: 0.8053 (m-30) cc_final: 0.7563 (m-30) REVERT: Z 82 ASP cc_start: 0.7756 (t0) cc_final: 0.7253 (t0) outliers start: 138 outliers final: 111 residues processed: 748 average time/residue: 0.5293 time to fit residues: 661.9476 Evaluate side-chains 744 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 625 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 36 THR Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 437 VAL Chi-restraints excluded: chain 1 residue 463 SER Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 493 LEU Chi-restraints excluded: chain 1 residue 497 LEU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 3 residue 117 SER Chi-restraints excluded: chain 3 residue 195 LEU Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 97 SER Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 15 LEU Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 73 TRP Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 104 LEU Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 294 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 185 VAL Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 192 LYS Chi-restraints excluded: chain P residue 216 GLU Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 512 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain U residue 559 LEU Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 89 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 253 GLN Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 473 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 93 THR Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 452 VAL Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 531 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 140 ILE Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 124 VAL Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 297 VAL Chi-restraints excluded: chain Z residue 440 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 416 optimal weight: 0.6980 chunk 268 optimal weight: 0.4980 chunk 401 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 132 optimal weight: 0.2980 chunk 130 optimal weight: 0.9980 chunk 427 optimal weight: 4.9990 chunk 458 optimal weight: 0.1980 chunk 332 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 528 optimal weight: 10.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 59 ASN 8 78 HIS 9 27 ASN E 98 GLN F 98 GLN R 181 ASN S 41 GLN T 134 ASN T 461 GLN T 539 ASN U 515 GLN V 121 ASN ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 54694 Z= 0.152 Angle : 0.513 10.162 74172 Z= 0.263 Chirality : 0.041 0.156 8690 Planarity : 0.004 0.060 9512 Dihedral : 5.978 163.969 7675 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.40 % Favored : 96.52 % Rotamer: Outliers : 2.04 % Allowed : 13.21 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.22 (0.10), residues: 7039 helix: 0.81 (0.09), residues: 3861 sheet: -0.64 (0.21), residues: 599 loop : -0.54 (0.13), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.005 0.001 HIS V 83 PHE 0.028 0.001 PHE J 107 TYR 0.022 0.001 TYR 4 211 ARG 0.013 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 675 time to evaluate : 4.