Starting phenix.real_space_refine on Mon Aug 10 07:08:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8p4f_17408/08_2026/8p4f_17408.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p4f_17408/08_2026/8p4f_17408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8p4f_17408/08_2026/8p4f_17408.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8p4f_17408/08_2026/8p4f_17408.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p4f_17408/08_2026/8p4f_17408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p4f_17408/08_2026/8p4f_17408.map" model { file = "/net/cci-nas-00/data/ceres_data/8p4f_17408/08_2026/8p4f_17408.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p4f_17408/08_2026/8p4f_17408.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.005 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 8 6.06 5 P 107 5.49 5 Mg 1 5.21 5 S 259 5.16 5 C 27302 2.51 5 N 7653 2.21 5 O 8356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.17s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43686 Number of models: 1 Model: "" Number of chains: 26 Chain: "P" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 622 Classifications: {'RNAv2': 29} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 17, 'rna3p_pyr': 8} Link IDs: {'rna2p': 4, 'rna3p': 24} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 11261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1421, 11261 Classifications: {'peptide': 1421} Link IDs: {'PCIS': 2, 'PTRANS': 68, 'TRANS': 1350} Chain breaks: 4 Chain: "B" Number of atoms: 9142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1147, 9142 Classifications: {'peptide': 1147} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 53, 'TRANS': 1093} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 2079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2079 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 15, 'TRANS': 243} Chain breaks: 1 Chain: "E" Number of atoms: 1711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1711 Classifications: {'peptide': 209} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 11, 'TRANS': 197} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 379 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 610 Classifications: {'DNA': 38} Incomplete info: {'p_only': 9} Link IDs: {'rna3p': 37} Unresolved chain links: 9 Chain breaks: 1 Unresolved chain link angles: 39 Unresolved chain link dihedrals: 29 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {' DT:plan': 5, ' DC:plan': 1, ' DC:plan2': 1, ' DA:plan': 2, ' DA:plan2': 2, ' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 101 Chain: "T" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 774 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3894 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 17, 'TRANS': 470} Chain breaks: 3 Chain: "G" Number of atoms: 1341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1341 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1008 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 3, 'TRANS': 124} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "O" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 695, 5643 Classifications: {'peptide': 695} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 27, 'TRANS': 663} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'MGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1086 SG CYS A 71 73.616 71.615 117.804 1.00174.43 S ATOM 1108 SG CYS A 74 77.003 71.714 117.951 1.00166.79 S ATOM 1155 SG CYS A 81 74.842 73.152 115.095 1.00162.13 S ATOM 1390 SG CYS A 111 87.055 39.794 81.979 1.00183.09 S ATOM 1418 SG CYS A 114 88.720 38.471 84.647 1.00182.27 S ATOM 1764 SG CYS A 184 86.209 36.272 82.465 1.00191.04 S ATOM 20595 SG CYS B1119 90.391 64.924 112.279 1.00148.10 S ATOM 20617 SG CYS B1122 88.560 63.624 109.561 1.00143.35 S ATOM 20732 SG CYS B1137 87.279 63.612 112.688 1.00165.79 S ATOM 20753 SG CYS B1140 89.477 60.627 110.822 1.00167.23 S ATOM 26725 SG CYS I 17 52.739 55.222 27.067 1.00155.52 S ATOM 26749 SG CYS I 20 52.005 54.156 30.974 1.00158.58 S ATOM 26910 SG CYS I 39 55.377 53.769 30.694 1.00159.23 S ATOM 26935 SG CYS I 42 53.411 51.662 28.290 1.00157.72 S ATOM 27287 SG CYS I 86 55.600 99.307 19.418 1.00154.36 S ATOM 27311 SG CYS I 89 52.124 100.294 18.297 1.00162.90 S ATOM 27515 SG CYS I 114 53.806 100.005 22.307 1.00146.80 S ATOM 27550 SG CYS I 119 52.501 97.406 20.192 1.00147.95 S ATOM 27660 SG CYS J 7 57.100 135.003 85.471 1.00 75.68 S ATOM 27684 SG CYS J 10 58.624 138.388 86.231 1.00 78.13 S ATOM 27948 SG CYS J 44 59.391 137.446 83.108 1.00 83.70 S ATOM 27954 SG CYS J 45 56.076 138.623 84.092 1.00 86.52 S ATOM 29107 SG CYS L 19 27.934 105.836 101.379 1.00138.04 S ATOM 29126 SG CYS L 22 24.939 107.539 101.745 1.00137.85 S ATOM 29243 SG CYS L 36 26.085 105.317 104.737 1.00146.22 S ATOM 29269 SG CYS L 39 25.156 103.889 101.248 1.00145.80 S ATOM 30940 SG CYS Y 16 33.114 24.951 95.418 1.00484.94 S ATOM 30962 SG CYS Y 19 34.344 25.347 91.802 1.00462.52 S ATOM 31074 SG CYS Y 33 30.815 25.374 92.193 1.00506.45 S ATOM 31096 SG CYS Y 36 32.757 22.048 92.841 1.00521.18 S Time building chain proxies: 7.83, per 1000 atoms: 0.18 Number of scatterers: 43686 At special positions: 0 Unit cell: (155.4, 176.4, 219.45, 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 8 29.99 S 259 16.00 P 107 15.00 Mg 1 11.99 O 8356 8.00 N 7653 7.00 C 27302 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 36 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " Number of angles added : 39 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9780 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 62 sheets defined 35.8% alpha, 20.0% beta 35 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 4.82 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.621A pdb=" N LYS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 151 removed outlier: 3.932A pdb=" N LEU A 141 " --> pdb=" O PRO A 137 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 227 removed outlier: 4.068A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.537A pdb=" N LEU A 236 " --> pdb=" O GLU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 274 through 296 removed outlier: 3.535A pdb=" N ILE A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 319 removed outlier: 3.571A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.764A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.774A pdb=" N ASN A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 removed outlier: 3.804A pdb=" N GLU A 404 " --> pdb=" O ASP A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 508 through 519 removed outlier: 3.903A pdb=" N GLU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 515 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 Processing helix chain 'A' and resid 539 through 550 removed outlier: 3.870A pdb=" N ARG A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 567 removed outlier: 3.556A pdb=" N MET A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 562 " --> pdb=" O GLY A 558 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 4.113A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 660 Processing helix chain 'A' and resid 665 through 678 removed outlier: 3.540A pdb=" N TYR A 669 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A 670 " --> pdb=" O ARG A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.749A pdb=" N GLU A 683 " --> pdb=" O TRP A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 697 through 722 removed outlier: 3.530A pdb=" N THR A 705 " --> pdb=" O ASP A 701 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 722 " --> pdb=" O GLU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 758 removed outlier: 3.649A pdb=" N ASN A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 747 " --> pdb=" O ARG A 743 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER A 754 " --> pdb=" O ASP A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.769A pdb=" N SER A 772 " --> pdb=" O SER A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.711A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 783 " --> pdb=" O ILE A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.730A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG A 863 " --> pdb=" O TYR A 859 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 865 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 920 removed outlier: 3.671A pdb=" N GLU A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 918 " --> pdb=" O LYS A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.631A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 3.538A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 967 " --> pdb=" O ARG A 963 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 974 removed outlier: 4.165A pdb=" N ASP A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 971 through 974' Processing helix chain 'A' and resid 982 through 993 removed outlier: 3.682A pdb=" N LYS A 992 " --> pdb=" O TRP A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1018 removed outlier: 3.736A pdb=" N VAL A1010 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 removed outlier: 3.566A pdb=" N ALA A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1049 removed outlier: 3.737A pdb=" N LEU A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1056 removed outlier: 3.530A pdb=" N ALA A1055 " --> pdb=" O SER A1051 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.545A pdb=" N GLY A1070 " --> pdb=" O ASP A1066 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A1071 " --> pdb=" O TRP A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1087 through 1097 removed outlier: 3.529A pdb=" N LEU A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A1096 " --> pdb=" O ALA A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1120 through 1130 removed outlier: 3.855A pdb=" N GLU A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.600A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A1162 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.064A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1180 through 1184 Processing helix chain 'A' and resid 1189 through 1199 removed outlier: 4.362A pdb=" N MET A1199 " --> pdb=" O VAL A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.507A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1262 through 1267 removed outlier: 3.828A pdb=" N GLU A1266 " --> pdb=" O MET A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1296 removed outlier: 4.175A pdb=" N THR A1294 " --> pdb=" O SER A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1342 through 1349 removed outlier: 3.673A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A1349 " --> pdb=" O ARG A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1370 removed outlier: 3.588A pdb=" N VAL A1368 " --> pdb=" O GLU A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1387 removed outlier: 3.578A pdb=" N VAL A1374 " --> pdb=" O GLY A1370 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A1379 " --> pdb=" O ARG A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1407 removed outlier: 3.652A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1401 " --> pdb=" O HIS A1397 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A1406 " --> pdb=" O CYS