Starting phenix.real_space_refine on Tue Jun 24 15:02:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hkk_34853/06_2025/8hkk_34853.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hkk_34853/06_2025/8hkk_34853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hkk_34853/06_2025/8hkk_34853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hkk_34853/06_2025/8hkk_34853.map" model { file = "/net/cci-nas-00/data/ceres_data/8hkk_34853/06_2025/8hkk_34853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hkk_34853/06_2025/8hkk_34853.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.044 sd= 0.156 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 K 18 8.98 5 Zn 4 6.06 5 S 212 5.16 5 Na 1 4.78 5 C 18576 2.51 5 N 4768 2.21 5 O 5108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.43s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28687 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7166 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7166 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "C" Number of atoms: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7166 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "D" Number of atoms: 7166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7166 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 42, 'TRANS': 856} Chain breaks: 7 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 81 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' K': 6, ' NA': 1, ' ZN': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' ZN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' ZN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' K': 4, ' ZN': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4448 SG CYS A 777 94.859 62.372 128.271 1.00 77.48 S ATOM 4454 SG CYS A 778 98.691 61.972 128.072 1.00 86.07 S ATOM 4508 SG CYS A 785 97.156 65.349 129.088 1.00116.80 S ATOM 11614 SG CYS B 777 85.146 94.663 128.336 1.00 79.33 S ATOM 11620 SG CYS B 778 85.637 98.482 128.141 1.00 90.83 S ATOM 11674 SG CYS B 785 82.198 97.031 129.102 1.00112.95 S ATOM 18780 SG CYS C 777 53.019 84.899 128.309 1.00 77.01 S ATOM 18786 SG CYS C 778 49.203 85.387 128.159 1.00 84.04 S ATOM 18840 SG CYS C 785 50.660 81.951 129.111 1.00117.77 S ATOM 25946 SG CYS D 777 62.637 52.726 128.313 1.00 74.25 S ATOM 25952 SG CYS D 778 62.212 48.895 128.101 1.00 84.06 S ATOM 26006 SG CYS D 785 65.618 50.419 129.067 1.00105.77 S Time building chain proxies: 16.86, per 1000 atoms: 0.59 Number of scatterers: 28687 At special positions: 0 Unit cell: (148.72, 148.72, 142.48, 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 4 29.99 K 18 19.00 S 212 16.00 Na 1 11.00 O 5108 8.00 N 4768 7.00 C 18576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.78 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1301 " - pdb=" SG CYS A 778 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 777 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1301 " - pdb=" SG CYS B 778 " pdb=" ZN C1301 " pdb="ZN ZN C1301 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 777 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1301 " - pdb=" SG CYS C 778 " pdb=" ZN D1301 " pdb="ZN ZN D1301 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 785 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 777 " pdb="ZN ZN D1301 " - pdb=" SG CYS D 778 " Number of angles added : 12 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 20 sheets defined 53.3% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 110 through 136 Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.633A pdb=" N LEU A 141 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 173 through 198 removed outlier: 3.606A pdb=" N ALA A 178 " --> pdb=" O MET A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 225 Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 226 through 227 No H-bonds generated for 'chain 'A' and resid 226 through 227' Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.565A pdb=" N LEU A 231 " --> pdb=" O TRP A 228 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN A 233 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 240 through 256 removed outlier: 4.084A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 293 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 324 through 357 Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 382 through 394 Processing helix chain 'A' and resid 395 through 400 removed outlier: 6.716A pdb=" N ARG A 398 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.550A pdb=" N ILE A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 463 through 482 Processing helix chain 'A' and resid 493 through 500 removed outlier: 4.686A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS A 499 " --> pdb=" O ASN A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 3.533A pdb=" N CYS A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 547 through 557 Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 579 through 592 Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.580A pdb=" N PHE A 637 " --> pdb=" O SER A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 797 removed outlier: 3.545A pdb=" N TYR A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 822 Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 843 through 851 Processing helix chain 'A' and resid 865 through 873 Processing helix chain 'A' and resid 893 through 897 Processing helix chain 'A' and resid 898 through 912 Processing helix chain 'A' and resid 923 through 930 removed outlier: 4.228A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET A 930 " --> pdb=" O MET A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 952 removed outlier: 3.895A pdb=" N SER A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 960 removed outlier: 3.964A pdb=" N PHE A 960 " --> pdb=" O ALA A 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 957 through 960' Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 972 through 982 removed outlier: 3.825A pdb=" N ASP A 976 " --> pdb=" O ILE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 996 Processing helix chain 'A' and resid 1013 through 1017 Processing helix chain 'A' and resid 1021 through 1033 Processing helix chain 'A' and resid 1129 through 1143 Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'B' and resid 111 through 137 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.636A pdb=" N LEU B 141 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 173 through 198 removed outlier: 3.515A pdb=" N ALA B 178 " --> pdb=" O MET B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 226 Proline residue: B 221 - end of helix removed outlier: 3.762A pdb=" N ILE B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Proline residue: B 230 - end of helix No H-bonds generated for 'chain 'B' and resid 227 through 232' Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 240 through 256 removed outlier: 3.889A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP B 255 " --> pdb=" O ASN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 293 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 324 through 357 Proline residue: B 343 - end of helix removed outlier: 3.538A pdb=" N GLU B 355 " --> pdb=" O TYR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 394 Processing helix chain 'B' and resid 395 through 400 removed outlier: 6.728A pdb=" N ARG B 398 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 400 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 422 removed outlier: 3.513A pdb=" N VAL B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 463 through 482 Processing helix chain 'B' and resid 493 through 500 removed outlier: 4.669A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B 499 " --> pdb=" O ASN B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 removed outlier: 3.525A pdb=" N CYS B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 534 Processing helix chain 'B' and resid 547 through 557 Processing helix chain 'B' and resid 572 through 576 Processing helix chain 'B' and resid 579 through 592 Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.594A pdb=" N PHE B 637 " --> pdb=" O SER B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.524A pdb=" N TYR B 796 " --> pdb=" O ASP B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 811 through 822 Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 843 through 851 Processing helix chain 'B' and resid 865 through 873 Processing helix chain 'B' and resid 893 through 897 Processing helix chain 'B' and resid 898 through 912 Processing helix chain 'B' and resid 923 through 930 removed outlier: 4.217A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B 930 " --> pdb=" O MET B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 952 removed outlier: 3.949A pdb=" N SER B 943 " --> pdb=" O SER B 939 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 960 removed outlier: 3.856A pdb=" N PHE B 960 " --> pdb=" O ALA B 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 957 through 960' Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 972 through 982 removed outlier: 3.751A pdb=" N ASP B 976 " --> pdb=" O ILE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 997 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1021 