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 216 LEU cc_start: 0.8778 (mt) cc_final: 0.8316 (tt) REVERT: 1 276 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8948 (pt) REVERT: 1 399 MET cc_start: 0.8687 (mmt) cc_final: 0.8393 (mmt) REVERT: 1 486 ASP cc_start: 0.7667 (m-30) cc_final: 0.7464 (m-30) REVERT: 1 572 ASP cc_start: 0.7937 (m-30) cc_final: 0.7656 (m-30) REVERT: 1 613 ASP cc_start: 0.7661 (m-30) cc_final: 0.7288 (m-30) REVERT: 2 74 ASN cc_start: 0.8173 (t0) cc_final: 0.7793 (t0) REVERT: 2 131 LYS cc_start: 0.7641 (mppt) cc_final: 0.7178 (ptpt) REVERT: 2 154 ASP cc_start: 0.6881 (t0) cc_final: 0.5877 (p0) REVERT: 2 358 LYS cc_start: 0.8512 (mttp) cc_final: 0.8225 (mttt) REVERT: 3 151 ASN cc_start: 0.7381 (t0) cc_final: 0.7158 (t0) REVERT: 4 54 GLU cc_start: 0.7970 (pt0) cc_final: 0.7743 (pt0) REVERT: 6 76 LYS cc_start: 0.7578 (mtmt) cc_final: 0.6952 (mttt) REVERT: 8 39 LYS cc_start: 0.8829 (tttm) cc_final: 0.8452 (tppt) REVERT: 8 69 LYS cc_start: 0.7969 (mttt) cc_final: 0.5987 (tmtt) REVERT: 9 1 MET cc_start: 0.1404 (ptt) cc_final: 0.0060 (mpp) REVERT: 9 80 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7639 (mm110) REVERT: A 81 MET cc_start: 0.7938 (ttp) cc_final: 0.7659 (ttp) REVERT: A 102 TYR cc_start: 0.7681 (m-80) cc_final: 0.6954 (m-80) REVERT: B 81 MET cc_start: 0.8743 (ttp) cc_final: 0.8537 (ttp) REVERT: B 92 ASN cc_start: 0.9088 (p0) cc_final: 0.8611 (p0) REVERT: H 107 PHE cc_start: 0.8449 (t80) cc_final: 0.8104 (t80) REVERT: J 119 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.6416 (mt) REVERT: M 168 MET cc_start: 0.8024 (mmt) cc_final: 0.7767 (mmt) REVERT: M 187 SER cc_start: 0.8574 (m) cc_final: 0.8315 (m) REVERT: M 275 PHE cc_start: 0.7547 (t80) cc_final: 0.7273 (t80) REVERT: M 324 LYS cc_start: 0.7196 (tptt) cc_final: 0.6610 (tmtt) REVERT: P 66 GLN cc_start: 0.8488 (mt0) cc_final: 0.8139 (mt0) REVERT: P 136 GLU cc_start: 0.7943 (mp0) cc_final: 0.7427 (mp0) REVERT: P 192 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8434 (mtpt) REVERT: P 227 LEU cc_start: 0.8617 (mt) cc_final: 0.8416 (mt) REVERT: Q 10 ARG cc_start: 0.8430 (tpp-160) cc_final: 0.8044 (mmt180) REVERT: Q 52 TYR cc_start: 0.7143 (m-80) cc_final: 0.6582 (m-80) REVERT: S 48 ARG cc_start: 0.7183 (ttt-90) cc_final: 0.6873 (ttt-90) REVERT: S 62 MET cc_start: 0.7728 (mmm) cc_final: 0.7443 (mmm) REVERT: S 153 ILE cc_start: 0.7032 (tt) cc_final: 0.6655 (pt) REVERT: S 158 TYR cc_start: 0.8093 (t80) cc_final: 0.7833 (t80) REVERT: S 220 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7877 (mm) REVERT: S 244 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7477 (ttp80) REVERT: T 49 ARG cc_start: 0.8361 (mtp-110) cc_final: 0.7865 (mtp85) REVERT: T 447 LYS cc_start: 0.8421 (ptpt) cc_final: 0.8195 (ptpp) REVERT: T 475 GLU cc_start: 0.6109 (tm-30) cc_final: 0.5607 (mm-30) REVERT: T 479 ARG cc_start: 0.6797 (mmp-170) cc_final: 0.5105 (tpt170) REVERT: U 72 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7727 (tm-30) REVERT: U 74 GLU cc_start: 0.8223 (pp20) cc_final: 0.7560 (pm20) REVERT: U 474 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7285 (mp) REVERT: U 476 ARG cc_start: 0.7289 (tpt-90) cc_final: 0.6950 (ttt180) REVERT: U 539 ASN cc_start: 0.8163 (m-40) cc_final: 0.7622 (m110) REVERT: V 43 LYS cc_start: 0.6956 (mmmm) cc_final: 0.6744 (mmmt) REVERT: V 61 HIS cc_start: 0.7731 (t-170) cc_final: 0.7498 (t-170) REVERT: V 449 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7437 (mt-10) REVERT: V 515 GLN cc_start: 0.7790 (mt0) cc_final: 0.7438 (pm20) REVERT: Y 371 LEU cc_start: 0.8348 (mp) cc_final: 0.8109 (mp) REVERT: Y 430 LYS cc_start: 0.6242 (ptmt) cc_final: 0.5908 (mtmm) REVERT: Z 49 ASP cc_start: 0.7980 (m-30) cc_final: 0.7517 (m-30) REVERT: Z 82 ASP cc_start: 0.7678 (t0) cc_final: 0.7232 (t0) REVERT: Z 198 ASN cc_start: 0.8466 (t0) cc_final: 0.8167 (t0) REVERT: Z 422 MET cc_start: 0.7846 (mmm) cc_final: 0.7447 (mmm) outliers start: 115 outliers final: 84 residues processed: 757 average time/residue: 0.5662 time to fit residues: 715.3009 Evaluate side-chains 708 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 619 time to evaluate : 4.