A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1422 removed outlier: 3.886A pdb=" N GLN A1422 " --> pdb=" O GLY A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 Processing helix chain 'A' and resid 1435 through 1445 removed outlier: 3.640A pdb=" N GLU A1441 " --> pdb=" O ASP A1437 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A1445 " --> pdb=" O GLU A1441 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.780A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.589A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 3.989A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 31 " --> pdb=" O TRP B 27 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 33 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 61 removed outlier: 3.502A pdb=" N ILE B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 246 through 253 removed outlier: 3.551A pdb=" N ALA B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.686A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.674A pdb=" N GLU B 307 " --> pdb=" O PRO B 303 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 345 Processing helix chain 'B' and resid 356 through 378 removed outlier: 4.191A pdb=" N LYS B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 364 " --> pdb=" O LYS B 360 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 424 removed outlier: 4.307A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 451 removed outlier: 3.551A pdb=" N GLY B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 removed outlier: 3.985A pdb=" N SER B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 516 through 520 removed outlier: 4.226A pdb=" N ALA B 519 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 547 removed outlier: 3.673A pdb=" N GLU B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.563A pdb=" N LEU B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.805A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 658 Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.577A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 704 " --> pdb=" O SER B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 718 removed outlier: 3.613A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLN B 718 " --> pdb=" O ASP B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 729 removed outlier: 3.662A pdb=" N THR B 723 " --> pdb=" O SER B 719 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 725 " --> pdb=" O ARG B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 767 Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 874 through 879 Processing helix chain 'B' and resid 950 through 954 removed outlier: 3.660A pdb=" N MET B 954 " --> pdb=" O GLN B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.703A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 993 removed outlier: 3.540A pdb=" N CYS B 984 " --> pdb=" O HIS B 980 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 989 " --> pdb=" O LEU B 985 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 removed outlier: 3.727A pdb=" N LEU B1014 " --> pdb=" O LYS B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1087 through 1097 removed outlier: 3.560A pdb=" N ALA B1096 " --> pdb=" O ASP B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1108 removed outlier: 3.785A pdb=" N LEU B1103 " --> pdb=" O ALA B1099 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU B1105 " --> pdb=" O GLN B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1164 removed outlier: 3.515A pdb=" N SER B1164 " --> pdb=" O GLN B1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 removed outlier: 3.565A pdb=" N ARG C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 71 removed outlier: 3.575A pdb=" N GLY C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.565A pdb=" N GLU C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP C 203 " --> pdb=" O PRO C 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 199 through 203' Processing helix chain 'C' and resid 241 through 271 removed outlier: 3.895A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 24 removed outlier: 3.654A pdb=" N ARG E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.508A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 4.148A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET E 121 " --> pdb=" O SER E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.677A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.822A pdb=" N PHE E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 74 removed outlier: 3.581A pdb=" N LEU F 66 " --> pdb=" O ARG F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 99 removed outlier: 3.545A pdb=" N LYS F 98 " --> pdb=" O MET F 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 removed outlier: 3.539A pdb=" N THR I 66 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 Processing helix chain 'J' and resid 17 through 26 removed outlier: 3.788A pdb=" N GLY J 23 " --> pdb=" O GLU J 19 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 4.085A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 9 removed outlier: 3.652A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.846A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 removed outlier: 3.554A pdb=" N ILE K 91 " --> pdb=" O PHE K 87 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU K 100 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU K 103 " --> pdb=" O SER K 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 6 Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 75 removed outlier: 3.703A pdb=" N LYS Y 73 " --> pdb=" O SER Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 104 Processing helix chain 'Z' and resid 188 through 204 Processing helix chain 'Z' and resid 231 through 240 removed outlier: 3.561A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 249 removed outlier: 5.202A pdb=" N LEU Z 247 " --> pdb=" O ASN Z 244 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 265 removed outlier: 4.976A pdb=" N THR Z 261 " --> pdb=" O LYS Z 258 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 349 Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 464 through 466 No H-bonds generated for 'chain 'Z' and resid 464 through 466' Processing helix chain 'Z' and resid 514 through 516 No H-bonds generated for 'chain 'Z' and resid 514 through 516' Processing helix chain 'Z' and resid 573 through 575 No H-bonds generated for 'chain 'Z' and resid 573 through 575' Processing helix chain 'Z' and resid 630 through 633 removed outlier: 3.560A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 111 through 113 No H-bonds generated for 'chain 'G' and resid 111 through 113' Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 89 Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'O' and resid 169 through 174 removed outlier: 4.400A pdb=" N ASP O 173 " --> pdb=" O GLU O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 205 Processing helix chain 'O' and resid 210 through 222 Processing helix chain 'O' and resid 224 through 228 Processing helix chain 'O' and resid 234 through 247 removed outlier: 4.219A pdb=" N MET O 238 " --> pdb=" O ASN O 234 " (cutoff:3.500A) Processing helix chain 'O' and resid 281 through 292 Processing helix chain 'O' and resid 309 through 313 Processing helix chain 'O' and resid 317 through 319 No H-bonds generated for 'chain 'O' and resid 317 through 319' Processing helix chain 'O' and resid 328 through 332 removed outlier: 3.662A pdb=" N GLY O 332 " --> pdb=" O GLY O 329 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 352 Processing helix chain 'O' and resid 372 through 374 No H-bonds generated for 'chain 'O' and resid 372 through 374' Processing helix chain 'O' and resid 375 through 394 removed outlier: 5.275A pdb=" N GLN O 382 " --> pdb=" O ILE O 378 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU O 383 " --> pdb=" O LEU O 379 " (cutoff:3.500A) Processing helix chain 'O' and resid 410 through 423 Processing helix chain 'O' and resid 453 through 471 Processing helix chain 'O' and resid 482 through 489 Processing helix chain 'O' and resid 489 through 520 Processing helix chain 'O' and resid 527 through 540 Processing helix chain 'O' and resid 553 through 563 Processing helix chain 'O' and resid 566 through 572 removed outlier: 3.830A pdb=" N TYR O 572 " --> pdb=" O ILE O 569 " (cutoff:3.500A) Processing helix chain 'O' and resid 581 through 586 Processing helix chain 'O' and resid 587 through 589 No H-bonds generated for 'chain 'O' and resid 587 through 589' Processing helix chain 'O' and resid 648 through 652 Processing helix chain 'O' and resid 675 through 690 removed outlier: 3.529A pdb=" N LYS O 688 " --> pdb=" O GLU O 684 " (cutoff:3.500A) Processing helix chain 'O' and resid 712 through 717 removed outlier: 3.816A pdb=" N PHE O 716 " --> pdb=" O MET O 712 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL O 717 " --> pdb=" O GLU O 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 712 through 717' Processing helix chain 'O' and resid 784 through 788 Processing helix chain 'O' and resid 790 through 797 Processing helix chain 'O' and resid 822 through 833 Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 95 removed outlier: 7.161A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.368A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.578A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 200 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 265 Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 359 removed outlier: 3.754A pdb=" N LEU B1084 " --> pdb=" O VAL A 359 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.872A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE A 482 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 366 " --> pdb=" O PHE A 482 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU A 484 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR A 368 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.707A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 5.812A pdb=" N ILE A 579 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR H 93 " --> pdb=" O ILE A 579 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 581 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP H 11 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP H 38 " --> pdb=" O GLN H 126 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 605 removed outlier: 3.766A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.903A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.797A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1243 through 1247 removed outlier: 4.399A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1320 through 1322 Processing sheet with id=AB8, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.638A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE G 54 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS G 71 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL G 48 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N PHE G 77 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE G 46 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 115 through 119 removed outlier: 5.638A pdb=" N LEU A1473 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY G 57 " --> pdb=" O LEU A1475 