through 1033 Processing helix chain 'B' and resid 1129 through 1143 Processing helix chain 'B' and resid 1144 through 1161 Processing helix chain 'C' and resid 111 through 137 Processing helix chain 'C' and resid 138 through 142 removed outlier: 3.663A pdb=" N LEU C 141 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 173 through 198 removed outlier: 3.594A pdb=" N ALA C 178 " --> pdb=" O MET C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 225 Proline residue: C 221 - end of helix Processing helix chain 'C' and resid 229 through 233 removed outlier: 4.348A pdb=" N ASN C 233 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 239 No H-bonds generated for 'chain 'C' and resid 237 through 239' Processing helix chain 'C' and resid 240 through 254 removed outlier: 4.000A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET C 252 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 293 removed outlier: 4.448A pdb=" N GLN C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 324 through 357 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 382 through 394 Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 438 through 445 Processing helix chain 'C' and resid 446 through 450 Processing helix chain 'C' and resid 463 through 482 Processing helix chain 'C' and resid 493 through 500 removed outlier: 4.681A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS C 499 " --> pdb=" O ASN C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 removed outlier: 3.544A pdb=" N CYS C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 534 Processing helix chain 'C' and resid 547 through 557 Processing helix chain 'C' and resid 572 through 576 Processing helix chain 'C' and resid 579 through 592 Processing helix chain 'C' and resid 633 through 644 removed outlier: 3.592A pdb=" N PHE C 637 " --> pdb=" O SER C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 797 removed outlier: 3.543A pdb=" N TYR C 796 " --> pdb=" O ASP C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 811 through 822 Proline residue: C 820 - end of helix Processing helix chain 'C' and resid 843 through 851 Processing helix chain 'C' and resid 865 through 873 Processing helix chain 'C' and resid 893 through 897 Processing helix chain 'C' and resid 898 through 912 Processing helix chain 'C' and resid 923 through 930 removed outlier: 4.228A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 930 " --> pdb=" O MET C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 952 removed outlier: 3.903A pdb=" N SER C 943 " --> pdb=" O SER C 939 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 960 removed outlier: 3.855A pdb=" N PHE C 960 " --> pdb=" O ALA C 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 957 through 960' Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 972 through 982 removed outlier: 3.664A pdb=" N ASP C 976 " --> pdb=" O ILE C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 997 Processing helix chain 'C' and resid 1013 through 1017 Processing helix chain 'C' and resid 1021 through 1033 Processing helix chain 'C' and resid 1129 through 1143 Processing helix chain 'C' and resid 1144 through 1161 Processing helix chain 'D' and resid 111 through 136 Processing helix chain 'D' and resid 138 through 142 removed outlier: 3.596A pdb=" N LEU D 141 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 173 through 198 removed outlier: 3.538A pdb=" N ALA D 178 " --> pdb=" O MET D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 225 Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 226 through 227 No H-bonds generated for 'chain 'D' and resid 226 through 227' Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 240 through 256 removed outlier: 4.059A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 254 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASP D 255 " --> pdb=" O ASN D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 293 removed outlier: 4.481A pdb=" N GLN D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 324 through 357 Proline residue: D 343 - end of helix removed outlier: 3.846A pdb=" N GLU D 355 " --> pdb=" O TYR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 394 Processing helix chain 'D' and resid 395 through 400 removed outlier: 6.717A pdb=" N ARG D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 400 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 422 removed outlier: 3.510A pdb=" N VAL D 419 " --> pdb=" O GLN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 Processing helix chain 'D' and resid 446 through 450 Processing helix chain 'D' and resid 463 through 482 Processing helix chain 'D' and resid 493 through 500 removed outlier: 4.673A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS D 499 " --> pdb=" O ASN D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 removed outlier: 3.519A pdb=" N CYS D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 534 Processing helix chain 'D' and resid 547 through 557 Processing helix chain 'D' and resid 572 through 576 Processing helix chain 'D' and resid 579 through 592 Processing helix chain 'D' and resid 633 through 644 removed outlier: 3.593A pdb=" N PHE D 637 " --> pdb=" O SER D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 792 through 797 removed outlier: 3.543A pdb=" N TYR D 796 " --> pdb=" O ASP D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 811 through 822 Proline residue: D 820 - end of helix Processing helix chain 'D' and resid 843 through 851 Processing helix chain 'D' and resid 865 through 873 Processing helix chain 'D' and resid 893 through 897 Processing helix chain 'D' and resid 898 through 912 Processing helix chain 'D' and resid 923 through 930 removed outlier: 4.231A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET D 930 " --> pdb=" O MET D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 936 through 952 removed outlier: 3.951A pdb=" N SER D 943 " --> pdb=" O SER D 939 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 960 removed outlier: 4.036A pdb=" N PHE D 960 " --> pdb=" O ALA D 957 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 957 through 960' Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 972 through 982 removed outlier: 3.652A pdb=" N ASP D 976 " --> pdb=" O ILE D 972 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1013 through 1017 Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1129 through 1143 Processing helix chain 'D' and resid 1144 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 432 removed outlier: 6.198A pdb=" N VAL A 404 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU A 432 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE A 406 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N PHE A 454 " --> pdb=" O HIS A 373 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL A 375 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS A 453 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLN A 490 " --> pdb=" O CYS A 453 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE A 455 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.522A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA4, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.103A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LEU A 802 " --> pdb=" O ALA A 877 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 879 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 916 " --> pdb=" O ASP A 878 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 920 " --> pdb=" O VAL A 882 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 3.964A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY A1039 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A1199 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 429 through 432 removed outlier: 6.288A pdb=" N VAL B 404 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU B 432 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE B 406 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 453 " --> pdb=" O TYR B 488 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N GLN B 490 " --> pdb=" O CYS B 453 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 455 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.527A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 750 through 752 Processing sheet with id=AA9, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.065A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU B 802 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 879 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B 916 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU B 920 " --> pdb=" O VAL B 882 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 3.933A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY B1039 " --> pdb=" O TYR B1197 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE B1199 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 429 through 432 removed outlier: 6.272A pdb=" N VAL C 404 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU C 432 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE C 406 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 9.069A pdb=" N PHE C 454 " --> pdb=" O HIS C 373 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL C 375 " --> pdb=" O PHE C 454 