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 493 LEU Chi-restraints excluded: chain 1 residue 497 LEU Chi-restraints excluded: chain 2 residue 8 VAL Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 73 TRP Chi-restraints excluded: chain 9 residue 87 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 192 LYS Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 63 SER Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 93 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 311 GLN Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 611 optimal weight: 3.9990 chunk 644 optimal weight: 0.5980 chunk 588 optimal weight: 3.9990 chunk 626 optimal weight: 3.9990 chunk 377 optimal weight: 0.6980 chunk 273 optimal weight: 6.9990 chunk 492 optimal weight: 4.9990 chunk 192 optimal weight: 0.5980 chunk 566 optimal weight: 1.9990 chunk 592 optimal weight: 5.9990 chunk 624 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 59 ASN 7 184 ASN 8 78 HIS E 98 GLN F 94 ASN F 98 GLN H 98 GLN P 59 GLN P 76 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN S 41 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 461 GLN T 539 ASN U 515 GLN ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 54694 Z= 0.198 Angle : 0.535 9.979 74172 Z= 0.273 Chirality : 0.042 0.277 8690 Planarity : 0.004 0.061 9512 Dihedral : 5.924 149.990 7675 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.38 % Rotamer: Outliers : 1.95 % Allowed : 13.58 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.28 (0.10), residues: 7039 helix: 0.86 (0.09), residues: 3871 sheet: -0.67 (0.21), residues: 618 loop : -0.51 (0.13), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 9 73 HIS 0.006 0.001 HIS V 83 PHE 0.029 0.001 PHE J 107 TYR 0.022 0.001 TYR 4 211 ARG 0.014 0.000 ARG V 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 631 time to evaluate : 4.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 1 216 LEU cc_start: 0.8773 (mt) cc_final: 0.8308 (tt) REVERT: 1 276 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8946 (pt) REVERT: 1 399 MET cc_start: 0.8693 (mmt) cc_final: 0.8394 (mmt) REVERT: 1 486 ASP cc_start: 0.7608 (m-30) cc_final: 0.7404 (m-30) REVERT: 1 572 ASP cc_start: 0.7944 (m-30) cc_final: 0.7657 (m-30) REVERT: 1 613 ASP cc_start: 0.7716 (m-30) cc_final: 0.7355 (m-30) REVERT: 2 74 ASN cc_start: 0.8161 (t0) cc_final: 0.7811 (t0) REVERT: 2 131 LYS cc_start: 0.7680 (mppt) cc_final: 0.7224 (ptpt) REVERT: 2 154 ASP cc_start: 0.6809 (t0) cc_final: 0.5755 (p0) REVERT: 4 54 GLU cc_start: 0.7987 (pt0) cc_final: 0.7753 (pt0) REVERT: 6 76 LYS cc_start: 0.7567 (mtmt) cc_final: 0.6937 (mttt) REVERT: 8 39 LYS cc_start: 0.8856 (tttm) cc_final: 0.8483 (tppt) REVERT: 8 69 LYS cc_start: 0.7989 (mttt) cc_final: 0.5992 (tmtt) REVERT: 9 1 MET cc_start: 0.1360 (ptt) cc_final: 0.0233 (mpp) REVERT: A 81 MET cc_start: 0.7993 (ttp) cc_final: 0.7715 (ttp) REVERT: B 92 ASN cc_start: 0.9093 (p0) cc_final: 0.8638 (p0) REVERT: H 107 PHE cc_start: 0.8457 (t80) cc_final: 0.8115 (t80) REVERT: J 119 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.6403 (mt) REVERT: M 168 MET cc_start: 0.8017 (mmt) cc_final: 0.7764 (mmt) REVERT: M 187 SER cc_start: 0.8586 (m) cc_final: 0.8316 (m) REVERT: M 275 PHE cc_start: 0.7545 (t80) cc_final: 0.7263 (t80) REVERT: M 294 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8744 (mp) REVERT: M 324 LYS cc_start: 0.7215 (tptt) cc_final: 0.6617 (tmtt) REVERT: P 66 GLN cc_start: 0.8494 (mt0) cc_final: 0.8099 (mt0) REVERT: P 136 GLU cc_start: 0.7958 (mp0) cc_final: 0.7433 (mp0) REVERT: P 192 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8469 (mtpt) REVERT: P 218 PHE cc_start: 0.8617 (t80) cc_final: 0.8292 (t80) REVERT: P 227 LEU cc_start: 0.8619 (mt) cc_final: 0.8410 (mt) REVERT: Q 52 TYR cc_start: 0.7188 (m-80) cc_final: 0.6608 (m-80) REVERT: S 48 ARG cc_start: 0.7111 (ttt-90) cc_final: 0.6808 (ttt-90) REVERT: S 62 MET cc_start: 0.7747 (mmm) cc_final: 0.7506 (mmm) REVERT: S 153 ILE cc_start: 0.6994 (tt) cc_final: 0.6596 (pt) REVERT: S 158 TYR cc_start: 0.8096 (t80) cc_final: 0.7855 (t80) REVERT: S 220 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7876 (mm) REVERT: S 244 ARG cc_start: 0.7921 (ttm-80) cc_final: 0.7553 (ttp80) REVERT: T 49 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.7881 (mtp85) REVERT: T 447 LYS cc_start: 0.8426 (ptpt) cc_final: 0.8192 (ptpp) REVERT: T 475 GLU cc_start: 0.6045 (tm-30) cc_final: 0.5472 (mm-30) REVERT: T 479 ARG cc_start: 0.6810 (mmp-170) cc_final: 0.5117 (tpt170) REVERT: U 72 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7702 (tm-30) REVERT: U 74 GLU cc_start: 0.8279 (pp20) cc_final: 0.7638 (pm20) REVERT: U 449 GLU cc_start: 0.6183 (tt0) cc_final: 0.5903 (tt0) REVERT: U 474 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7254 (mp) REVERT: V 61 HIS cc_start: 0.7769 (t-170) cc_final: 0.7525 (t-170) REVERT: V 449 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7417 (mt-10) REVERT: V 515 GLN cc_start: 0.7787 (mt0) cc_final: 0.7424 (pm20) REVERT: X 538 VAL cc_start: 0.6873 (OUTLIER) cc_final: 0.6540 (m) REVERT: Y 371 LEU cc_start: 0.8384 (mp) cc_final: 0.8130 (mp) REVERT: Y 430 LYS cc_start: 0.6258 (ptmt) cc_final: 0.5919 (mtmm) REVERT: Z 49 ASP cc_start: 0.8030 (m-30) cc_final: 0.7543 (m-30) REVERT: Z 82 ASP cc_start: 0.7672 (t0) cc_final: 0.7253 (t0) outliers start: 110 outliers final: 89 residues processed: 709 average time/residue: 0.5657 time to fit residues: 668.4998 Evaluate side-chains 709 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 613 time to evaluate : 4.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 476 VAL Chi-restraints excluded: chain 1 residue 493 LEU Chi-restraints excluded: chain 1 residue 497 LEU Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 4 residue 187 CYS Chi-restraints excluded: chain 4 residue 199 VAL Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 90 GLU Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 72 SER Chi-restraints excluded: chain 6 residue 107 VAL Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 73 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 66 CYS Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain M residue 254 LEU Chi-restraints excluded: chain M residue 294 LEU Chi-restraints excluded: chain P residue 77 PHE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 108 VAL Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 192 LYS Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain Q residue 69 ILE Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 213 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 187 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 391 SER Chi-restraints excluded: chain U residue 411 GLU Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 