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE G 2 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.675A pdb=" N ASP B 127 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE B 91 " --> pdb=" O TYR B 125 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TYR B 125 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU B 93 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA B 122 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLY B 150 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 124 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B 148 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL B 126 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS B 146 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 97 through 99 Processing sheet with id=AC3, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.512A pdb=" N GLN B 468 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC5, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.831A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU B 225 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 531 through 532 removed outlier: 3.566A pdb=" N ARG B 623 " --> pdb=" O ILE B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC8, first strand: chain 'B' and resid 572 through 577 removed outlier: 7.030A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.216A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.216A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL B 926 " --> pdb=" O GLY B 902 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N GLY B 902 " --> pdb=" O VAL B 926 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD3, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.026A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD5, first strand: chain 'B' and resid 865 through 867 removed outlier: 3.602A pdb=" N ILE B 867 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 956 through 957 Processing sheet with id=AD7, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD8, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.608A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE C 21 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.654A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 removed outlier: 3.558A pdb=" N VAL C 151 " --> pdb=" O VAL C 115 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 61 removed outlier: 6.210A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.553A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.523A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AE7, first strand: chain 'I' and resid 94 through 97 Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AF1, first strand: chain 'Y' and resid 83 through 89 removed outlier: 7.071A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 115 through 116 removed outlier: 7.314A pdb=" N ILE Y 115 " --> pdb=" O LYS Z 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'Z' and resid 352 through 355 removed outlier: 4.705A pdb=" N TYR Z 366 " --> pdb=" O PHE Z 373 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS Z 306 " --> pdb=" O VAL Z 293 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL Z 293 " --> pdb=" O LYS Z 306 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 452 through 454 Processing sheet with id=AF5, first strand: chain 'Z' and resid 510 through 513 removed outlier: 3.547A pdb=" N ARG Z 494 " --> pdb=" O ILE Z 501 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE Z 503 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE Z 492 " --> pdb=" O PHE Z 503 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.064A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 585 through 587 Processing sheet with id=AF8, first strand: chain 'Z' and resid 635 through 639 removed outlier: 6.381A pdb=" N HIS Z 625 " --> pdb=" O ILE Z 614 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE Z 614 " --> pdb=" O HIS Z 625 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.789A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.609A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL G 152 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER G 105 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER G 109 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU G 97 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU G 100 " --> pdb=" O VAL G 89 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL G 89 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 145 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 176 through 179 removed outlier: 6.726A pdb=" N VAL O 176 " --> pdb=" O ASN O 478 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 321 through 323 removed outlier: 7.911A pdb=" N TYR O 272 " --> pdb=" O HIS O 359 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU O 361 " --> pdb=" O TYR O 272 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA O 274 " --> pdb=" O LEU O 361 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ALA O 363 " --> pdb=" O ALA O 274 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL O 276 " --> pdb=" O ALA O 363 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL O 358 " --> pdb=" O ARG O 396 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLY O 398 " --> pdb=" O VAL O 358 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE O 360 " --> pdb=" O GLY O 398 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS O 400 " --> pdb=" O PHE O 360 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N MET O 362 " --> pdb=" O HIS O 400 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE O 402 " --> pdb=" O MET O 362 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLY O 399 " --> pdb=" O GLY O 448 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU O 449 " --> pdb=" O PHE O 424 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N PHE O 424 " --> pdb=" O LEU O 449 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 575 through 576 removed outlier: 6.217A pdb=" N THR O 575 " --> pdb=" O PHE O 800 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLU O 802 " --> pdb=" O THR O 575 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY O 747 " --> pdb=" O SER O 596 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 623 through 624 removed outlier: 7.972A pdb=" N LEU O 636 " --> pdb=" O VAL O 663 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL O 663 " --> pdb=" O LEU O 636 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER O 638 " --> pdb=" O LEU O 661 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 623 through 624 removed outlier: 7.972A pdb=" N LEU O 636 " --> pdb=" O VAL O 663 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL O 663 " --> pdb=" O LEU O 636 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER O 638 " --> pdb=" O LEU O 661 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 719 through 723 Processing sheet with id=AG8, first strand: chain 'O' and resid 758 through 763 removed outlier: 3.548A pdb=" N LYS O 768 " --> pdb=" O SER O 763 " (cutoff:3.500A) 1619 hydrogen bonds defined for protein. 4401 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 13.44 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.47: 24573 1.47 - 1.73: 19740 1.73 - 2.00: 410 2.00 - 2.26: 2 2.26 - 2.53: 1 Bond restraints: 44726 Sorted by residual: bond pdb=" CE1 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 1.321 2.527 -1.206 1.00e-02 1.00e+04 1.46e+04 bond pdb=" ND1 HIS O 659 " pdb=" CE1 HIS O 659 " ideal model delta sigma weight residual 1.321 2.154 -0.833 1.00e-02 1.00e+04 6.93e+03 bond pdb=" CD2 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 1.374 2.142 -0.768 1.10e-02 8.26e+03 4.87e+03 bond pdb=" C PRO O 549 " pdb=" N SER O 550 " ideal model delta sigma weight residual 1.332 1.661 -0.329 1.37e-02 5.33e+03 5.76e+02 bond pdb=" CA GLY Y 105 " pdb=" C GLY Y 105 " ideal model delta sigma weight residual 1.511 1.685 -0.173 1.40e-02 5.10e+03 1.53e+02 ... (remaining 44721 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.80: 60803 12.80 - 25.59: 15 25.59 - 38.39: 2 38.39 - 51.19: 4 51.19 - 63.99: 1 Bond angle restraints: 60825 Sorted by residual: angle pdb=" CA PRO O 549 " pdb=" C PRO O 549 " pdb=" N SER O 550 " ideal model delta sigma weight residual 115.71 65.16 50.55 1.19e+00 7.06e-01 1.80e+03 angle pdb=" O PRO O 549 " pdb=" C PRO O 549 " pdb=" N SER O 550 " ideal model delta sigma weight residual 122.98 165.67 -42.69 1.09e+00 8.42e-01 1.53e+03 angle pdb=" C PRO O 549 " pdb=" N SER O 550 " pdb=" CA SER O 550 " ideal model delta sigma weight residual 121.31 76.04 45.27 1.49e+00 4.50e-01 9.23e+02 angle pdb=" ND1 HIS O 659 " pdb=" CE1 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 108.40 84.96 23.44 1.00e+00 1.00e+00 5.49e+02 angle pdb=" CG HIS O 659 " pdb=" CD2 HIS O 659 " pdb=" NE2 HIS O 659 " ideal model delta sigma weight residual 107.20 128.81 -21.61 1.00e+00 1.00e+00 4.67e+02 ... (remaining 60820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 26477 33.94 - 67.89: 551 67.89 - 101.83: 31 101.83 - 135.77: 2 135.77 - 169.72: 2 Dihedral angle restraints: 27063 sinusoidal: 11932 harmonic: 15131 Sorted by residual: dihedral pdb=" C4' A P 27 " pdb=" C3' A P 27 " pdb=" C2' A P 27 " pdb=" C1' A P 27 " ideal model delta sinusoidal sigma weight residual 36.34 -39.68 76.02 1 3.10e+00 1.04e-01 7.58e+02 dihedral pdb=" C4' A P 28 " pdb=" C3' A P 28 " pdb=" C2' A P 28 " pdb=" C1' A P 28 " ideal model delta sinusoidal sigma weight residual 36.34 -34.71 71.05 1 3.10e+00 1.04e-01 6.75e+02 dihedral pdb=" C4' U P 35 " pdb=" C3' U P 35 " pdb=" C2' U P 35 " pdb=" C1' U P 35 " ideal model delta sinusoidal sigma weight residual 36.34 -25.87 62.22 1 3.10e+00 1.04e-01 5.33e+02 ... (remaining 27060 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.907: 6774 0.907 - 1.814: 1 1.814 - 2.720: 1 2.720 - 3.627: 0 3.627 - 4.534: 2 Chirality restraints: 6778 Sorted by residual: chirality pdb=" C1' G P 31 " pdb=" O4' G P 31 " pdb=" C2' G P 31 " pdb=" N9 G P 31 " both_signs ideal model delta sigma weight residual False 2.46 -2.08 4.53 2.00e-01 2.50e+01 5.14e+02 chirality pdb=" C1' C P 33 " pdb=" O4' C P 33 " pdb=" C2' C P 33 " pdb=" N1 C P 33 " both_signs ideal model delta sigma weight residual False 2.46 -2.04 4.50 2.00e-01 2.50e+01 5.06e+02 chirality pdb=" P A P 34 " pdb=" OP1 A P 34 " pdb=" OP2 A P 34 " pdb=" O5' A P 34 " both_signs ideal model delta sigma weight residual True 2.17 0.01 2.16 2.00e-01 2.50e+01 1.17e+02 ... (remaining 6775 not shown) Planarity restraints: 7524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 314 " -0.114 2.00e-02 2.50e+03 7.21e-02 1.04e+02 pdb=" CG TYR O 314 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR O 314 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR O 314 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 TYR O 314 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR O 314 " 0.061 2.00e-02 2.50e+03 pdb=" CZ TYR O 314 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR O 314 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 443 " -0.102 2.00e-02 2.50e+03 5.81e-02 6.74e+01 pdb=" CG TYR O 443 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR O 443 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR O 443 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR O 443 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR O 443 " 0.038 2.00e-02 2.50e+03 pdb=" CZ TYR O 443 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR O 443 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE O 791 " 0.086 2.00e-02 2.50e+03 5.34e-02 4.99e+01 pdb=" CG PHE O 791 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE O 791 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 PHE O 791 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE O 791 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE O 791 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE O 791 " 0.057 2.00e-02 2.50e+03 ... (remaining 7521 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 11 2.08 - 2.78: 9491 2.78 - 3.49: 57037 3.49 - 4.19: 105487 4.19 - 4.90: 182802 Nonbonded interactions: 354828 Sorted by model distance: nonbonded pdb=" OP1 A P 23 " pdb=" NH1 ARG O 235 " model vdw 1.370 3.120 nonbonded pdb=" O3' A P 32 " pdb=" P A P 34 " model vdw 1.643 3.400 nonbonded pdb=" O GLU O 311 " pdb=" NZ LYS O 608 " model vdw 1.779 3.120 nonbonded pdb=" OD2 ASP G 141 " pdb=" NZ LYS O 725 " model vdw 1.784 3.120 nonbonded pdb=" OG SER O 317 " pdb=" ND2 ASN O 667 " model vdw 1.810 3.120 ... (remaining 354823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.65 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.660 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: 0.030 Extract box with map and model: 0.680 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 47.390 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 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 : 0.015 1.206 44759 Z= 1.025 Angle : 1.369 63.987 60864 Z= 0.825 Chirality : 0.109 4.534 6778 Planarity : 0.008 0.123 7524 Dihedral : 12.816 169.715 17283 Min Nonbonded Distance : 1.370 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.24 % Favored : 95.47 % Rotamer: Outliers : 1.05 % Allowed : 1.26 % Favored : 97.69 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.10), residues: 5160 helix: -3.24 (0.09), residues: 1568 sheet: -1.43 (0.15), residues: 828 loop : -1.12 (0.10), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG A 797 TYR 0.128 0.006 TYR O 314 PHE 0.086 0.005 PHE O 791 TRP 0.063 0.007 TRP O 622 HIS 0.037 0.003 HIS O 659 Details of bonding type rmsd/Z covalent geometry : bond 0.01433 / 0.98 (44726) covalent geometry : angle 1.32042 / 0.82 (60825) hydrogen bonds : bond 0.25356 / 14.96 ( 1646) hydrogen bonds : angle 9.69492 / 6.23 ( 4561) metal coordination : bond 0.16210 / 8.15 ( 31) metal coordination : angle 14.36493 / 6.61 ( 39) Misc. bond : bond 0.39818 / 19.91 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 532 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1090 LEU cc_start: 0.9054 (mt) cc_final: 0.8810 (mm) REVERT: B 863 ASP cc_start: 0.8929 (m-30) cc_final: 0.8673 (t0) REVERT: B 954 MET cc_start: 0.8605 (mmm) cc_final: 0.8370 (mmt) REVERT: B 1081 ASP cc_start: 0.8089 (t0) cc_final: 0.7708 (t0) REVERT: F 95 LYS cc_start: 0.8911 (tttt) cc_final: 0.8542 (ttpt) REVERT: Y 42 MET cc_start: -0.3237 (ptp) cc_final: -0.3714 (tmm) REVERT: Y 48 MET cc_start: 0.0069 (tpt) cc_final: -0.0284 (tpt) REVERT: Y 57 PHE cc_start: 0.5702 (p90) cc_final: 0.5269 (p90) REVERT: Y 64 MET cc_start: 0.6952 (mtt) cc_final: 0.6179 (mpp) REVERT: Z 460 MET cc_start: 0.6347 (mmt) cc_final: 0.5500 (mmt) REVERT: G 33 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8704 (mt-10) REVERT: G 41 LYS cc_start: 0.9345 (tttt) cc_final: 0.9064 (tttt) REVERT: G 86 ASP cc_start: 0.6319 (t0) cc_final: 0.5513 (p0) REVERT: G 88 VAL cc_start: 0.9293 (OUTLIER) cc_final: 0.8940 (t) REVERT: G 89 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.8703 (p) REVERT: G 92 VAL cc_start: 0.8884 (OUTLIER) cc_final: 0.8665 (t) REVERT: G 122 ASN cc_start: 0.8922 (m-40) cc_final: 0.8616 (p0) REVERT: G 166 ASP cc_start: 0.9551 (m-30) cc_final: 0.9306 (p0) REVERT: O 653 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.6021 (mtp180) REVERT: O 685 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7876 (pttt) outliers start: 48 outliers final: 9 residues processed: 578 average time/residue: 0.2760 time to fit residues: 258.0813 Evaluate side-chains 288 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 274 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 129 LYS Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 653 ARG Chi-restraints excluded: chain O residue 656 SER Chi-restraints excluded: chain O residue 685 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 7.9990 chunk 497 optimal weight: 30.0000 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 8.9990 chunk 366 optimal weight: 50.0000 chunk 223 optimal weight: 8.9990 chunk 516 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 HIS A 301 HIS ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 GLN A 671 ASN ** A 757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 GLN A1093 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1230 GLN ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 56 GLN B 111 ASN B 265 GLN B 312 GLN B 518 HIS B 537 GLN B 825 GLN B 842 HIS B1021 HIS B1097 HIS C 32 ASN C 145 GLN C 260 GLN I 22 ASN I 45 GLN K 69 HIS Y 41 GLN Z 534 HIS Z 625 HIS G 4 HIS G 9 HIS ** G 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN D 38 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 ASN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 515 HIS O 667 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.054709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.035372 restraints weight = 339801.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.036331 restraints weight = 173938.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037052 restraints weight = 111480.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.037494 restraints weight = 83848.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.037734 restraints weight = 70315.169| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 44759 Z= 0.279 Angle : 0.924 23.613 60864 Z= 0.455 Chirality : 0.089 3.996 6778 Planarity : 0.006 0.063 7524 Dihedral : 14.088 175.744 6814 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 1.42 % Allowed : 5.69 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.11), residues: 5160 helix: -1.15 (0.11), residues: 1632 sheet: -1.06 (0.15), residues: 884 loop : -0.60 (0.12), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 235 TYR 0.033 0.002 TYR B 766 PHE 0.024 0.002 PHE H 88 TRP 0.019 0.002 TRP Y 70 HIS 0.015 0.002 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.28 (44726) covalent geometry : angle 0.90600 / 0.45 (60825) hydrogen bonds : bond 0.05541 / 3.34 ( 1646) hydrogen bonds : angle 6.08256 / 3.98 ( 4561) metal coordination : bond 0.02035 / 1.04 ( 31) metal coordination : angle 7.17523 / 3.04 ( 39) Misc. bond : bond 0.03126 / 1.56 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 293 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9240 (ptm) cc_final: 0.8978 (ptp) REVERT: A 78 MET cc_start: 0.8992 (tmm) cc_final: 0.8723 (ttm) REVERT: A 104 MET cc_start: 0.9498 (ptp) cc_final: 0.9154 (ptp) REVERT: A 238 MET cc_start: 0.7927 (ttt) cc_final: 0.7629 (ttt) REVERT: A 248 MET cc_start: 0.9375 (mtm) cc_final: 0.8937 (mpp) REVERT: A 329 MET cc_start: 0.9268 (mmp) cc_final: 0.8875 (mmp) REVERT: A 355 MET cc_start: 0.8573 (mmp) cc_final: 0.7774 (mmm) REVERT: A 467 MET cc_start: 0.9288 (mmt) cc_final: 0.8808 (mmm) REVERT: A 469 MET cc_start: 0.9289 (mtp) cc_final: 0.8274 (tpp) REVERT: A 561 MET cc_start: 0.9384 (mmm) cc_final: 0.9061 (mmm) REVERT: A 660 MET cc_start: 0.8842 (tpp) cc_final: 0.8629 (mmm) REVERT: A 1228 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8335 (ttm) REVERT: A 1412 MET cc_start: 0.8409 (tmm) cc_final: 0.7784 (tmm) REVERT: B 260 LEU cc_start: 0.9527 (mp) cc_final: 0.9288 (mt) REVERT: B 347 MET cc_start: 0.9152 (tpp) cc_final: 0.8430 (tpp) REVERT: B 491 ARG cc_start: 0.8702 (mmt-90) cc_final: 0.7189 (mtt180) REVERT: B 508 MET cc_start: 0.8858 (mtp) cc_final: 0.8436 (mtp) REVERT: B 529 MET cc_start: 0.9425 (mmm) cc_final: 0.8795 (mmm) REVERT: B 584 MET cc_start: 0.9263 (tpp) cc_final: 0.8954 (tpp) REVERT: B 764 MET cc_start: 0.8729 (mtt) cc_final: 0.8269 (mtt) REVERT: B 863 ASP cc_start: 0.9352 (m-30) cc_final: 0.8917 (t0) REVERT: B 976 MET cc_start: 0.8245 (mpp) cc_final: 0.7956 (mpp) REVERT: B 1081 ASP cc_start: 0.8994 (t0) cc_final: 0.8493 (t0) REVERT: C 145 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6844 (pm20) REVERT: E 110 MET cc_start: 0.8887 (tpp) cc_final: 0.8671 (tpp) REVERT: F 95 LYS cc_start: 0.9282 (tttt) cc_final: 0.8808 (tppt) REVERT: H 84 ARG cc_start: 0.7378 (ptp90) cc_final: 0.7125 (ptp90) REVERT: H 118 TYR cc_start: 0.8160 (m-80) cc_final: 0.7124 (m-80) REVERT: H 123 MET cc_start: 0.8562 (tmm) cc_final: 0.8297 (tmm) REVERT: H 141 VAL cc_start: 0.9600 (OUTLIER) cc_final: 0.9182 (p) REVERT: J 28 GLU cc_start: 0.8603 (mp0) cc_final: 0.8356 (mp0) REVERT: L 44 MET cc_start: 0.8029 (mmp) cc_final: 0.7792 (mmm) REVERT: Y 42 MET cc_start: 0.2078 (ptp) cc_final: 0.1797 (ttp) REVERT: Z 746 ASP cc_start: 0.9552 (m-30) cc_final: 0.9185 (p0) REVERT: G 10 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8670 (mm-30) REVERT: G 33 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8963 (mt-10) REVERT: G 41 LYS cc_start: 0.9317 (tttt) cc_final: 0.9089 (tptt) REVERT: G 89 VAL cc_start: 0.9557 (OUTLIER) cc_final: 0.8888 (p) REVERT: G 104 MET cc_start: 0.8862 (ttp) cc_final: 0.8508 (tmm) REVERT: G 122 ASN cc_start: 0.9095 (m-40) cc_final: 0.8708 (p0) REVERT: G 166 ASP cc_start: 0.9591 (m-30) cc_final: 0.9355 (p0) REVERT: D 47 GLN cc_start: 0.9369 (pt0) cc_final: 0.9111 (tm-30) REVERT: O 300 MET cc_start: 0.2122 (tpp) cc_final: 0.1585 (tpt) REVERT: O 496 MET cc_start: 0.8813 (tpp) cc_final: 0.8555 (tpp) REVERT: O 686 PHE cc_start: 0.8756 (t80) cc_final: 0.8171 (t80) REVERT: O 712 MET cc_start: 0.8519 (ttp) cc_final: 0.8183 (ptt) outliers start: 65 outliers final: 26 residues processed: 346 average time/residue: 0.2794 time to fit residues: 158.4568 Evaluate side-chains 277 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 242 ARG Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 145 GLN Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 76 CYS Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 141 VAL Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 331 ASP Chi-restraints excluded: chain O residue 352 ASN Chi-restraints excluded: chain O residue 642 VAL Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 656 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 288 optimal weight: 0.2980 chunk 435 optimal weight: 20.0000 chunk 385 optimal weight: 50.0000 chunk 67 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 484 optimal weight: 40.0000 chunk 90 optimal weight: 3.9990 chunk 516 optimal weight: 50.0000 chunk 254 optimal weight: 7.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 HIS ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 757 GLN A 945 ASN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 537 GLN B 731 GLN B 825 GLN B1120 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN G 93 ASN D 43 HIS D 47 GLN D 128 GLN O 643 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.055186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036088 restraints weight = 327760.