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N CYS C 453 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLN C 490 " --> pdb=" O CYS C 453 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE C 455 " --> pdb=" O GLN C 490 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.520A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 750 through 752 Processing sheet with id=AB5, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.100A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU C 802 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 879 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER C 916 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 920 " --> pdb=" O VAL C 882 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 3.962A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY C1039 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C1199 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 429 through 432 removed outlier: 6.148A pdb=" N VAL D 404 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU D 432 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE D 406 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N PHE D 454 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL D 375 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU D 456 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N CYS D 377 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS D 453 " --> pdb=" O TYR D 488 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLN D 490 " --> pdb=" O CYS D 453 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE D 455 " --> pdb=" O GLN D 490 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.560A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 750 through 752 Processing sheet with id=AC1, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.073A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU D 802 " --> pdb=" O ALA D 877 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D 879 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 920 " --> pdb=" O VAL D 882 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 3.954A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY D1039 " --> pdb=" O TYR D1197 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE D1199 " --> pdb=" O PRO D1037 " (cutoff:3.500A) 1393 hydrogen bonds defined for protein. 3903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.92 Time building geometry restraints manager: 7.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 1.03: 3 1.03 - 1.40: 11880 1.40 - 1.77: 17130 1.77 - 2.13: 313 2.13 - 2.50: 2 Bond restraints: 29328 Sorted by residual: bond pdb=" CG PRO D 237 " pdb=" CD PRO D 237 " ideal model delta sigma weight residual 1.503 0.662 0.841 3.40e-02 8.65e+02 6.12e+02 bond pdb=" CB PRO C 237 " pdb=" CG PRO C 237 " ideal model delta sigma weight residual 1.492 2.502 -1.010 5.00e-02 4.00e+02 4.08e+02 bond pdb=" CB PRO B 237 " pdb=" CG PRO B 237 " ideal model delta sigma weight residual 1.492 2.493 -1.001 5.00e-02 4.00e+02 4.01e+02 bond pdb=" CG PRO B 237 " pdb=" CD PRO B 237 " ideal model delta sigma weight residual 1.503 0.978 0.525 3.40e-02 8.65e+02 2.39e+02 bond pdb=" CG PRO C 237 " pdb=" CD PRO C 237 " ideal model delta sigma weight residual 1.503 0.991 0.512 3.40e-02 8.65e+02 2.26e+02 ... (remaining 29323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 21.22: 39787 21.22 - 42.43: 5 42.43 - 63.65: 2 63.65 - 84.87: 0 84.87 - 106.09: 2 Bond angle restraints: 39796 Sorted by residual: angle pdb=" CB PRO C 237 " pdb=" CG PRO C 237 " pdb=" CD PRO C 237 " ideal model delta sigma weight residual 106.10 0.01 106.09 3.20e+00 9.77e-02 1.10e+03 angle pdb=" CB PRO B 237 " pdb=" CG PRO B 237 " pdb=" CD PRO B 237 " ideal model delta sigma weight residual 106.10 2.52 103.58 3.20e+00 9.77e-02 1.05e+03 angle pdb=" N GLY C 147 " pdb=" CA GLY C 147 " pdb=" C GLY C 147 " ideal model delta sigma weight residual 113.18 169.32 -56.14 2.37e+00 1.78e-01 5.61e+02 angle pdb=" C TRP A 146 " pdb=" CA TRP A 146 " pdb=" CB TRP A 146 " ideal model delta sigma weight residual 112.06 76.20 35.86 1.57e+00 4.06e-01 5.22e+02 angle pdb=" C GLY C 147 " pdb=" N CYS C 148 " pdb=" CA CYS C 148 " ideal model delta sigma weight residual 121.80 170.51 -48.71 2.44e+00 1.68e-01 3.99e+02 ... (remaining 39791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.80: 16557 27.80 - 55.60: 922 55.60 - 83.40: 97 83.40 - 111.20: 11 111.20 - 138.99: 1 Dihedral angle restraints: 17588 sinusoidal: 6976 harmonic: 10612 Sorted by residual: dihedral pdb=" C TRP A 146 " pdb=" N TRP A 146 " pdb=" CA TRP A 146 " pdb=" CB TRP A 146 " ideal model delta harmonic sigma weight residual -122.60 -90.31 -32.29 0 2.50e+00 1.60e-01 1.67e+02 dihedral pdb=" N PRO D 149 " pdb=" C PRO D 149 " pdb=" CA PRO D 149 " pdb=" CB PRO D 149 " ideal model delta harmonic sigma weight residual 115.10 136.11 -21.01 0 2.50e+00 1.60e-01 7.06e+01 dihedral pdb=" C PRO D 149 " pdb=" N PRO D 149 " pdb=" CA PRO D 149 " pdb=" CB PRO D 149 " ideal model delta harmonic sigma weight residual -120.70 -140.75 20.05 0 2.50e+00 1.60e-01 6.43e+01 ... (remaining 17585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 4533 0.224 - 0.449: 10 0.449 - 0.673: 2 0.673 - 0.898: 2 0.898 - 1.122: 1 Chirality restraints: 4548 Sorted by residual: chirality pdb=" CA PRO D 149 " pdb=" N PRO D 149 " pdb=" C PRO D 149 " pdb=" CB PRO D 149 " both_signs ideal model delta sigma weight residual False 2.72 1.60 1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" CA PRO B 149 " pdb=" N PRO B 149 " pdb=" C PRO B 149 " pdb=" CB PRO B 149 " both_signs ideal model delta sigma weight residual False 2.72 1.92 0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CA CYS C 148 " pdb=" N CYS C 148 " pdb=" C CYS C 148 " pdb=" CB CYS C 148 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.21e+01 ... (remaining 4545 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 228 " 0.106 5.00e-02 4.00e+02 1.52e-01 3.68e+01 pdb=" N PRO A 229 " -0.262 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 147 " -0.030 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C GLY C 147 " 0.099 2.00e-02 2.50e+03 pdb=" O GLY C 147 " -0.034 2.00e-02 2.50e+03 pdb=" N CYS C 148 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 148 " -0.093 5.00e-02 4.00e+02 1.39e-01 3.11e+01 pdb=" N PRO B 149 " 0.241 5.00e-02 4.00e+02 pdb=" CA PRO B 149 " -0.075 5.00e-02 4.00e+02 pdb=" CD PRO B 149 " -0.073 5.00e-02 4.00e+02 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.40: 113 2.40 - 3.08: 19327 3.08 - 3.77: 51748 3.77 - 4.45: 84905 4.45 - 5.14: 133006 Nonbonded interactions: 289099 Sorted by model distance: nonbonded pdb=" CE MET B 267 " pdb=" CD2 LEU B 349 " model vdw 1.710 3.880 nonbonded pdb=" O TRP A 146 " pdb=" CG TRP A 146 " model vdw 1.802 3.260 nonbonded pdb=" O TRP A 146 " pdb=" CB TRP A 146 " model vdw 1.866 2.752 nonbonded pdb=" CD1 PHE B 235 " pdb=" NE2 HIS B 291 " model vdw 1.914 3.420 nonbonded pdb=" OD1 ASP C 782 " pdb=" CG MET C 859 " model vdw 1.970 3.440 ... (remaining 289094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 110 through 1205 or resid 1301 or resid 1303 through 1305) \ ) selection = (chain 'B' and (resid 110 through 1205 or resid 1301 or resid 1303 through 1305) \ ) selection = (chain 'C' and (resid 110 through 1205 or resid 1301 or resid 1303 through 1305) \ ) selection = (chain 'D' and (resid 110 through 1205 or resid 1301 or resid 1303 through 1305) \ ) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 70.530 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:15.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 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 : 0.012 1.010 29344 Z= 0.328 Angle : 1.187 106.087 39808 Z= 0.547 Chirality : 0.051 1.122 4548 Planarity : 0.008 0.152 4992 Dihedral : 16.136 138.994 10700 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.10 % Favored : 97.79 % Rotamer: Outliers : 0.92 % Allowed : 20.87 % Favored : 78.21 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 3532 helix: -0.12 (0.12), residues: 1704 sheet: -0.27 (0.25), residues: 348 loop : -0.24 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 177 HIS 0.014 0.001 HIS C1159 PHE 0.043 0.001 PHE D 235 TYR 0.023 0.001 TYR A 317 ARG 0.008 0.000 ARG A 398 Details of bonding type rmsd hydrogen bonds : bond 0.20708 ( 1393) hydrogen bonds : angle 6.93007 ( 3903) metal coordination : bond 0.00197 ( 16) metal coordination : angle 0.37298 ( 12) covalent geometry : bond 0.01184 (29328) covalent geometry : angle 1.18741 (39796) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 517 time to evaluate : 3.576 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: A 228 TRP cc_start: 0.6715 (m100) cc_final: 0.5643 (m-10) REVERT: A 292 LEU cc_start: 0.8823 (tp) cc_final: 0.8578 (tt) REVERT: A 385 LEU cc_start: 0.8933 (tt) cc_final: 0.8718 (tp) REVERT: A 582 TYR cc_start: 0.8236 (t80) cc_final: 0.7888 (t80) REVERT: A 859 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.8150 (ttt) REVERT: B 124 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8317 (pp) REVERT: C 174 MET cc_start: 0.6820 (ptp) cc_final: 0.6500 (pmm) REVERT: C 182 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8250 (pp) REVERT: C 234 LEU cc_start: 0.8720 (tm) cc_final: 0.8481 (tt) REVERT: C 252 MET cc_start: 0.6833 (ttt) cc_final: 0.6614 (tmt) REVERT: C 293 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7646 (mt-10) REVERT: D 174 MET cc_start: 0.6994 (tpp) cc_final: 0.5872 (mpm) REVERT: D 237 PRO cc_start: 0.8556 (Cg_exo) cc_final: 0.8055 (Cg_endo) REVERT: D 243 TRP cc_start: 0.6892 (m-10) cc_final: 0.6571 (m-90) REVERT: D 293 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7776 (mt-10) REVERT: D 385 LEU cc_start: 0.8938 (tt) cc_final: 0.8710 (tp) REVERT: D 908 MET cc_start: 0.8386 (mmt) cc_final: 0.7897 (mmt) REVERT: D 944 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7919 (mmtm) outliers start: 29 outliers final: 13 residues processed: 535 average time/residue: 1.4481 time to fit residues: 910.0350 Evaluate side-chains 471 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 455 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 1176 THR Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 1045 SER Chi-restraints excluded: chain D residue 1176 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 300 optimal weight: 4.9990 chunk 269 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 182 optimal weight: 40.0000 chunk 144 optimal weight: 6.9990 chunk 279 optimal weight: 40.0000 chunk 107 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 323 optimal weight: 4.