93 THR Chi-restraints excluded: chain X residue 261 VAL Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain X residue 538 VAL Chi-restraints excluded: chain Y residue 58 SER Chi-restraints excluded: chain Y residue 69 SER Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 266 LEU Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 311 GLN Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 200 VAL Chi-restraints excluded: chain Z residue 440 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 411 optimal weight: 0.3980 chunk 662 optimal weight: 2.9990 chunk 404 optimal weight: 0.3980 chunk 314 optimal weight: 4.9990 chunk 460 optimal weight: 0.6980 chunk 695 optimal weight: 4.9990 chunk 640 optimal weight: 0.0470 chunk 553 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 427 optimal weight: 0.1980 chunk 339 optimal weight: 9.9990 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 562 ASN ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 59 ASN 8 78 HIS F 98 GLN H 98 GLN P 59 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 41 GLN S 45 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 GLN T 539 ASN U 515 GLN ** Y 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 440 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 54694 Z= 0.139 Angle : 0.519 19.488 74172 Z= 0.264 Chirality : 0.041 0.285 8690 Planarity : 0.004 0.059 9512 Dihedral : 5.666 135.672 7675 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 1.49 % Allowed : 14.20 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.49 (0.10), residues: 7039 helix: 1.06 (0.09), residues: 3863 sheet: -0.62 (0.21), residues: 591 loop : -0.45 (0.13), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.006 0.001 HIS V 83 PHE 0.033 0.001 PHE 3 115 TYR 0.022 0.001 TYR 4 211 ARG 0.014 0.000 ARG V 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14078 Ramachandran restraints generated. 7039 Oldfield, 0 Emsley, 7039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 663 time to evaluate : 4.605 Fit side-chains REVERT: 0 41 GLU cc_start: 0.7757 (mt-10) cc_final: 0.6991 (pm20) REVERT: 1 216 LEU cc_start: 0.8817 (mt) cc_final: 0.8322 (tt) REVERT: 1 276 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8928 (pt) REVERT: 1 399 MET cc_start: 0.8674 (mmt) cc_final: 0.8387 (mmt) REVERT: 1 572 ASP cc_start: 0.7940 (m-30) cc_final: 0.7673 (m-30) REVERT: 1 613 ASP cc_start: 0.7659 (m-30) cc_final: 0.7311 (m-30) REVERT: 2 74 ASN cc_start: 0.8110 (t0) cc_final: 0.7791 (t0) REVERT: 2 131 LYS cc_start: 0.7584 (mppt) cc_final: 0.7162 (ptpt) REVERT: 2 142 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7939 (mtm-85) REVERT: 2 154 ASP cc_start: 0.6811 (t0) cc_final: 0.5834 (p0) REVERT: 4 54 GLU cc_start: 0.7926 (pt0) cc_final: 0.7694 (pt0) REVERT: 6 76 LYS cc_start: 0.7583 (mtmt) cc_final: 0.6936 (mttt) REVERT: 7 60 GLN cc_start: 0.7355 (tt0) cc_final: 0.7138 (tt0) REVERT: 7 106 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8584 (mm-40) REVERT: 8 39 LYS cc_start: 0.8804 (tttm) cc_final: 0.8427 (tppt) REVERT: 8 69 LYS cc_start: 0.7942 (mttt) cc_final: 0.5987 (tmtt) REVERT: 9 1 MET cc_start: 0.0992 (ptt) cc_final: 0.0454 (mpp) REVERT: 9 80 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7596 (mm110) REVERT: A 81 MET cc_start: 0.7959 (ttp) cc_final: 0.7697 (ttp) REVERT: B 92 ASN cc_start: 0.9063 (p0) cc_final: 0.8570 (p0) REVERT: H 107 PHE cc_start: 0.8432 (t80) cc_final: 0.8110 (t80) REVERT: I 60 LYS cc_start: 0.7783 (mttm) cc_final: 0.7449 (ttmm) REVERT: J 119 