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.037139 restraints weight = 172728.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.037827 restraints weight = 112959.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.038259 restraints weight = 85253.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.038528 restraints weight = 71236.905| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 44759 Z= 0.153 Angle : 0.752 17.746 60864 Z= 0.367 Chirality : 0.077 3.656 6778 Planarity : 0.004 0.065 7524 Dihedral : 13.857 178.160 6797 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.64 % Favored : 96.28 % Rotamer: Outliers : 1.33 % Allowed : 6.08 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.11), residues: 5160 helix: -0.22 (0.12), residues: 1648 sheet: -0.76 (0.16), residues: 847 loop : -0.42 (0.12), residues: 2665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 695 TYR 0.026 0.001 TYR B 766 PHE 0.027 0.002 PHE A1202 TRP 0.016 0.001 TRP C 49 HIS 0.014 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (44726) covalent geometry : angle 0.73773 / 0.37 (60825) hydrogen bonds : bond 0.04439 / 2.64 ( 1646) hydrogen bonds : angle 5.50687 / 3.61 ( 4561) metal coordination : bond 0.00781 / 0.39 ( 31) metal coordination : angle 5.86883 / 2.32 ( 39) Misc. bond : bond 0.01082 / 0.54 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9401 (ptp) cc_final: 0.9000 (ptp) REVERT: A 238 MET cc_start: 0.7816 (ttt) cc_final: 0.7534 (ttt) REVERT: A 248 MET cc_start: 0.9225 (mtm) cc_final: 0.8869 (mpp) REVERT: A 388 MET cc_start: 0.8875 (mmm) cc_final: 0.8550 (mmt) REVERT: A 469 MET cc_start: 0.8984 (mtp) cc_final: 0.8073 (tpp) REVERT: A 501 MET cc_start: 0.8566 (mtp) cc_final: 0.8364 (mtp) REVERT: A 535 MET cc_start: 0.8608 (mmm) cc_final: 0.8367 (mmt) REVERT: A 561 MET cc_start: 0.9200 (mmm) cc_final: 0.8951 (mmm) REVERT: A 637 MET cc_start: 0.8935 (ppp) cc_final: 0.8366 (ppp) REVERT: A 1228 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8291 (ttt) REVERT: A 1296 MET cc_start: 0.8347 (mmm) cc_final: 0.8138 (mmm) REVERT: A 1412 MET cc_start: 0.8649 (tmm) cc_final: 0.7994 (tmm) REVERT: A 1451 MET cc_start: 0.9033 (mmm) cc_final: 0.8350 (mmm) REVERT: A 1459 MET cc_start: 0.8985 (mmm) cc_final: 0.8687 (mmp) REVERT: B 200 MET cc_start: 0.8770 (tpp) cc_final: 0.8433 (tpp) REVERT: B 347 MET cc_start: 0.8926 (tpp) cc_final: 0.7719 (mmp) REVERT: B 491 ARG cc_start: 0.8522 (mmt-90) cc_final: 0.7167 (mtt180) REVERT: B 508 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: B 529 MET cc_start: 0.9405 (mmm) cc_final: 0.8927 (mmm) REVERT: B 584 MET cc_start: 0.9055 (tpp) cc_final: 0.8707 (tpp) REVERT: B 764 MET cc_start: 0.8650 (mtt) cc_final: 0.8205 (mtt) REVERT: B 863 ASP cc_start: 0.9167 (m-30) cc_final: 0.8796 (t0) REVERT: B 1081 ASP cc_start: 0.8868 (t0) cc_final: 0.8420 (t0) REVERT: E 151 MET cc_start: 0.8770 (mtp) cc_final: 0.8503 (mtm) REVERT: H 84 ARG cc_start: 0.7301 (ptp90) cc_final: 0.7014 (ptp90) REVERT: Y 42 MET cc_start: 0.2288 (ptp) cc_final: 0.1972 (ttp) REVERT: Z 460 MET cc_start: 0.6939 (mmt) cc_final: 0.6223 (mmt) REVERT: Z 508 MET cc_start: 0.7845 (mmm) cc_final: 0.7620 (mmp) REVERT: Z 746 ASP cc_start: 0.9500 (m-30) cc_final: 0.9140 (p0) REVERT: G 10 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8485 (mm-30) REVERT: G 33 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8863 (mt-10) REVERT: G 104 MET cc_start: 0.9052 (ttp) cc_final: 0.8825 (tmm) REVERT: G 122 ASN cc_start: 0.9069 (m-40) cc_final: 0.8689 (p0) REVERT: G 130 THR cc_start: 0.6207 (OUTLIER) cc_final: 0.5699 (p) REVERT: G 163 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7383 (mm) REVERT: G 166 ASP cc_start: 0.9533 (m-30) cc_final: 0.9273 (p0) REVERT: D 43 HIS cc_start: 0.9182 (OUTLIER) cc_final: 0.8951 (m90) REVERT: D 47 GLN cc_start: 0.9280 (pt0) cc_final: 0.8972 (tm-30) REVERT: O 300 MET cc_start: 0.0715 (tpp) cc_final: 0.0281 (tpt) REVERT: O 362 MET cc_start: 0.7831 (mtm) cc_final: 0.7516 (mpp) REVERT: O 496 MET cc_start: 0.8919 (tpp) cc_final: 0.8658 (tpp) REVERT: O 686 PHE cc_start: 0.8974 (t80) cc_final: 0.8325 (t80) REVERT: O 698 MET cc_start: 0.8043 (tmm) cc_final: 0.7785 (tmm) REVERT: O 712 MET cc_start: 0.8448 (ttp) cc_final: 0.8061 (ptt) outliers start: 61 outliers final: 24 residues processed: 324 average time/residue: 0.2671 time to fit residues: 144.0057 Evaluate side-chains 269 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 921 ILE Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 331 ASP Chi-restraints excluded: chain O residue 352 ASN Chi-restraints excluded: chain O residue 642 VAL Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 656 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 215 optimal weight: 0.0370 chunk 332 optimal weight: 0.0000 chunk 503 optimal weight: 20.0000 chunk 199 optimal weight: 2.9990 chunk 409 optimal weight: 8.9990 chunk 43 optimal weight: 0.0060 chunk 396 optimal weight: 30.0000 chunk 112 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 475 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS Y 95 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.054991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.036073 restraints weight = 332993.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.037045 restraints weight = 173682.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.037749 restraints weight = 112947.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.038177 restraints weight = 84997.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.038433 restraints weight = 71164.160| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 44759 Z= 0.138 Angle : 0.713 15.384 60864 Z= 0.348 Chirality : 0.067 3.411 6778 Planarity : 0.004 0.055 7524 Dihedral : 13.685 179.251 6795 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.45 % Favored : 96.45 % Rotamer: Outliers : 1.09 % Allowed : 6.73 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.11), residues: 5160 helix: 0.28 (0.13), residues: 1664 sheet: -0.60 (0.17), residues: 840 loop : -0.31 (0.12), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Z 494 TYR 0.021 0.001 TYR B 766 PHE 0.026 0.001 PHE O 247 TRP 0.024 0.001 TRP Y 70 HIS 0.015 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (44726) covalent geometry : angle 0.70333 / 0.35 (60825) hydrogen bonds : bond 0.03786 / 2.24 ( 1646) hydrogen bonds : angle 5.23178 / 3.41 ( 4561) metal coordination : bond 0.00712 / 0.36 ( 31) metal coordination : angle 4.65765 / 1.83 ( 39) Misc. bond : bond 0.00213 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.9490 (ppp) cc_final: 0.9137 (ppp) REVERT: A 238 MET cc_start: 0.8055 (ttt) cc_final: 0.7783 (ttt) REVERT: A 248 MET cc_start: 0.9205 (mtm) cc_final: 0.8874 (mpp) REVERT: A 329 MET cc_start: 0.9339 (mmp) cc_final: 0.7422 (ttt) REVERT: A 388 MET cc_start: 0.8887 (mmm) cc_final: 0.8470 (mmm) REVERT: A 470 MET cc_start: 0.8919 (mtp) cc_final: 0.8420 (mmm) REVERT: A 524 MET cc_start: 0.8327 (mtp) cc_final: 0.8006 (mtp) REVERT: A 561 MET cc_start: 0.9183 (mmm) cc_final: 0.8950 (mmm) REVERT: A 637 MET cc_start: 0.8995 (ppp) cc_final: 0.8423 (ppp) REVERT: A 1228 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8409 (ttt) REVERT: A 1412 MET cc_start: 0.8741 (tmm) cc_final: 0.8230 (tmm) REVERT: A 1484 MET cc_start: 0.7575 (pmm) cc_final: 0.7327 (pmm) REVERT: B 347 MET cc_start: 0.8722 (tpp) cc_final: 0.7788 (mmm) REVERT: B 491 ARG cc_start: 0.8441 (mmt-90) cc_final: 0.7277 (mtt180) REVERT: B 508 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8293 (mtp) REVERT: B 529 MET cc_start: 0.9362 (mmm) cc_final: 0.8856 (mmm) REVERT: B 550 MET cc_start: 0.8356 (tmm) cc_final: 0.7414 (tmm) REVERT: B 764 MET cc_start: 0.8626 (mtt) cc_final: 0.8150 (mtt) REVERT: B 863 ASP cc_start: 0.9156 (m-30) cc_final: 0.8763 (t0) REVERT: B 976 MET cc_start: 0.8562 (mpp) cc_final: 0.8001 (mpp) REVERT: B 1081 ASP cc_start: 0.8995 (t0) cc_final: 0.8552 (t0) REVERT: B 1165 MET cc_start: 0.9367 (mtm) cc_final: 0.9068 (ptp) REVERT: E 151 MET cc_start: 0.8716 (mtp) cc_final: 0.8445 (mtm) REVERT: F 72 GLN cc_start: 0.9585 (mt0) cc_final: 0.9202 (pt0) REVERT: H 84 ARG cc_start: 0.7344 (ptp90) cc_final: 0.7009 (ptp90) REVERT: I 108 MET cc_start: 0.9175 (mmm) cc_final: 0.8867 (mpp) REVERT: Y 42 MET cc_start: 0.2219 (ptp) cc_final: 0.1943 (ttp) REVERT: Z 460 MET cc_start: 0.6752 (mmt) cc_final: 0.5848 (mmt) REVERT: Z 474 MET cc_start: 0.8344 (mmt) cc_final: 0.7787 (mmt) REVERT: Z 746 ASP cc_start: 0.9504 (m-30) cc_final: 0.9205 (p0) REVERT: G 10 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8499 (mm-30) REVERT: G 122 ASN cc_start: 0.9103 (m-40) cc_final: 0.8721 (p0) REVERT: G 163 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7191 (mm) REVERT: G 166 ASP cc_start: 0.9501 (m-30) cc_final: 0.9227 (p0) REVERT: D 43 HIS cc_start: 0.9308 (m90) cc_final: 0.9020 (m90) REVERT: D 47 GLN cc_start: 0.9261 (pt0) cc_final: 0.8938 (tm-30) REVERT: O 300 MET cc_start: 0.0552 (tpp) cc_final: 0.0255 (tpp) REVERT: O 362 MET cc_start: 0.7790 (mtm) cc_final: 0.7455 (mpp) REVERT: O 496 MET cc_start: 0.8908 (tpp) cc_final: 0.8616 (tpp) REVERT: O 686 PHE cc_start: 0.9052 (t80) cc_final: 0.8388 (t80) REVERT: O 698 MET cc_start: 0.8106 (tmm) cc_final: 0.7852 (tmm) outliers start: 50 outliers final: 24 residues processed: 293 average time/residue: 0.2821 time to fit residues: 137.9008 Evaluate side-chains 265 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 145 GLN Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain Y residue 70 TRP Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain O residue 250 MET Chi-restraints excluded: chain O residue 331 ASP Chi-restraints excluded: chain O residue 352 ASN Chi-restraints excluded: chain O residue 642 VAL Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 656 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 380 optimal weight: 40.0000 chunk 140 optimal weight: 3.9990 chunk 323 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 484 optimal weight: 30.0000 chunk 496 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 291 optimal weight: 6.9990 chunk 420 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS Z 592 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 833 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.053664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.034685 restraints weight = 344653.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.035306 restraints weight = 181587.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.035989 restraints weight = 117576.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.036428 restraints weight = 89099.