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 GLN A 470 GLN A 490 GLN A 505 HIS A 535 HIS A 632 ASN A 816 ASN A 845 HIS A 904 ASN A1159 HIS A1174 GLN B 156 ASN ** B 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN B 490 GLN B 505 HIS B 535 HIS B 632 ASN B 816 ASN B 845 HIS B 865 ASN ** B 904 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1159 HIS C 156 ASN C 218 ASN C 415 GLN C 470 GLN C 490 GLN C 505 HIS C 535 HIS C 632 ASN C 816 ASN C 904 ASN C1159 HIS D 156 ASN D 180 GLN D 218 ASN D 490 GLN D 505 HIS D 535 HIS D 632 ASN D 816 ASN D 904 ASN D1159 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.129237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.094958 restraints weight = 53802.095| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.38 r_work: 0.3140 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.132 29344 Z= 0.227 Angle : 0.673 14.517 39808 Z= 0.337 Chirality : 0.045 0.294 4548 Planarity : 0.007 0.152 4992 Dihedral : 5.037 59.988 3926 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 4.36 % Allowed : 19.85 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3532 helix: 0.53 (0.12), residues: 1708 sheet: -0.67 (0.25), residues: 356 loop : -0.05 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 177 HIS 0.011 0.002 HIS C 291 PHE 0.025 0.002 PHE C 307 TYR 0.025 0.002 TYR A 351 ARG 0.010 0.001 ARG C 232 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 1393) hydrogen bonds : angle 4.91999 ( 3903) metal coordination : bond 0.00320 ( 16) metal coordination : angle 0.99800 ( 12) covalent geometry : bond 0.00574 (29328) covalent geometry : angle 0.67310 (39796) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 477 time to evaluate : 2.923 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: A 177 TRP cc_start: 0.6637 (t60) cc_final: 0.6106 (t60) REVERT: A 228 TRP cc_start: 0.6857 (m100) cc_final: 0.5714 (m-10) REVERT: A 241 ASN cc_start: 0.8341 (t0) cc_final: 0.7918 (t0) REVERT: A 252 MET cc_start: 0.6644 (tmt) cc_final: 0.5770 (mpt) REVERT: A 267 MET cc_start: 0.7350 (tmm) cc_final: 0.6290 (pmt) REVERT: A 323 LYS cc_start: 0.8531 (mmtt) cc_final: 0.8266 (mmtm) REVERT: A 540 GLN cc_start: 0.8237 (mt0) cc_final: 0.7905 (mm-40) REVERT: A 576 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7087 (tp30) REVERT: A 770 LEU cc_start: 0.8341 (mt) cc_final: 0.8128 (mt) REVERT: A 859 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8291 (ttt) REVERT: A 935 LYS cc_start: 0.8021 (mmtm) cc_final: 0.7768 (mtmm) REVERT: A 959 MET cc_start: 0.8756 (ttp) cc_final: 0.8493 (ttm) REVERT: B 372 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8010 (mmtp) REVERT: C 174 MET cc_start: 0.7145 (ptp) cc_final: 0.6771 (pmm) REVERT: C 177 TRP cc_start: 0.7527 (t60) cc_final: 0.6987 (t60) REVERT: C 182 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8308 (pp) REVERT: C 188 PHE cc_start: 0.7715 (t80) cc_final: 0.7063 (t80) REVERT: C 200 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5943 (mptt) REVERT: C 237 PRO cc_start: 0.8525 (Cg_exo) cc_final: 0.8316 (Cg_endo) REVERT: C 241 ASN cc_start: 0.7758 (t0) cc_final: 0.7517 (t0) REVERT: C 252 MET cc_start: 0.6902 (ttt) cc_final: 0.6433 (tmt) REVERT: C 354 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7473 (ppp) REVERT: D 182 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7962 (tp) REVERT: D 200 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6808 (tppt) REVERT: D 204 TRP cc_start: 0.6054 (OUTLIER) cc_final: 0.5439 (t60) REVERT: D 241 ASN cc_start: 0.7914 (t0) cc_final: 0.7696 (t0) REVERT: D 250 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8397 (tm-30) REVERT: D 278 LEU cc_start: 0.8886 (tt) cc_final: 0.8680 (mt) REVERT: D 293 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7800 (mt-10) REVERT: D 548 GLN cc_start: 0.8375 (tp40) cc_final: 0.8053 (tp40) REVERT: D 944 LYS cc_start: 0.8383 (mtmm) cc_final: 0.7885 (mmtm) outliers start: 137 outliers final: 56 residues processed: 545 average time/residue: 1.4049 time to fit residues: 901.0306 Evaluate side-chains 520 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 455 time to evaluate : 3.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 149 PRO Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 149 PRO Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 414 VAL Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 32 optimal weight: 3.9990 chunk 182 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 325 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 178 optimal weight: 40.0000 chunk 250 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS B 904 ASN B1159 HIS B1174 GLN C 632 ASN C1159 HIS D 470 GLN D 632 ASN D1159 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.129213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095283 restraints weight = 54071.371| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.35 r_work: 0.3120 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 29344 Z= 0.184 Angle : 0.609 11.321 39808 Z= 0.302 Chirality : 0.044 0.288 4548 Planarity : 0.006 0.146 4992 Dihedral : 4.674 47.272 3911 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.75 % Favored : 97.14 % Rotamer: Outliers : 4.83 % Allowed : 19.59 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3532 helix: 0.81 (0.12), residues: 1708 sheet: -0.86 (0.25), residues: 356 loop : 0.06 (0.16), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 177 HIS 0.010 0.002 HIS C1159 PHE 0.029 0.002 PHE A 307 TYR 0.019 0.002 TYR A1022 ARG 0.004 0.000 ARG D 968 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 1393) hydrogen bonds : angle 4.67418 ( 3903) metal coordination : bond 0.00281 ( 16) metal coordination : angle 0.90047 ( 12) covalent geometry : bond 0.00466 (29328) covalent geometry : angle 0.60904 (39796) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 468 time to evaluate : 3.460 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: A 177 TRP cc_start: 0.6678 (t60) cc_final: 0.6275 (t60) REVERT: A 228 TRP cc_start: 0.6693 (m100) cc_final: 0.5695 (m-10) REVERT: A 241 ASN cc_start: 0.8243 (t0) cc_final: 0.7824 (t0) REVERT: A 252 MET cc_start: 0.6448 (tmt) cc_final: 0.5766 (mpt) REVERT: A 267 MET cc_start: 0.7253 (tmm) cc_final: 0.6269 (pmt) REVERT: A 334 MET cc_start: 0.6539 (tmm) cc_final: 0.6247 (tmm) REVERT: A 585 PHE cc_start: 0.7773 (t80) cc_final: 0.7542 (t80) REVERT: A 770 LEU cc_start: 0.8265 (mt) cc_final: 0.8063 (mt) REVERT: A 829 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8360 (ptmm) REVERT: A 940 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7111 (mt) REVERT: A 969 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8524 (p) REVERT: B 200 LYS cc_start: 0.6633 (OUTLIER) cc_final: 0.6349 (mptt) REVERT: B 204 TRP cc_start: 0.5948 (OUTLIER) cc_final: 0.5288 (t60) REVERT: B 334 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6510 (tmm) REVERT: B 347 GLU cc_start: 0.7763 (pp20) cc_final: 0.7461 (mm-30) REVERT: B 372 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7660 (mttt) REVERT: B 976 ASP cc_start: 0.8030 (m-30) cc_final: 0.7799 (m-30) REVERT: B 1011 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8204 (tptt) REVERT: B 1194 ASP cc_start: 0.7389 (m-30) cc_final: 0.7100 (m-30) REVERT: C 174 MET cc_start: 0.6885 (ptp) cc_final: 0.6575 (pmm) REVERT: C 182 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8290 (pp) REVERT: C 200 LYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5851 (mptt) REVERT: C 234 LEU cc_start: 0.8731 (tm) cc_final: 0.8529 (tp) REVERT: C 237 PRO cc_start: 0.8626 (Cg_exo) cc_final: 0.8386 (Cg_endo) REVERT: C 354 MET cc_start: 0.7980 (mtm) cc_final: 0.7455 (ppp) REVERT: C 566 MET cc_start: 0.8182 (ttp) cc_final: 0.7888 (tmt) REVERT: D 182 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7965 (tp) REVERT: D 200 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6703 (tppt) REVERT: D 204 TRP cc_start: 0.6021 (OUTLIER) cc_final: 0.5393 (t60) REVERT: D 235 PHE cc_start: 0.8218 (t80) cc_final: 0.7974 (t80) REVERT: D 241 ASN cc_start: 0.7974 (t0) cc_final: 0.7655 (t0) REVERT: D 250 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8544 (tm-30) REVERT: D 278 LEU cc_start: 0.8897 (tt) cc_final: 0.8675 (mt) REVERT: D 293 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7666 (mt-10) REVERT: D 412 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8202 (ttp) REVERT: D 548 GLN cc_start: 0.8245 (tp40) cc_final: 0.7978 (tp40) REVERT: D 782 ASP cc_start: 0.7749 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: D 944 LYS cc_start: 0.8332 (mtmm) cc_final: 0.7928 (mmtm) outliers start: 152 outliers final: 70 residues processed: 554 average time/residue: 1.4025 time to fit residues: 917.5051 Evaluate side-chains 530 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 445 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 974 MET Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 859 MET Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1143 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 353 TRP Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 950 ARG Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 160 optimal weight: 0.5980 chunk 223 optimal weight: 5.9990 chunk 189 optimal weight: 20.0000 chunk 274 optimal weight: 3.9990 chunk 218 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 60 optimal weight: 0.4980 chunk 139 optimal weight: 5.9990 chunk 309 optimal weight: 0.8980 chunk 332 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 632 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS B1159 HIS ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 632 ASN C 845 HIS C1159 HIS C1174 GLN D 490 GLN D 632 ASN D1159 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.131000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096976 restraints weight = 54323.641| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.41 r_work: 0.3127 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 29344 Z= 0.139 Angle : 0.582 9.784 39808 Z= 0.286 Chirality : 0.042 0.274 4548 Planarity : 0.005 0.140 4992 Dihedral : 4.466 50.157 3908 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.89 % Favored : 97.00 % Rotamer: Outliers : 4.58 % Allowed : 20.42 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3532 helix: 1.10 (0.13), residues: 1676 sheet: -0.81 (0.26), residues: 356 loop : 0.17 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 177 HIS 0.010 0.001 HIS C1159 PHE 0.028 0.001 PHE A 307 TYR 0.017 0.002 TYR A 553 ARG 0.003 0.000 ARG A1200 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 1393) hydrogen bonds : angle 4.50140 ( 3903) metal coordination : bond 0.00327 ( 16) metal coordination : angle 0.94469 ( 12) covalent geometry : bond 0.00349 (29328) covalent geometry : angle 0.58148 (39796) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 457 time to evaluate : 2.992 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: A 177 TRP cc_start: 0.6545 (t60) cc_final: 0.6208 (t60) REVERT: A 228 TRP cc_start: 0.6720 (m100) cc_final: 0.5724 (m-10) REVERT: A 241 ASN cc_start: 0.8217 (t0) cc_final: 0.7779 (t0) REVERT: A 267 MET cc_start: 0.7218 (tmm) cc_final: 0.6343 (pmt) REVERT: A 334 MET cc_start: 0.6627 (tmm) cc_final: 0.6285 (tmm) REVERT: A 585 PHE cc_start: 0.7973 (t80) cc_final: 0.7771 (t80) REVERT: A 829 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8370 (ptmm) REVERT: A 940 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.7050 (mt) REVERT: B 200 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.6322 (mptt) REVERT: B 204 TRP cc_start: 0.6062 (OUTLIER) cc_final: 0.5401 (t60) REVERT: B 334 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6553 (tmm) REVERT: B 372 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7758 (mttt) REVERT: B 969 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8655 (p) REVERT: B 976 ASP cc_start: 0.8262 (m-30) cc_final: 0.7990 (m-30) REVERT: C 168 LEU cc_start: 0.8396 (tm) cc_final: 0.7695 (mt) REVERT: C 174 MET cc_start: 0.6986 (ptp) cc_final: 0.6618 (pmm) REVERT: C 182 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8348 (pp) REVERT: C 200 LYS cc_start: 0.6103 (OUTLIER) cc_final: 0.5829 (mptt) REVERT: C 237 PRO cc_start: 0.8542 (Cg_exo) cc_final: 0.8261 (Cg_endo) REVERT: C 354 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7424 (ppp) REVERT: C 490 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8427 (mt0) REVERT: C 566 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8155 (tmt) REVERT: D 182 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7963 (tp) REVERT: D 200 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6785 (tppt) REVERT: D 204 TRP cc_start: 0.6144 (OUTLIER) cc_final: 0.5516 (t60) REVERT: D 235 PHE cc_start: 0.8196 (t80) cc_final: 0.7970 (t80) REVERT: D 241 ASN cc_start: 0.7928 (t0) cc_final: 0.7607 (t0) REVERT: D 278 LEU cc_start: 0.8920 (tt) cc_final: 0.8699 (mt) REVERT: D 281 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8959 (tt) REVERT: D 293 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7670 (mt-10) REVERT: D 548 GLN cc_start: 0.8353 (tp40) cc_final: 0.8042 (tp40) REVERT: D 566 MET cc_start: 0.8425 (ttp) cc_final: 0.8079 (tmt) REVERT: D 782 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7621 (m-30) REVERT: D 944 LYS cc_start: 0.8460 (mtmm) cc_final: 0.8025 (mmtm) outliers start: 144 outliers final: 64 residues processed: 533 average time/residue: 1.3094 time to fit residues: 823.3798 Evaluate side-chains 527 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 446 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 242 CYS Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 794 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 974 MET Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 490 GLN Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 576 GLU Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 277 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 chunk 221 optimal weight: 0.3980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 603 ASN A 632 ASN A 845 HIS A1159 HIS B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS B1159 HIS C 180 GLN ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 632 ASN C 845 HIS C1159 HIS D 632 ASN D1159 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.129535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095689 restraints weight = 54029.039| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.33 r_work: 0.3144 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 29344 Z= 0.185 Angle : 0.610 11.012 39808 Z= 0.298 Chirality : 0.043 0.267 4548 Planarity : 0.005 0.136 4992 Dihedral : 4.519 54.024 3908 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.89 % Favored : 97.00 % Rotamer: Outliers : 4.96 % Allowed : 20.39 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.14), residues: 3532 helix: 1.13 (0.12), residues: 1676 sheet: -0.85 (0.26), residues: 356 loop : 0.18 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 177 HIS 0.010 0.002 HIS B 844 PHE 0.030 0.002 PHE A 307 TYR 0.018 0.002 TYR A 351 ARG 0.005 0.000 ARG C 133 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 1393) hydrogen bonds : angle 4.48327 ( 3903) metal coordination : bond 0.00247 ( 16) metal coordination : angle 0.83154 ( 12) covalent geometry : bond 0.00468 (29328) covalent geometry : angle 0.60957 (39796) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 461 time to evaluate : 3.207 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: A 177 TRP cc_start: 0.6534 (t60) cc_final: 0.6118 (t60) REVERT: A 228 TRP cc_start: 0.6734 (m100) cc_final: 0.5722 (m-10) REVERT: A 241 ASN cc_start: 0.8283 (t0) cc_final: 0.7776 (t0) REVERT: A 267 MET cc_start: 0.7047 (tmm) cc_final: 0.6405 (pmt) REVERT: A 334 MET cc_start: 0.6679 (tmm) cc_final: 0.6316 (tmm) REVERT: A 355 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: A 585 PHE cc_start: 0.7992 (t80) cc_final: 0.7775 (t80) REVERT: A 829 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8403 (ptmm) REVERT: A 940 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7113 (mt) REVERT: A 969 VAL cc_start: 0.8925 (OUTLIER) cc_final: 0.8721 (p) REVERT: B 204 TRP cc_start: 0.5986 (OUTLIER) cc_final: 0.5317 (t60) REVERT: B 334 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6728 (tmm) REVERT: B 347 GLU cc_start: 0.7852 (pp20) cc_final: 0.7438 (mm-30) REVERT: B 372 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7805 (mttt) REVERT: B 413 ASP cc_start: 0.6771 (t0) cc_final: 0.6544 (t0) REVERT: B 566 MET cc_start: 0.8358 (tmt) cc_final: 0.8045 (tmt) REVERT: B 969 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8696 (p) REVERT: B 976 ASP cc_start: 0.8271 (m-30) cc_final: 0.8047 (m-30) REVERT: C 169 TRP cc_start: 0.7975 (m100) cc_final: 0.7378 (m-10) REVERT: C 182 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8351 (pp) REVERT: C 192 MET cc_start: 0.7439 (mtm) cc_final: 0.7183 (mtt) REVERT: C 200 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5796 (mptt) REVERT: C 234 LEU cc_start: 0.8757 (tm) cc_final: 0.8547 (tp) REVERT: C 354 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7448 (ppp) REVERT: C 566 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7304 (tmt) REVERT: C 1140 LEU cc_start: 0.8236 (tp) cc_final: 0.8004 (tp) REVERT: D 182 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7984 (tp) REVERT: D 193 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6667 (mt) REVERT: D 200 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6708 (tppt) REVERT: D 204 TRP cc_start: 0.5885 (OUTLIER) cc_final: 0.5278 (t60) REVERT: D 241 ASN cc_start: 0.7967 (t0) cc_final: 0.7578 (t0) REVERT: D 278 LEU cc_start: 0.8931 (tt) cc_final: 0.8714 (mt) REVERT: D 293 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7653 (mt-10) REVERT: D 426 SER cc_start: 0.9012 (OUTLIER) cc_final: 0.8595 (m) REVERT: D 566 MET cc_start: 0.8410 (ttp) cc_final: 0.7333 (tmt) REVERT: D 782 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: D 944 LYS cc_start: 0.8451 (mtmm) cc_final: 0.8006 (mmtm) outliers start: 156 outliers final: 76 residues processed: 552 average time/residue: 1.3527 time to fit residues: 890.8713 Evaluate side-chains 541 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 447 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 766 LEU Chi-restraints excluded: chain B residue 794 LYS Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 135 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1138 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 80 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 301 optimal weight: 0.9980 chunk 255 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 298 ASN A 603 ASN A 632 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 GLN B 632 ASN B 845 HIS B1159 HIS C 241 ASN C 632 ASN C 845 HIS C1159 HIS D 632 ASN D1159 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.129857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.096998 restraints weight = 54053.280| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.06 r_work: 0.3175 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 29344 Z= 0.147 Angle : 0.601 10.968 39808 Z= 0.292 Chirality : 0.042 0.260 4548 Planarity : 0.005 0.133 4992 Dihedral : 4.457 58.193 3908 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.97 % Favored : 96.91 % Rotamer: Outliers : 4.48 % Allowed : 21.25 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3532 helix: 1.22 (0.13), residues: 1680 sheet: -0.87 (0.25), residues: 372 loop : 0.26 (0.16), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 177 HIS 0.010 0.001 HIS C 844 PHE 0.031 0.002 PHE A 307 TYR 0.018 0.002 TYR D 938 ARG 0.006 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03511 ( 1393) hydrogen bonds : angle 4.40230 ( 3903) metal coordination : bond 0.00287 ( 16) metal coordination : angle 0.91307 ( 12) covalent geometry : bond 0.00368 (29328) covalent geometry : angle 0.60101 (39796) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 459 time to evaluate : 3.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TRP cc_start: 0.6452 (t60) cc_final: 0.6077 (t60) REVERT: A 193 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5374 (mt) REVERT: A 228 TRP cc_start: 0.6699 (m100) cc_final: 0.5723 (m-10) REVERT: A 241 ASN cc_start: 0.8267 (t0) cc_final: 0.7641 (t0) REVERT: A 252 MET cc_start: 0.6331 (tmt) cc_final: 0.5457 (mmt) REVERT: A 267 MET cc_start: 0.7040 (tmm) cc_final: 0.6436 (pmt) REVERT: A 334 MET cc_start: 0.6669 (tmm) cc_final: 0.6377 (tmm) REVERT: A 355 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: A 829 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8332 (ptmm) REVERT: A 876 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7288 (p90) REVERT: A 940 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.7030 (mt) REVERT: A 969 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8677 (p) REVERT: B 192 MET cc_start: 0.7602 (mtp) cc_final: 0.7398 (mtp) REVERT: B 204 TRP cc_start: 0.6176 (OUTLIER) cc_final: 0.5505 (t60) REVERT: B 334 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6714 (tmm) REVERT: B 372 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7720 (mttt) REVERT: B 876 TYR cc_start: 0.8021 (OUTLIER) cc_final: 0.7339 (p90) REVERT: B 969 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8651 (p) REVERT: B 976 ASP cc_start: 0.8194 (m-30) cc_final: 0.7966 (m-30) REVERT: C 133 ARG cc_start: 0.7977 (tmm160) cc_final: 0.7624 (tmt170) REVERT: C 168 LEU cc_start: 0.8367 (tm) cc_final: 0.7681 (mt) REVERT: C 174 MET cc_start: 0.7499 (tpp) cc_final: 0.6856 (pmm) REVERT: C 182 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8343 (pp) REVERT: C 200 LYS cc_start: 0.6169 (OUTLIER) cc_final: 0.5864 (mptt) REVERT: C 354 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7381 (ppp) REVERT: C 566 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7683 (tmt) REVERT: C 969 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8637 (p) REVERT: C 1140 LEU cc_start: 0.8270 (tp) cc_final: 0.8022 (tp) REVERT: D 182 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7960 (tp) REVERT: D 193 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6729 (mt) REVERT: D 200 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6740 (tppt) REVERT: D 204 TRP cc_start: 0.6086 (OUTLIER) cc_final: 0.5442 (t60) REVERT: D 241 ASN cc_start: 0.7975 (t0) cc_final: 0.7603 (t0) REVERT: D 278 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8761 (mt) REVERT: D 293 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7767 (mt-10) REVERT: D 355 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: D 426 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8599 (m) REVERT: D 447 MET cc_start: 0.8764 (tpt) cc_final: 0.8364 (tpt) REVERT: D 548 GLN cc_start: 0.8235 (tp40) cc_final: 0.8035 (tp40) REVERT: D 566 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7543 (tmt) REVERT: D 576 GLU cc_start: 0.7272 (mm-30) cc_final: 0.6953 (mm-30) REVERT: D 585 PHE cc_start: 0.8091 (t80) cc_final: 0.7831 (t80) REVERT: D 782 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: D 944 LYS cc_start: 0.8488 (mtmm) cc_final: 0.8016 (mmtm) outliers start: 141 outliers final: 70 residues processed: 536 average time/residue: 1.2916 time to fit residues: 816.6432 Evaluate side-chains 541 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 446 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 940 LEU Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 794 LYS Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 969 VAL Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 984 VAL Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 566 MET Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 214 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 198 optimal weight: 6.9990 chunk 187 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 39 optimal weight: 0.0670 chunk 240 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A 632 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS B1159 HIS C 241 ASN C 632 ASN C 845 HIS C 865 ASN C1159 HIS D 632 ASN D1159 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.130270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.096793 restraints weight = 54085.018| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.31 r_work: 0.3176 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 29344 Z= 0.118 Angle : 0.586 11.561 39808 Z= 0.285 Chirality : 0.041 0.258 4548 Planarity : 0.005 0.130 4992 Dihedral : 4.328 58.238 3908 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.60 % Favored : 97.28 % Rotamer: Outliers : 3.75 % Allowed : 22.42 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.14), residues: 3532 helix: 1.34 (0.13), residues: 1680 sheet: -0.77 (0.26), residues: 380 loop : 0.35 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 177 HIS 0.010 0.001 HIS C 844 PHE 0.031 0.001 PHE A 307 TYR 0.022 0.001 TYR B 582 ARG 0.022 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 1393) hydrogen bonds : angle 4.30609 ( 3903) metal coordination : bond 0.00326 ( 16) metal coordination : angle 0.96131 ( 12) covalent geometry : bond 0.00292 (29328) covalent geometry : angle 0.58632 (39796) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 467 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LEU cc_start: 0.9020 (mm) cc_final: 0.8812 (tp) REVERT: A 177 TRP cc_start: 0.6548 (t60) cc_final: 0.6162 (t60) REVERT: A 193 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5312 (mt) REVERT: A 228 TRP cc_start: 0.6678 (m100) cc_final: 0.5717 (m-10) REVERT: A 241 ASN cc_start: 0.8210 (t0) cc_final: 0.7577 (t0) REVERT: A 252 MET cc_start: 0.6273 (tmt) cc_final: 0.5361 (mmt) REVERT: A 267 MET cc_start: 0.6688 (tmm) cc_final: 0.6260 (pmt) REVERT: A 334 MET cc_start: 0.6597 (tmm) cc_final: 0.6293 (tmm) REVERT: A 355 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: A 829 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8328 (ptmm) REVERT: A 876 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.7228 (p90) REVERT: A 1011 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8268 (tptt) REVERT: B 204 TRP cc_start: 0.6078 (OUTLIER) cc_final: 0.5387 (t60) REVERT: B 334 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6749 (tmm) REVERT: B 372 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7692 (mttt) REVERT: B 566 MET cc_start: 0.8277 (tmt) cc_final: 0.8009 (tmt) REVERT: B 867 ASP cc_start: 0.7880 (m-30) cc_final: 0.7557 (m-30) REVERT: B 876 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7227 (p90) REVERT: C 133 ARG cc_start: 0.7920 (tmm160) cc_final: 0.7640 (tmt170) REVERT: C 168 LEU cc_start: 0.8391 (tm) cc_final: 0.7686 (mt) REVERT: C 174 MET cc_start: 0.7539 (tpp) cc_final: 0.6842 (pmm) REVERT: C 182 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8334 (pp) REVERT: C 200 LYS cc_start: 0.6163 (OUTLIER) cc_final: 0.5886 (tppt) REVERT: C 234 LEU cc_start: 0.8832 (tm) cc_final: 0.8530 (tp) REVERT: C 293 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7330 (mt-10) REVERT: C 354 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7425 (ppp) REVERT: C 566 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7957 (tmt) REVERT: C 969 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8634 (p) REVERT: C 1017 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8421 (mt) REVERT: D 182 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7989 (tp) REVERT: D 193 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6651 (mt) REVERT: D 200 LYS cc_start: 0.7021 (OUTLIER) cc_final: 0.6723 (tppt) REVERT: D 204 TRP cc_start: 0.5961 (OUTLIER) cc_final: 0.5260 (t60) REVERT: D 241 ASN cc_start: 0.8006 (t0) cc_final: 0.7592 (t0) REVERT: D 293 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7673 (mt-10) REVERT: D 415 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: D 426 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8613 (m) REVERT: D 447 MET cc_start: 0.8737 (tpt) cc_final: 0.8368 (tpt) REVERT: D 566 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7453 (tmt) REVERT: D 782 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: D 867 ASP cc_start: 0.7935 (m-30) cc_final: 0.7691 (m-30) REVERT: D 944 LYS cc_start: 0.8390 (mtmm) cc_final: 0.8008 (mmtm) outliers start: 118 outliers final: 57 residues processed: 529 average time/residue: 1.3149 time to fit residues: 821.1944 Evaluate side-chains 539 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 460 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 794 LYS Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 566 MET Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 566 MET Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 251 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 340 optimal weight: 0.0870 chunk 157 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 316 optimal weight: 5.9990 chunk 317 optimal weight: 1.9990 chunk 349 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN B 291 HIS B 490 GLN B 632 ASN B 845 HIS B1159 HIS C 845 HIS C1159 HIS D 632 ASN D 845 HIS D 931 GLN D1159 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.130223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.096016 restraints weight = 54309.212| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.39 r_work: 0.3133 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 29344 Z= 0.138 Angle : 0.611 12.174 39808 Z= 0.294 Chirality : 0.042 0.249 4548 Planarity : 0.005 0.127 4992 Dihedral : 4.306 54.760 3906 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.77 % Favored : 97.11 % Rotamer: Outliers : 4.01 % Allowed : 22.52 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.14), residues: 3532 helix: 1.40 (0.13), residues: 1680 sheet: -0.75 (0.26), residues: 380 loop : 0.35 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 177 HIS 0.011 0.001 HIS A 844 PHE 0.032 0.002 PHE A 307 TYR 0.023 0.002 TYR C 582 ARG 0.012 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 1393) hydrogen bonds : angle 4.30333 ( 3903) metal coordination : bond 0.00291 ( 16) metal coordination : angle 0.97365 ( 12) covalent geometry : bond 0.00344 (29328) covalent geometry : angle 0.61082 (39796) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 457 time to evaluate : 3.037 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: A 177 TRP cc_start: 0.6520 (t60) cc_final: 0.6132 (t60) REVERT: A 193 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5325 (mt) REVERT: A 228 TRP cc_start: 0.6789 (m100) cc_final: 0.5742 (m-10) REVERT: A 241 ASN cc_start: 0.8159 (t0) cc_final: 0.7449 (t0) REVERT: A 252 MET cc_start: 0.6246 (tmt) cc_final: 0.5355 (mmt) REVERT: A 267 MET cc_start: 0.6635 (tmm) cc_final: 0.6244 (pmt) REVERT: A 334 MET cc_start: 0.6716 (tmm) cc_final: 0.6348 (tmm) REVERT: A 355 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7422 (mp0) REVERT: A 876 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.7033 (p90) REVERT: A 1011 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8171 (tptt) REVERT: B 334 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6772 (tmm) REVERT: B 372 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7586 (mttt) REVERT: B 566 MET cc_start: 0.8083 (tmt) cc_final: 0.7814 (tmt) REVERT: B 876 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7048 (p90) REVERT: C 168 LEU cc_start: 0.8362 (tm) cc_final: 0.7666 (mt) REVERT: C 174 MET cc_start: 0.7349 (tpp) cc_final: 0.6732 (pmm) REVERT: C 182 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8318 (pp) REVERT: C 200 LYS cc_start: 0.6121 (OUTLIER) cc_final: 0.5850 (tppt) REVERT: C 234 LEU cc_start: 0.8823 (tm) cc_final: 0.8517 (tp) REVERT: C 293 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7328 (mt-10) REVERT: C 354 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7378 (ppp) REVERT: C 782 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7613 (m-30) REVERT: C 969 VAL cc_start: 0.8760 (OUTLIER) cc_final: 0.8544 (p) REVERT: C 1017 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8335 (mt) REVERT: D 182 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.8002 (tp) REVERT: D 200 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6753 (tppt) REVERT: D 204 TRP cc_start: 0.5913 (OUTLIER) cc_final: 0.5215 (t60) REVERT: D 241 ASN cc_start: 0.8016 (t0) cc_final: 0.7540 (t0) REVERT: D 293 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7625 (mt-10) REVERT: D 415 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: D 426 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8573 (m) REVERT: D 566 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7695 (tmt) REVERT: D 782 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7477 (m-30) REVERT: D 859 MET cc_start: 0.8491 (ttt) cc_final: 0.8085 (ttp) REVERT: D 944 LYS cc_start: 0.8283 (mtmm) cc_final: 0.7920 (mmtm) outliers start: 126 outliers final: 68 residues processed: 531 average time/residue: 1.3126 time to fit residues: 822.7813 Evaluate side-chains 537 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 450 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 919 THR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 794 LYS Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 566 MET Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 260 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 336 optimal weight: 0.9990 chunk 329 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 337 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN B 291 HIS B 490 GLN B 632 ASN B 845 HIS B1159 HIS C 241 ASN C 845 HIS C1159 HIS D 490 GLN D 632 ASN D 845 HIS D1159 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.130132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.097402 restraints weight = 54057.417| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.09 r_work: 0.3183 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 29344 Z= 0.134 Angle : 0.611 12.428 39808 Z= 0.297 Chirality : 0.042 0.249 4548 Planarity : 0.005 0.124 4992 Dihedral : 4.252 49.392 3906 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.58 % Favored : 97.31 % Rotamer: Outliers : 3.34 % Allowed : 23.00 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.14), residues: 3532 helix: 1.42 (0.13), residues: 1680 sheet: -0.89 (0.25), residues: 404 loop : 0.37 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 177 HIS 0.011 0.001 HIS B 844 PHE 0.034 0.002 PHE A 307 TYR 0.023 0.001 TYR B 582 ARG 0.005 0.000 ARG C 948 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 1393) hydrogen bonds : angle 4.27611 ( 3903) metal coordination : bond 0.00274 ( 16) metal coordination : angle 0.97500 ( 12) covalent geometry : bond 0.00333 (29328) covalent geometry : angle 0.61079 (39796) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 457 time to evaluate : 3.192 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: A 177 TRP cc_start: 0.6558 (t60) cc_final: 0.6140 (t60) REVERT: A 193 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5341 (mt) REVERT: A 228 TRP cc_start: 0.6700 (m100) cc_final: 0.5684 (m-10) REVERT: A 241 ASN cc_start: 0.8177 (t0) cc_final: 0.7529 (t0) REVERT: A 252 MET cc_start: 0.6253 (tmt) cc_final: 0.5332 (mmt) REVERT: A 267 MET cc_start: 0.6589 (tmm) cc_final: 0.6122 (pmt) REVERT: A 334 MET cc_start: 0.6817 (tmm) cc_final: 0.6395 (tmm) REVERT: A 355 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: A 576 GLU cc_start: 0.6598 (mm-30) cc_final: 0.5844 (mp0) REVERT: A 876 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7155 (p90) REVERT: A 1011 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8231 (mmtt) REVERT: B 372 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7752 (mttt) REVERT: B 