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.6368 (mt) REVERT: M 168 MET cc_start: 0.8021 (mmt) cc_final: 0.7774 (mmt) REVERT: M 187 SER cc_start: 0.8565 (m) cc_final: 0.8304 (m) REVERT: M 230 THR cc_start: 0.9117 (t) cc_final: 0.8799 (m) REVERT: M 270 MET cc_start: 0.6288 (tmm) cc_final: 0.5387 (mmt) REVERT: M 275 PHE cc_start: 0.7489 (t80) cc_final: 0.7205 (t80) REVERT: M 324 LYS cc_start: 0.7169 (tptt) cc_final: 0.6588 (tmtt) REVERT: P 66 GLN cc_start: 0.8450 (mt0) cc_final: 0.8086 (mt0) REVERT: P 136 GLU cc_start: 0.8007 (mp0) cc_final: 0.7631 (mp0) REVERT: P 191 ASP cc_start: 0.7772 (t0) cc_final: 0.7454 (p0) REVERT: P 192 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8298 (mtpt) REVERT: P 218 PHE cc_start: 0.8646 (t80) cc_final: 0.8320 (t80) REVERT: P 227 LEU cc_start: 0.8597 (mt) cc_final: 0.8384 (mt) REVERT: Q 10 ARG cc_start: 0.8285 (tpp-160) cc_final: 0.7892 (mmt180) REVERT: Q 52 TYR cc_start: 0.7111 (m-80) cc_final: 0.6637 (m-80) REVERT: S 62 MET cc_start: 0.7679 (mmm) cc_final: 0.7461 (mmm) REVERT: S 153 ILE cc_start: 0.6900 (tt) cc_final: 0.6546 (pt) REVERT: S 158 TYR cc_start: 0.8071 (t80) cc_final: 0.7853 (t80) REVERT: S 220 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7870 (mm) REVERT: S 244 ARG cc_start: 0.7914 (ttm-80) cc_final: 0.7507 (ttp80) REVERT: T 49 ARG cc_start: 0.8340 (mtp-110) cc_final: 0.7845 (mtp85) REVERT: T 447 LYS cc_start: 0.8408 (ptpt) cc_final: 0.8197 (ptpp) REVERT: T 479 ARG cc_start: 0.6708 (mmp-170) cc_final: 0.5181 (tpt170) REVERT: T 539 ASN cc_start: 0.8237 (m110) cc_final: 0.7702 (p0) REVERT: U 72 GLU cc_start: 0.8355 (tm-30) cc_final: 0.7714 (tm-30) REVERT: U 74 GLU cc_start: 0.8274 (pp20) cc_final: 0.7618 (pm20) REVERT: U 474 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7192 (mp) REVERT: U 512 VAL cc_start: 0.7657 (OUTLIER) cc_final: 0.7414 (t) REVERT: V 449 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7403 (mt-10) REVERT: V 515 GLN cc_start: 0.7813 (mt0) cc_final: 0.7470 (pm20) REVERT: Y 371 LEU cc_start: 0.8413 (mp) cc_final: 0.8185 (mp) REVERT: Y 430 LYS cc_start: 0.6213 (ptmt) cc_final: 0.5900 (mtmm) REVERT: Y 437 ARG cc_start: 0.8339 (mtp85) cc_final: 0.7824 (mtp85) REVERT: Y 441 ARG cc_start: 0.8492 (mmt-90) cc_final: 0.8060 (mpt180) REVERT: Y 493 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7513 (mmmt) REVERT: Z 49 ASP cc_start: 0.7992 (m-30) cc_final: 0.7537 (m-30) REVERT: Z 82 ASP cc_start: 0.7632 (t0) cc_final: 0.7220 (t0) REVERT: Z 198 ASN cc_start: 0.8488 (t0) cc_final: 0.8229 (t0) REVERT: Z 422 MET cc_start: 0.7821 (mmm) cc_final: 0.7507 (mmm) REVERT: Z 488 MET cc_start: 0.8091 (mmp) cc_final: 0.7512 (mmp) outliers start: 84 outliers final: 62 residues processed: 723 average time/residue: 0.5426 time to fit residues: 648.7996 Evaluate side-chains 688 residues out of total 5637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 620 time to evaluate : 4.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 68 VAL Chi-restraints excluded: chain 1 residue 102 LEU Chi-restraints excluded: chain 1 residue 256 VAL Chi-restraints excluded: chain 1 residue 276 ILE Chi-restraints excluded: chain 1 residue 335 VAL Chi-restraints excluded: chain 1 residue 493 LEU Chi-restraints excluded: chain 1 residue 497 LEU Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 2 residue 359 THR Chi-restraints excluded: chain 2 residue 416 VAL Chi-restraints excluded: chain 5 residue 59 ASN Chi-restraints excluded: chain 5 residue 90 GLU Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 