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.036668 restraints weight = 74494.901| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 44759 Z= 0.185 Angle : 0.698 15.620 60864 Z= 0.341 Chirality : 0.061 2.982 6778 Planarity : 0.004 0.054 7524 Dihedral : 13.542 174.879 6795 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.64 % Favored : 96.24 % Rotamer: Outliers : 1.24 % Allowed : 7.17 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.12), residues: 5160 helix: 0.77 (0.13), residues: 1668 sheet: -0.58 (0.16), residues: 877 loop : -0.20 (0.12), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 106 TYR 0.019 0.001 TYR B 766 PHE 0.021 0.001 PHE A 458 TRP 0.014 0.001 TRP C 49 HIS 0.008 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (44726) covalent geometry : angle 0.68798 / 0.34 (60825) hydrogen bonds : bond 0.03707 / 2.26 ( 1646) hydrogen bonds : angle 5.09088 / 3.30 ( 4561) metal coordination : bond 0.01363 / 0.69 ( 31) metal coordination : angle 4.65025 / 1.82 ( 39) Misc. bond : bond 0.00129 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.8137 (ttt) cc_final: 0.7813 (ttt) REVERT: A 248 MET cc_start: 0.9237 (mtm) cc_final: 0.8833 (mpp) REVERT: A 329 MET cc_start: 0.9452 (mmp) cc_final: 0.7576 (ttt) REVERT: A 470 MET cc_start: 0.9147 (mtp) cc_final: 0.8572 (mmm) REVERT: A 561 MET cc_start: 0.9217 (mmm) cc_final: 0.8914 (mmm) REVERT: A 637 MET cc_start: 0.9134 (ppp) cc_final: 0.8482 (ppp) REVERT: A 959 MET cc_start: 0.9362 (mmm) cc_final: 0.9069 (mmm) REVERT: A 1228 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8449 (ttt) REVERT: A 1296 MET cc_start: 0.8319 (mmm) cc_final: 0.7927 (mmm) REVERT: A 1412 MET cc_start: 0.8764 (tmm) cc_final: 0.8316 (tmm) REVERT: A 1484 MET cc_start: 0.7714 (pmm) cc_final: 0.7481 (pmm) REVERT: B 347 MET cc_start: 0.8682 (tpp) cc_final: 0.7895 (mmm) REVERT: B 491 ARG cc_start: 0.8484 (mmt-90) cc_final: 0.7291 (mtt180) REVERT: B 508 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8606 (mtp) REVERT: B 529 MET cc_start: 0.9394 (mmm) cc_final: 0.9035 (mmm) REVERT: B 550 MET cc_start: 0.8448 (tmm) cc_final: 0.7644 (tmm) REVERT: B 764 MET cc_start: 0.8693 (mtt) cc_final: 0.8210 (mtt) REVERT: B 863 ASP cc_start: 0.9194 (m-30) cc_final: 0.8789 (t0) REVERT: B 908 MET cc_start: 0.8722 (ppp) cc_final: 0.8485 (ppp) REVERT: B 976 MET cc_start: 0.8478 (mpp) cc_final: 0.8240 (mpp) REVERT: B 1075 MET cc_start: 0.9179 (mmm) cc_final: 0.8723 (mmm) REVERT: B 1081 ASP cc_start: 0.9137 (t0) cc_final: 0.8788 (t0) REVERT: B 1171 MET cc_start: 0.8651 (mpp) cc_final: 0.8425 (mpp) REVERT: E 151 MET cc_start: 0.8764 (mtp) cc_final: 0.8495 (mtm) REVERT: F 72 GLN cc_start: 0.9588 (mt0) cc_final: 0.9296 (pt0) REVERT: H 37 MET cc_start: 0.8966 (mmt) cc_final: 0.8706 (mmt) REVERT: H 84 ARG cc_start: 0.7272 (ptp90) cc_final: 0.7003 (ptp90) REVERT: Y 42 MET cc_start: 0.2562 (ptp) cc_final: 0.2311 (ttp) REVERT: Z 460 MET cc_start: 0.6929 (mmt) cc_final: 0.6107 (mmt) REVERT: Z 508 MET cc_start: 0.7665 (mmm) cc_final: 0.7389 (mmp) REVERT: Z 746 ASP cc_start: 0.9488 (m-30) cc_final: 0.9237 (p0) REVERT: G 33 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8843 (mt-10) REVERT: G 104 MET cc_start: 0.8782 (tmm) cc_final: 0.8203 (tmm) REVERT: G 122 ASN cc_start: 0.9166 (m-40) cc_final: 0.8792 (p0) REVERT: G 163 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7086 (mm) REVERT: G 166 ASP cc_start: 0.9517 (m-30) cc_final: 0.9233 (p0) REVERT: O 300 MET cc_start: 0.0948 (tpp) cc_final: 0.0542 (tpp) REVERT: O 362 MET cc_start: 0.7823 (mtm) cc_final: 0.7510 (mpp) REVERT: O 496 MET cc_start: 0.8907 (tpp) cc_final: 0.8617 (tpp) REVERT: O 686 PHE cc_start: 0.9037 (t80) cc_final: 0.8329 (t80) REVERT: O 721 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.8102 (tpp) outliers start: 57 outliers final: 30 residues processed: 279 average time/residue: 0.2683 time to fit residues: 126.9550 Evaluate side-chains 262 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1228 MET Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Z residue 603 ILE Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 250 MET Chi-restraints excluded: chain O residue 331 ASP Chi-restraints excluded: chain O residue 352 ASN Chi-restraints excluded: chain O residue 642 VAL Chi-restraints excluded: chain O residue 650 LYS Chi-restraints excluded: chain O residue 721 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 60 optimal weight: 5.9990 chunk 497 optimal weight: 0.8980 chunk 167 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 459 optimal weight: 10.0000 chunk 307 optimal weight: 0.4980 chunk 317 optimal weight: 6.9990 chunk 321 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 455 optimal weight: 0.0070 chunk 191 optimal weight: 5.9990 overall best weight: 2.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 833 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.053938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.034963 restraints weight = 344562.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 73)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.035904 restraints weight = 176058.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.036576 restraints weight = 113576.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.036987 restraints weight = 85783.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 69)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.037221 restraints weight = 72368.937| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 44759 Z= 0.129 Angle : 0.675 14.487 60864 Z= 0.327 Chirality : 0.054 1.979 6778 Planarity : 0.004 0.057 7524 Dihedral : 13.437 172.316 6794 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.66 % Favored : 96.22 % Rotamer: Outliers : 1.00 % Allowed : 8.02 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.12), residues: 5160 helix: 0.95 (0.13), residues: 1672 sheet: -0.45 (0.16), residues: 865 loop : -0.20 (0.12), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG I 103 TYR 0.016 0.001 TYR B 160 PHE 0.030 0.001 PHE A 458 TRP 0.034 0.001 TRP Z 180 HIS 0.018 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (44726) covalent geometry : angle 0.66599 / 0.33 (60825) hydrogen bonds : bond 0.03328 / 1.99 ( 1646) hydrogen bonds : angle 4.92000 / 3.19 ( 4561) metal coordination : bond 0.00775 / 0.39 ( 31) metal coordination : angle 4.37633 / 1.68 ( 39) Misc. bond : bond 0.00042 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8571 (pmm) cc_final: 0.8333 (pmm) REVERT: A 78 MET cc_start: 0.9305 (tmm) cc_final: 0.8982 (ttm) REVERT: A 238 MET cc_start: 0.8111 (ttt) cc_final: 0.7732 (ttt) REVERT: A 248 MET cc_start: 0.9215 (mtm) cc_final: 0.8839 (mpp) REVERT: A 329 MET cc_start: 0.9461 (mmp) cc_final: 0.8960 (mmm) REVERT: A 388 MET cc_start: 0.8911 (mmm) cc_final: 0.8268 (mmt) REVERT: A 470 MET cc_start: 0.9087 (mtp) cc_final: 0.8570 (mmm) REVERT: A 561 MET cc_start: 0.9138 (mmm) cc_final: 0.8933 (mmm) REVERT: A 637 MET cc_start: 0.9137 (ppp) cc_final: 0.8466 (ppp) REVERT: A 1228 MET cc_start: 0.8989 (mmm) cc_final: 0.8492 (ttt) REVERT: A 1412 MET cc_start: 0.8679 (tmm) cc_final: 0.8188 (tmm) REVERT: A 1451 MET cc_start: 0.9093 (tpp) cc_final: 0.8581 (mpp) REVERT: B 347 MET cc_start: 0.8639 (tpp) cc_final: 0.7906 (mmm) REVERT: B 491 ARG cc_start: 0.8390 (mmt-90) cc_final: 0.7374 (mtt180) REVERT: B 508 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8626 (mtp) REVERT: B 529 MET cc_start: 0.9378 (mmm) cc_final: 0.9063 (mmm) REVERT: B 550 MET cc_start: 0.8514 (tmm) cc_final: 0.7564 (tmm) REVERT: B 764 MET cc_start: 0.8687 (mtt) cc_final: 0.8177 (mtt) REVERT: B 863 ASP cc_start: 0.9173 (m-30) cc_final: 0.8742 (t0) REVERT: B 908 MET cc_start: 0.8788 (ppp) cc_final: 0.8553 (ppp) REVERT: B 1081 ASP cc_start: 0.9124 (t0) cc_final: 0.8743 (t0) REVERT: B 1165 MET cc_start: 0.9379 (mtm) cc_final: 0.9163 (ptp) REVERT: B 1171 MET cc_start: 0.8682 (mpp) cc_final: 0.8451 (mpp) REVERT: E 151 MET cc_start: 0.8793 (mtp) cc_final: 0.8547 (mtm) REVERT: F 72 GLN cc_start: 0.9555 (mt0) cc_final: 0.9252 (pt0) REVERT: H 37 MET cc_start: 0.8837 (mmt) cc_final: 0.8488 (tmm) REVERT: I 108 MET cc_start: 0.9228 (mmm) cc_final: 0.8756 (mpp) REVERT: Y 42 MET cc_start: 0.2508 (ptp) cc_final: 0.2242 (ttp) REVERT: Z 460 MET cc_start: 0.6816 (mmt) cc_final: 0.5881 (mmt) REVERT: Z 474 MET cc_start: 0.8446 (mmt) cc_final: 0.7834 (mmt) REVERT: Z 508 MET cc_start: 0.7649 (mmm) cc_final: 0.7377 (mmp) REVERT: Z 746 ASP cc_start: 0.9544 (m-30) cc_final: 0.9223 (p0) REVERT: G 10 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8521 (mm-30) REVERT: G 33 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8772 (mt-10) REVERT: G 104 MET cc_start: 0.8784 (tmm) cc_final: 0.8218 (tmm) REVERT: G 122 ASN cc_start: 0.9186 (m-40) cc_final: 0.8789 (p0) REVERT: G 163 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6998 (mm) REVERT: G 166 ASP cc_start: 0.9513 (m-30) cc_final: 0.9228 (p0) REVERT: O 300 MET cc_start: 0.0755 (OUTLIER) cc_final: 0.0400 (tpp) REVERT: O 362 MET cc_start: 0.7815 (mtm) cc_final: 0.7468 (mtm) REVERT: O 496 MET cc_start: 0.8931 (tpp) cc_final: 0.8634 (tpp) REVERT: O 686 PHE cc_start: 0.9022 (t80) cc_final: 0.8334 (t80) REVERT: O 698 MET cc_start: 0.8373 (tmm) cc_final: 0.8137 (tmm) REVERT: O 712 MET cc_start: 0.8193 (ppp) cc_final: 0.7724 (ppp) REVERT: O 721 MET cc_start: 0.8261 (tpt) cc_final: 0.7987 (tpp) outliers start: 46 outliers final: 28 residues processed: 276 average time/residue: 0.2576 time to fit residues: 120.2848 Evaluate side-chains 257 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 226 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain Z residue 603 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 250 MET Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 331 ASP Chi-restraints excluded: chain O residue 352 ASN Chi-restraints excluded: chain O residue 642 VAL Chi-restraints excluded: chain O residue 650 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 123 optimal weight: 30.0000 chunk 497 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 460 optimal weight: 30.0000 chunk 443 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 442 optimal weight: 0.0070 chunk 429 optimal weight: 9.9990 chunk 406 optimal weight: 0.4980 chunk 483 optimal weight: 7.9990 overall best weight: 1.9004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** O 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 833 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.053729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.034487 restraints weight = 341600.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.035411 restraints weight = 175806.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036096 restraints weight = 113914.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.036491 restraints weight = 86297.