52 LEU Chi-restraints excluded: chain 9 residue 73 TRP Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain H residue 62 VAL Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain P residue 163 ASP Chi-restraints excluded: chain P residue 190 ILE Chi-restraints excluded: chain P residue 192 LYS Chi-restraints excluded: chain Q residue 62 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 143 ASP Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 113 SER Chi-restraints excluded: chain T residue 180 VAL Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain T residue 559 LEU Chi-restraints excluded: chain U residue 62 VAL Chi-restraints excluded: chain U residue 81 VAL Chi-restraints excluded: chain U residue 180 VAL Chi-restraints excluded: chain U residue 213 VAL Chi-restraints excluded: chain U residue 287 MET Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 378 THR Chi-restraints excluded: chain U residue 421 LEU Chi-restraints excluded: chain U residue 448 LEU Chi-restraints excluded: chain U residue 474 LEU Chi-restraints excluded: chain U residue 487 LYS Chi-restraints excluded: chain U residue 512 VAL Chi-restraints excluded: chain V residue 130 VAL Chi-restraints excluded: chain V residue 185 VAL Chi-restraints excluded: chain V residue 445 THR Chi-restraints excluded: chain V residue 456 VAL Chi-restraints excluded: chain V residue 518 VAL Chi-restraints excluded: chain V residue 536 LEU Chi-restraints excluded: chain X residue 280 VAL Chi-restraints excluded: chain X residue 281 LEU Chi-restraints excluded: chain X residue 308 VAL Chi-restraints excluded: chain X residue 432 THR Chi-restraints excluded: chain X residue 495 VAL Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 308 VAL Chi-restraints excluded: chain Y residue 416 ILE Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 440 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 698 random chunks: chunk 439 optimal weight: 0.0770 chunk 589 optimal weight: 10.0000 chunk 169 optimal weight: 0.0670 chunk 510 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 554 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 569 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 24 GLN 8 78 HIS B 98 GLN F 98 GLN H 98 GLN P 59 GLN ** Q 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 41 GLN S 45 GLN ** S 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 ASN T 461 GLN U 134 ASN U 515 GLN ** Y 286 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 = 0.3578 r_free = 0.3578 target = 0.132264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.103201 restraints weight = 75544.659| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.65 r_work: 0.2922 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 54694 Z= 0.201 Angle : 0.638 59.167 74172 Z= 0.355 Chirality : 0.042 0.549 8690 Planarity : 0.004 0.101 9512 Dihedral : 5.684 135.586 7675 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 1.42 % Allowed : 14.47 % Favored : 84.11 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.05 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.49 (0.10), residues: 7039 helix: 1.06 (0.09), residues: 3863 sheet: -0.61 (0.21), residues: 592 loop : -0.45 (0.13), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 9 73 HIS 0.006 0.001 HIS P 84 PHE 0.027 0.001 PHE 3 105 TYR 0.026 0.001 TYR C 102 ARG 0.011 0.000 ARG V 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12922.88 seconds wall clock time: 224 minutes 40.79 seconds (13480.79 seconds total)