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.036715 restraints weight = 72769.588| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44759 Z= 0.127 Angle : 0.666 13.696 60864 Z= 0.321 Chirality : 0.049 0.955 6778 Planarity : 0.004 0.057 7524 Dihedral : 13.362 174.273 6794 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.53 % Favored : 96.36 % Rotamer: Outliers : 1.05 % Allowed : 8.67 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.12), residues: 5160 helix: 1.11 (0.13), residues: 1668 sheet: -0.37 (0.17), residues: 865 loop : -0.13 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 83 TYR 0.015 0.001 TYR B 160 PHE 0.026 0.001 PHE A 458 TRP 0.015 0.001 TRP Z 180 HIS 0.021 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (44726) covalent geometry : angle 0.65798 / 0.32 (60825) hydrogen bonds : bond 0.03226 / 1.94 ( 1646) hydrogen bonds : angle 4.83797 / 3.14 ( 4561) metal coordination : bond 0.00725 / 0.36 ( 31) metal coordination : angle 4.20987 / 1.59 ( 39) Misc. bond : bond 0.00021 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 232 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8602 (pmm) cc_final: 0.8352 (pmm) REVERT: A 78 MET cc_start: 0.9365 (tmm) cc_final: 0.8846 (ttm) REVERT: A 238 MET cc_start: 0.8319 (ttt) cc_final: 0.8006 (ttt) REVERT: A 248 MET cc_start: 0.9183 (mtm) cc_final: 0.8812 (mpp) REVERT: A 329 MET cc_start: 0.9511 (mmp) cc_final: 0.9038 (mmm) REVERT: A 388 MET cc_start: 0.8952 (mmm) cc_final: 0.8333 (mmt) REVERT: A 470 MET cc_start: 0.9147 (mtp) cc_final: 0.8930 (mmm) REVERT: A 561 MET cc_start: 0.9138 (mmm) cc_final: 0.8931 (mmm) REVERT: A 637 MET cc_start: 0.9143 (ppp) cc_final: 0.8433 (ppp) REVERT: A 959 MET cc_start: 0.9325 (mmm) cc_final: 0.9046 (mmm) REVERT: A 1228 MET cc_start: 0.8992 (mmm) cc_final: 0.8488 (ttt) REVERT: A 1405 MET cc_start: 0.8636 (mmp) cc_final: 0.8385 (mmp) REVERT: A 1412 MET cc_start: 0.8655 (tmm) cc_final: 0.8351 (tmm) REVERT: A 1451 MET cc_start: 0.9073 (tpp) cc_final: 0.8681 (mpp) REVERT: B 347 MET cc_start: 0.8773 (tpp) cc_final: 0.7902 (mmm) REVERT: B 491 ARG cc_start: 0.8426 (mmt-90) cc_final: 0.7254 (mtt180) REVERT: B 508 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8641 (mtp) REVERT: B 529 MET cc_start: 0.9369 (mmm) cc_final: 0.9025 (mmm) REVERT: B 550 MET cc_start: 0.8541 (tmm) cc_final: 0.7526 (tmm) REVERT: B 728 MET cc_start: 0.9021 (mtm) cc_final: 0.8707 (ptp) REVERT: B 764 MET cc_start: 0.8701 (mtt) cc_final: 0.8294 (mtt) REVERT: B 863 ASP cc_start: 0.9144 (m-30) cc_final: 0.8703 (t0) REVERT: B 908 MET cc_start: 0.8828 (ppp) cc_final: 0.8577 (ppp) REVERT: B 1081 ASP cc_start: 0.9140 (t0) cc_final: 0.8785 (t0) REVERT: B 1165 MET cc_start: 0.9339 (mtm) cc_final: 0.9117 (ptp) REVERT: B 1171 MET cc_start: 0.8740 (mpp) cc_final: 0.8474 (mpp) REVERT: E 72 MET cc_start: 0.9027 (tpp) cc_final: 0.8711 (tpt) REVERT: E 151 MET cc_start: 0.8775 (mtp) cc_final: 0.8507 (mtm) REVERT: F 72 GLN cc_start: 0.9510 (mt0) cc_final: 0.9255 (pt0) REVERT: F 94 MET cc_start: 0.8815 (tmm) cc_final: 0.8595 (tmm) REVERT: H 37 MET cc_start: 0.8774 (mmt) cc_final: 0.8335 (tmm) REVERT: H 145 MET cc_start: 0.8284 (mmm) cc_final: 0.7947 (tpt) REVERT: I 115 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.9200 (p) REVERT: Y 42 MET cc_start: 0.2552 (ptp) cc_final: 0.2330 (ttp) REVERT: Z 460 MET cc_start: 0.6864 (mmt) cc_final: 0.6032 (mmp) REVERT: Z 474 MET cc_start: 0.8467 (mmt) cc_final: 0.7838 (mmt) REVERT: Z 508 MET cc_start: 0.7616 (mmm) cc_final: 0.7362 (mmp) REVERT: Z 746 ASP cc_start: 0.9526 (m-30) cc_final: 0.9285 (p0) REVERT: G 10 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8516 (mm-30) REVERT: G 33 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8753 (mt-10) REVERT: G 104 MET cc_start: 0.8722 (tmm) cc_final: 0.8295 (tmm) REVERT: G 122 ASN cc_start: 0.9209 (m-40) cc_final: 0.8826 (p0) REVERT: G 166 ASP cc_start: 0.9495 (m-30) cc_final: 0.9198 (p0) REVERT: O 300 MET cc_start: 0.0826 (tpp) cc_final: 0.0465 (tpp) REVERT: O 362 MET cc_start: 0.7761 (mtm) cc_final: 0.7417 (mtm) REVERT: O 496 MET cc_start: 0.8951 (tpp) cc_final: 0.8655 (tpp) REVERT: O 686 PHE cc_start: 0.9030 (t80) cc_final: 0.8324 (t80) REVERT: O 712 MET cc_start: 0.8213 (ppp) cc_final: 0.7810 (ppp) REVERT: O 721 MET cc_start: 0.8241 (tpt) cc_final: 0.8015 (tpp) outliers start: 48 outliers final: 31 residues processed: 269 average time/residue: 0.2497 time to fit residues: 115.6780 Evaluate side-chains 254 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain Z residue 603 ILE Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 250 MET Chi-restraints excluded: chain O residue 331 ASP Chi-restraints excluded: chain O residue 352 ASN Chi-restraints excluded: chain O residue 642 VAL Chi-restraints excluded: chain O residue 650 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 392 optimal weight: 50.0000 chunk 336 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 462 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 395 optimal weight: 50.0000 chunk 74 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 286 optimal weight: 10.0000 chunk 483 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 HIS A1230 GLN ** A1457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 833 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.052624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.033046 restraints weight = 344254.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.033994 restraints weight = 180454.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.034674 restraints weight = 117703.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.035094 restraints weight = 89187.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.035332 restraints weight = 75498.208| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 44759 Z= 0.193 Angle : 0.684 14.495 60864 Z= 0.333 Chirality : 0.047 0.633 6778 Planarity : 0.004 0.057 7524 Dihedral : 13.340 179.078 6794 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 1.07 % Allowed : 8.91 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.12), residues: 5160 helix: 1.24 (0.13), residues: 1674 sheet: -0.30 (0.16), residues: 896 loop : -0.08 (0.13), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 927 TYR 0.018 0.001 TYR A 413 PHE 0.023 0.001 PHE A 458 TRP 0.014 0.002 TRP A1210 HIS 0.022 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (44726) covalent geometry : angle 0.67577 / 0.33 (60825) hydrogen bonds : bond 0.03476 / 2.11 ( 1646) hydrogen bonds : angle 4.87448 / 3.14 ( 4561) metal coordination : bond 0.01198 / 0.60 ( 31) metal coordination : angle 4.26894 / 1.65 ( 39) Misc. bond : bond 0.00046 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8632 (pmm) cc_final: 0.8372 (pmm) REVERT: A 78 MET cc_start: 0.9380 (tmm) cc_final: 0.8795 (ttm) REVERT: A 238 MET cc_start: 0.8357 (ttt) cc_final: 0.8016 (ttt) REVERT: A 248 MET cc_start: 0.9229 (mtm) cc_final: 0.8804 (mpp) REVERT: A 329 MET cc_start: 0.9537 (mmp) cc_final: 0.9168 (mmp) REVERT: A 388 MET cc_start: 0.8984 (mmm) cc_final: 0.8362 (mmt) REVERT: A 458 PHE cc_start: 0.9420 (OUTLIER) cc_final: 0.8501 (t80) REVERT: A 470 MET cc_start: 0.9201 (mtp) cc_final: 0.8581 (mmm) REVERT: A 561 MET cc_start: 0.9170 (mmm) cc_final: 0.8893 (mmm) REVERT: A 637 MET cc_start: 0.9135 (ppp) cc_final: 0.8404 (ppp) REVERT: A 959 MET cc_start: 0.9361 (mmm) cc_final: 0.9047 (mmm) REVERT: A 1228 MET cc_start: 0.9031 (mmm) cc_final: 0.8578 (ttt) REVERT: A 1296 MET cc_start: 0.8475 (mmm) cc_final: 0.8272 (mmm) REVERT: A 1405 MET cc_start: 0.8686 (mmp) cc_final: 0.8404 (mmp) REVERT: A 1412 MET cc_start: 0.8612 (tmm) cc_final: 0.8310 (tmm) REVERT: A 1428 MET cc_start: 0.7626 (mmt) cc_final: 0.7348 (mmt) REVERT: A 1451 MET cc_start: 0.9071 (tpp) cc_final: 0.8613 (mpp) REVERT: B 347 MET cc_start: 0.8794 (tpp) cc_final: 0.7962 (mmm) REVERT: B 491 ARG cc_start: 0.8397 (mmt-90) cc_final: 0.7235 (mtt180) REVERT: B 508 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8668 (mtp) REVERT: B 529 MET cc_start: 0.9458 (mmm) cc_final: 0.8953 (mmm) REVERT: B 550 MET cc_start: 0.8679 (tmm) cc_final: 0.7734 (tmm) REVERT: B 863 ASP cc_start: 0.9133 (m-30) cc_final: 0.8713 (t0) REVERT: B 908 MET cc_start: 0.8883 (ppp) cc_final: 0.8639 (ppp) REVERT: B 1165 MET cc_start: 0.9378 (mtm) cc_final: 0.9116 (ptp) REVERT: B 1171 MET cc_start: 0.8751 (mpp) cc_final: 0.8426 (mpp) REVERT: E 151 MET cc_start: 0.8807 (mtp) cc_final: 0.8513 (mtm) REVERT: I 115 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9073 (p) REVERT: Z 460 MET cc_start: 0.6861 (mmt) cc_final: 0.6025 (mmp) REVERT: Z 474 MET cc_start: 0.8534 (mmt) cc_final: 0.7881 (mmt) REVERT: Z 746 ASP cc_start: 0.9535 (m-30) cc_final: 0.9300 (p0) REVERT: G 104 MET cc_start: 0.8742 (tmm) cc_final: 0.8316 (tmm) REVERT: G 122 ASN cc_start: 0.9242 (m-40) cc_final: 0.8835 (p0) REVERT: G 166 ASP cc_start: 0.9459 (m-30) cc_final: 0.9166 (p0) REVERT: O 300 MET cc_start: 0.1143 (OUTLIER) cc_final: 0.0684 (tpp) REVERT: O 362 MET cc_start: 0.7747 (mtm) cc_final: 0.7414 (mtm) REVERT: O 496 MET cc_start: 0.8968 (tpp) cc_final: 0.8666 (tpp) REVERT: O 686 PHE cc_start: 0.9095 (t80) cc_final: 0.8399 (t80) REVERT: O 697 ASP cc_start: 0.8636 (m-30) cc_final: 0.8143 (p0) outliers start: 49 outliers final: 33 residues processed: 254 average time/residue: 0.2596 time to fit residues: 113.5680 Evaluate side-chains 253 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 216 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1133 LYS Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain Y residue 88 SER Chi-restraints excluded: chain Z residue 603 ILE Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 250 MET Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 331 ASP Chi-restraints excluded: chain O residue 352 ASN Chi-restraints excluded: chain O residue 642 VAL Chi-restraints excluded: chain O residue 650 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 481 optimal weight: 50.0000 chunk 130 optimal weight: 0.1980 chunk 308 optimal weight: 0.5980 chunk 509 optimal weight: 50.0000 chunk 317 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 501 optimal weight: 6.9990 chunk 498 optimal weight: 6.9990 chunk 324 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 333 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 HIS ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 60 HIS I 87 GLN ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 833 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.053429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034010 restraints weight = 327274.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.034961 restraints weight = 174241.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.035663 restraints weight = 114578.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036102 restraints weight = 86179.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.036356 restraints weight = 72207.131| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 44759 Z= 0.111 Angle : 0.663 14.635 60864 Z= 0.318 Chirality : 0.047 0.573 6778 Planarity : 0.004 0.058 7524 Dihedral : 13.262 178.402 6794 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.45 % Favored : 96.41 % Rotamer: Outliers : 0.94 % Allowed : 9.17 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.12), residues: 5160 helix: 1.26 (0.13), residues: 1673 sheet: -0.23 (0.17), residues: 872 loop : -0.07 (0.13), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 103 TYR 0.013 0.001 TYR B 160 PHE 0.023 0.001 PHE O 247 TRP 0.013 0.001 TRP C 49 HIS 0.022 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (44726) covalent geometry : angle 0.65521 / 0.32 (60825) hydrogen bonds : bond 0.03157 / 1.89 ( 1646) hydrogen bonds : angle 4.76974 / 3.08 ( 4561) metal coordination : bond 0.00558 / 0.28 ( 31) metal coordination : angle 3.97935 / 1.50 ( 39) Misc. bond : bond 0.00028 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8672 (pmm) cc_final: 0.8431 (pmm) REVERT: A 78 MET cc_start: 0.9363 (tmm) cc_final: 0.8853 (ttm) REVERT: A 238 MET cc_start: 0.8369 (ttt) cc_final: 0.8027 (ttt) REVERT: A 248 MET cc_start: 0.9138 (mtm) cc_final: 0.8793 (mpp) REVERT: A 317 MET cc_start: 0.9306 (tpp) cc_final: 0.8856 (mmt) REVERT: A 329 MET cc_start: 0.9548 (mmp) cc_final: 0.9066 (mmp) REVERT: A 388 MET cc_start: 0.8969 (mmm) cc_final: 0.8385 (mmt) REVERT: A 458 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.8454 (t80) REVERT: A 561 MET cc_start: 0.9095 (mmm) cc_final: 0.8800 (mmm) REVERT: A 637 MET cc_start: 0.9135 (ppp) cc_final: 0.8379 (ppp) REVERT: A 959 MET cc_start: 0.9311 (mmm) cc_final: 0.9019 (mmm) REVERT: A 1228 MET cc_start: 0.8954 (mmm) cc_final: 0.8424 (ttt) REVERT: A 1405 MET cc_start: 0.8680 (mmp) cc_final: 0.8395 (mmp) REVERT: A 1412 MET cc_start: 0.8618 (tmm) cc_final: 0.8347 (tmm) REVERT: A 1428 MET cc_start: 0.7788 (mmt) cc_final: 0.7363 (mmt) REVERT: A 1451 MET cc_start: 0.9047 (tpp) cc_final: 0.8620 (mpp) REVERT: B 347 MET cc_start: 0.8753 (tpp) cc_final: 0.7909 (mmm) REVERT: B 491 ARG cc_start: 0.8356 (mmt-90) cc_final: 0.7168 (mtt180) REVERT: B 508 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8679 (mtp) REVERT: B 529 MET cc_start: 0.9241 (mmm) cc_final: 0.8748 (mmm) REVERT: B 550 MET cc_start: 0.8608 (tmm) cc_final: 0.7637 (tmm) REVERT: B 863 ASP cc_start: 0.9081 (m-30) cc_final: 0.8662 (t0) REVERT: B 908 MET cc_start: 0.8909 (ppp) cc_final: 0.8654 (ppp) REVERT: B 1089 MET cc_start: 0.9012 (mpp) cc_final: 0.8738 (mtm) REVERT: B 1165 MET cc_start: 0.9349 (mtm) cc_final: 0.9091 (ptp) REVERT: B 1171 MET cc_start: 0.8704 (mpp) cc_final: 0.8454 (mpp) REVERT: E 151 MET cc_start: 0.8773 (mtp) cc_final: 0.8485 (mtm) REVERT: F 72 GLN cc_start: 0.9568 (mt0) cc_final: 0.9267 (pt0) REVERT: I 115 THR cc_start: 0.9394 (OUTLIER) cc_final: 0.9137 (p) REVERT: K 97 GLU cc_start: 0.8628 (tt0) cc_final: 0.8407 (tt0) REVERT: Z 460 MET cc_start: 0.6846 (mmt) cc_final: 0.5918 (mmp) REVERT: Z 474 MET cc_start: 0.8521 (mmt) cc_final: 0.7875 (mmt) REVERT: Z 746 ASP cc_start: 0.9513 (m-30) cc_final: 0.9301 (p0) REVERT: G 10 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8485 (mm-30) REVERT: G 33 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8748 (mt-10) REVERT: G 104 MET cc_start: 0.8704 (tmm) cc_final: 0.8314 (tmm) REVERT: G 117 MET cc_start: 0.8104 (tpp) cc_final: 0.7827 (tpp) REVERT: G 122 ASN cc_start: 0.9185 (m-40) cc_final: 0.8766 (p0) REVERT: G 166 ASP cc_start: 0.9450 (m-30) cc_final: 0.9152 (p0) REVERT: O 300 MET cc_start: 0.0344 (OUTLIER) cc_final: 0.0076 (tpp) REVERT: O 362 MET cc_start: 0.7697 (mtm) cc_final: 0.7352 (mtm) REVERT: O 496 MET cc_start: 0.8994 (tpp) cc_final: 0.8676 (tpp) REVERT: O 686 PHE cc_start: 0.9155 (t80) cc_final: 0.8451 (t80) REVERT: O 697 ASP cc_start: 0.8547 (m-30) cc_final: 0.7978 (p0) REVERT: O 746 MET cc_start: 0.8768 (ptt) cc_final: 0.8357 (mmt) outliers start: 43 outliers final: 27 residues processed: 253 average time/residue: 0.2444 time to fit residues: 106.2192 Evaluate side-chains 251 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 60 HIS Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain Z residue 603 ILE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 250 MET Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 331 ASP Chi-restraints excluded: chain O residue 352 ASN Chi-restraints excluded: chain O residue 642 VAL Chi-restraints excluded: chain O residue 650 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 261 optimal weight: 8.9990 chunk 409 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 381 optimal weight: 8.9990 chunk 371 optimal weight: 50.0000 chunk 255 optimal weight: 4.9990 chunk 445 optimal weight: 6.9990 chunk 413 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 833 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.052736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.033318 restraints weight = 335071.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.034194 restraints weight = 176950.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.034893 restraints weight = 116740.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.035320 restraints weight = 88276.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.035566 restraints weight = 74021.779| |-----------------------------------------------------------------------------| r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 44759 Z= 0.152 Angle : 0.675 13.382 60864 Z= 0.326 Chirality : 0.046 0.520 6778 Planarity : 0.004 0.057 7524 Dihedral : 13.208 177.310 6792 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.76 % Favored : 96.10 % Rotamer: Outliers : 0.74 % Allowed : 9.48 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.12), residues: 5160 helix: 1.35 (0.13), residues: 1676 sheet: -0.21 (0.17), residues: 889 loop : -0.04 (0.13), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 927 TYR 0.016 0.001 TYR B 766 PHE 0.024 0.001 PHE O 247 TRP 0.015 0.001 TRP A1192 HIS 0.033 0.001 HIS I 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (44726) covalent geometry : angle 0.66780 / 0.33 (60825) hydrogen bonds : bond 0.03278 / 1.98 ( 1646) hydrogen bonds : angle 4.77759 / 3.07 ( 4561) metal coordination : bond 0.00935 / 0.47 ( 31) metal coordination : angle 3.82553 / 1.45 ( 39) Misc. bond : bond 0.00027 / 0.01 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10320 Ramachandran restraints generated. 5160 Oldfield, 0 Emsley, 5160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8697 (pmm) cc_final: 0.8436 (pmm) REVERT: A 78 MET cc_start: 0.9404 (tmm) cc_final: 0.8801 (ttm) REVERT: A 238 MET cc_start: 0.8440 (ttt) cc_final: 0.8080 (ttt) REVERT: A 248 MET cc_start: 0.9165 (mtm) cc_final: 0.8762 (mpp) REVERT: A 317 MET cc_start: 0.9338 (tpp) cc_final: 0.8893 (mmt) REVERT: A 329 MET cc_start: 0.9559 (mmp) cc_final: 0.9132 (mmp) REVERT: A 388 MET cc_start: 0.9007 (mmm) cc_final: 0.8419 (mmt) REVERT: A 458 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8525 (t80) REVERT: A 561 MET cc_start: 0.9140 (mmm) cc_final: 0.8870 (mmm) REVERT: A 637 MET cc_start: 0.9170 (ppp) cc_final: 0.8398 (ppp) REVERT: A 959 MET cc_start: 0.9351 (mmm) cc_final: 0.9031 (mmm) REVERT: A 1228 MET cc_start: 0.8957 (mmm) cc_final: 0.8520 (ttt) REVERT: A 1405 MET cc_start: 0.8707 (mmp) cc_final: 0.8429 (mmp) REVERT: A 1412 MET cc_start: 0.8613 (tmm) cc_final: 0.8285 (tmm) REVERT: A 1428 MET cc_start: 0.7896 (mmt) cc_final: 0.7389 (mmt) REVERT: A 1451 MET cc_start: 0.9073 (tpp) cc_final: 0.8699 (mpp) REVERT: B 347 MET cc_start: 0.8779 (tpp) cc_final: 0.7952 (mmm) REVERT: B 491 ARG cc_start: 0.8366 (mmt-90) cc_final: 0.7171 (mtt180) REVERT: B 508 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8678 (mtp) REVERT: B 550 MET cc_start: 0.8734 (tmm) cc_final: 0.7766 (tmm) REVERT: B 863 ASP cc_start: 0.9085 (m-30) cc_final: 0.8656 (t0) REVERT: B 908 MET cc_start: 0.8936 (ppp) cc_final: 0.8685 (ppp) REVERT: B 1089 MET cc_start: 0.8956 (mpp) cc_final: 0.8448 (mtm) REVERT: B 1165 MET cc_start: 0.9389 (mtm) cc_final: 0.9110 (ptp) REVERT: B 1171 MET cc_start: 0.8732 (mpp) cc_final: 0.8436 (mpp) REVERT: E 18 MET cc_start: 0.9024 (ppp) cc_final: 0.8568 (ppp) REVERT: E 151 MET cc_start: 0.8790 (mtp) cc_final: 0.8581 (mtm) REVERT: F 72 GLN cc_start: 0.9587 (mt0) cc_final: 0.9379 (pt0) REVERT: I 115 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.9131 (p) REVERT: Y 42 MET cc_start: 0.1882 (ppp) cc_final: 0.1680 (tmm) REVERT: Z 460 MET cc_start: 0.6827 (mmt) cc_final: 0.5949 (mmp) REVERT: Z 563 MET cc_start: 0.8453 (pmm) cc_final: 0.7760 (pmm) REVERT: Z 746 ASP cc_start: 0.9535 (m-30) cc_final: 0.9328 (p0) REVERT: G 10 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8508 (mm-30) REVERT: G 100 GLU cc_start: 0.9343 (mp0) cc_final: 0.8910 (mp0) REVERT: G 104 MET cc_start: 0.8672 (tmm) cc_final: 0.8313 (tmm) REVERT: G 117 MET cc_start: 0.8166 (tpp) cc_final: 0.7884 (tpp) REVERT: G 122 ASN cc_start: 0.9184 (m-40) cc_final: 0.8766 (p0) REVERT: G 165 ASP cc_start: 0.7997 (t70) cc_final: 0.7555 (t70) REVERT: G 166 ASP cc_start: 0.9436 (m-30) cc_final: 0.9131 (p0) REVERT: O 300 MET cc_start: 0.0767 (OUTLIER) cc_final: 0.0399 (tpp) REVERT: O 362 MET cc_start: 0.7729 (mtm) cc_final: 0.7392 (mtm) REVERT: O 496 MET cc_start: 0.9005 (tpp) cc_final: 0.8692 (tpp) REVERT: O 686 PHE cc_start: 0.9155 (t80) cc_final: 0.8460 (t80) REVERT: O 697 ASP cc_start: 0.8545 (m-30) cc_final: 0.7950 (p0) REVERT: O 746 MET cc_start: 0.8780 (ptt) cc_final: 0.8364 (mmt) outliers start: 34 outliers final: 27 residues processed: 247 average time/residue: 0.2418 time to fit residues: 102.3191 Evaluate side-chains 251 residues out of total 4615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 220 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 883 ILE Chi-restraints excluded: chain A residue 1459 MET Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 508 MET Chi-restraints excluded: chain B residue 667 THR Chi-restraints excluded: chain B residue 840 MET Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1144 THR Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain Z residue 603 ILE Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain O residue 242 ASN Chi-restraints excluded: chain O residue 250 MET Chi-restraints excluded: chain O residue 300 MET Chi-restraints excluded: chain O residue 331 ASP Chi-restraints excluded: chain O residue 352 ASN Chi-restraints excluded: chain O residue 642 VAL Chi-restraints excluded: chain O residue 650 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 520 random chunks: chunk 20 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 451 optimal weight: 0.0570 chunk 34 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 chunk 453 optimal weight: 50.0000 chunk 488 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 overall best weight: 1.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN O 833 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.053039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.033489 restraints weight = 333788.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.034516 restraints weight = 176139.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.035191 restraints weight = 115148.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.035624 restraints weight = 86991.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.035876 restraints weight = 72911.009| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44759 Z= 0.121 Angle : 0.663 13.380 60864 Z= 0.318 Chirality : 0.046 0.492 6778 Planarity : 0.004 0.056 7524 Dihedral : 13.139 175.815 6792 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.68 % Favored : 96.20 % Rotamer: Outliers : 0.76 % Allowed : 9.69 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.12), residues: 5160 helix: 1.33 (0.13), residues: 1670 sheet: -0.15 (0.17), residues: 876 loop : -0.05 (0.13), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 927 TYR 0.013 0.001 TYR B 766 PHE 0.023 0.001 PHE O 247 TRP 0.014 0.001 TRP A1192 HIS 0.022 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (44726) covalent geometry : angle 0.65679 / 0.32 (60825) hydrogen bonds : bond 0.03134 / 1.87 ( 1646) hydrogen bonds : angle 4.72326 / 3.04 ( 4561) metal coordination : bond 0.00683 / 0.34 ( 31) metal coordination : angle 3.62844 / 1.36 ( 39) Misc. bond : bond 0.00021 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11286.72 seconds wall clock time: 194 minutes 17.06 seconds (11657.06 seconds total)