566 MET cc_start: 0.8239 (tmt) cc_final: 0.7961 (tmt) REVERT: B 585 PHE cc_start: 0.8026 (t80) cc_final: 0.7765 (t80) REVERT: B 862 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8543 (t) REVERT: B 876 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7178 (p90) REVERT: C 168 LEU cc_start: 0.8312 (tm) cc_final: 0.7443 (mt) REVERT: C 169 TRP cc_start: 0.7868 (m100) cc_final: 0.7222 (m-10) REVERT: C 174 MET cc_start: 0.7686 (tpp) cc_final: 0.6885 (pmm) REVERT: C 182 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8303 (pp) REVERT: C 200 LYS cc_start: 0.6181 (OUTLIER) cc_final: 0.5878 (tppt) REVERT: C 293 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7412 (mt-10) REVERT: C 354 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7354 (ppp) REVERT: C 566 MET cc_start: 0.8188 (tmt) cc_final: 0.7673 (tmt) REVERT: C 576 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6857 (mm-30) REVERT: C 782 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: C 892 GLU cc_start: 0.6670 (pp20) cc_final: 0.6125 (pp20) REVERT: C 969 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8626 (p) REVERT: D 182 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7957 (tp) REVERT: D 193 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6735 (pt) REVERT: D 200 LYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6771 (tppt) REVERT: D 204 TRP cc_start: 0.6050 (OUTLIER) cc_final: 0.5367 (t60) REVERT: D 241 ASN cc_start: 0.8043 (t0) cc_final: 0.7575 (t0) REVERT: D 293 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7633 (mt-10) REVERT: D 415 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: D 426 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8606 (m) REVERT: D 548 GLN cc_start: 0.8261 (tp40) cc_final: 0.8060 (tp40) REVERT: D 566 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7935 (tmt) REVERT: D 747 VAL cc_start: 0.6819 (OUTLIER) cc_final: 0.6389 (m) REVERT: D 782 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: D 944 LYS cc_start: 0.8393 (mtmm) cc_final: 0.7967 (mmtm) REVERT: D 1011 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8214 (mmtt) outliers start: 105 outliers final: 60 residues processed: 516 average time/residue: 1.3845 time to fit residues: 839.1801 Evaluate side-chains 534 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 454 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 974 MET Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 794 LYS Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 180 GLN Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 415 GLN Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 566 MET Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 238 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 314 optimal weight: 0.0470 chunk 151 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 146 optimal weight: 3.9990 chunk 181 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 139 optimal weight: 8.9990 chunk 202 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A 845 HIS A 865 ASN A1159 HIS B 241 ASN B 270 GLN B 291 HIS B 490 GLN B 632 ASN B 845 HIS B1159 HIS C 845 HIS C1159 HIS D 632 ASN D 845 HIS D1159 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.131068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.098910 restraints weight = 53865.910| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.19 r_work: 0.3187 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 29344 Z= 0.125 Angle : 0.620 13.035 39808 Z= 0.297 Chirality : 0.042 0.245 4548 Planarity : 0.005 0.121 4992 Dihedral : 4.189 45.400 3906 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.60 % Favored : 97.28 % Rotamer: Outliers : 2.99 % Allowed : 23.85 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3532 helix: 1.45 (0.13), residues: 1680 sheet: -0.79 (0.26), residues: 400 loop : 0.39 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 177 HIS 0.011 0.001 HIS B 844 PHE 0.043 0.002 PHE D 188 TYR 0.023 0.001 TYR B 582 ARG 0.011 0.000 ARG C 948 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 1393) hydrogen bonds : angle 4.26092 ( 3903) metal coordination : bond 0.00340 ( 16) metal coordination : angle 0.98811 ( 12) covalent geometry : bond 0.00308 (29328) covalent geometry : angle 0.61975 (39796) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 453 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TRP cc_start: 0.6442 (t60) cc_final: 0.6103 (t60) REVERT: A 228 TRP cc_start: 0.6706 (m100) cc_final: 0.5674 (m-10) REVERT: A 241 ASN cc_start: 0.8171 (t0) cc_final: 0.7512 (t0) REVERT: A 252 MET cc_start: 0.6294 (tmt) cc_final: 0.5393 (mmt) REVERT: A 267 MET cc_start: 0.6609 (tmm) cc_final: 0.6179 (pmt) REVERT: A 334 MET cc_start: 0.6882 (tmm) cc_final: 0.6445 (tmm) REVERT: A 355 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: A 867 ASP cc_start: 0.8083 (m-30) cc_final: 0.7829 (m-30) REVERT: A 876 TYR cc_start: 0.7976 (OUTLIER) cc_final: 0.7102 (p90) REVERT: A 1011 LYS cc_start: 0.8698 (mtpt) cc_final: 0.8300 (tptt) REVERT: B 372 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7734 (mttt) REVERT: B 566 MET cc_start: 0.8256 (tmt) cc_final: 0.7966 (tmt) REVERT: B 862 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8559 (t) REVERT: B 867 ASP cc_start: 0.7923 (m-30) cc_final: 0.7626 (m-30) REVERT: B 876 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7236 (p90) REVERT: C 168 LEU cc_start: 0.8335 (tm) cc_final: 0.7469 (mt) REVERT: C 169 TRP cc_start: 0.7844 (m100) cc_final: 0.7226 (m-10) REVERT: C 174 MET cc_start: 0.7609 (tpp) cc_final: 0.6846 (pmm) REVERT: C 200 LYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5922 (mptt) REVERT: C 293 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7416 (mt-10) REVERT: C 354 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7303 (ppp) REVERT: C 566 MET cc_start: 0.8142 (tmt) cc_final: 0.7903 (tmt) REVERT: C 782 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: C 892 GLU cc_start: 0.6730 (pp20) cc_final: 0.6178 (pp20) REVERT: C 969 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8619 (p) REVERT: D 182 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7992 (tp) REVERT: D 193 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6323 (mt) REVERT: D 200 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6769 (tppt) REVERT: D 204 TRP cc_start: 0.5893 (OUTLIER) cc_final: 0.5197 (t60) REVERT: D 241 ASN cc_start: 0.8057 (t0) cc_final: 0.7589 (t0) REVERT: D 250 GLU cc_start: 0.8678 (tt0) cc_final: 0.8123 (tm-30) REVERT: D 293 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7587 (mt-10) REVERT: D 426 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8595 (m) REVERT: D 566 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7948 (tmt) REVERT: D 747 VAL cc_start: 0.6795 (OUTLIER) cc_final: 0.6348 (m) REVERT: D 859 MET cc_start: 0.8660 (ttt) cc_final: 0.8360 (ttt) REVERT: D 867 ASP cc_start: 0.8013 (m-30) cc_final: 0.7774 (m-30) REVERT: D 944 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8034 (mmtm) REVERT: D 1011 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8202 (mmtt) outliers start: 94 outliers final: 55 residues processed: 508 average time/residue: 1.4370 time to fit residues: 861.2792 Evaluate side-chains 519 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 448 time to evaluate : 3.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 972 ILE Chi-restraints excluded: chain A residue 988 MET Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1176 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 789 SER Chi-restraints excluded: chain B residue 794 LYS Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 988 MET Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 919 THR Chi-restraints excluded: chain C residue 969 VAL Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 974 MET Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1159 HIS Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 354 MET Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 523 CYS Chi-restraints excluded: chain D residue 566 MET Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 850 ILE Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 988 MET Chi-restraints excluded: chain D residue 1021 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 266 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 219 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 249 optimal weight: 5.9990 chunk 172 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN B 291 HIS B 632 ASN B 845 HIS B1159 HIS C 845 HIS C1159 HIS D 632 ASN D 845 HIS D1159 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.131048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.098839 restraints weight = 53680.621| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.09 r_work: 0.3195 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 29344 Z= 0.122 Angle : 0.619 12.898 39808 Z= 0.299 Chirality : 0.042 0.244 4548 Planarity : 0.005 0.119 4992 Dihedral : 4.095 25.667 3903 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.55 % Favored : 97.34 % Rotamer: Outliers : 2.61 % Allowed : 24.08 % Favored : 73.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3532 helix: 1.48 (0.13), residues: 1680 sheet: -0.78 (0.26), residues: 400 loop : 0.42 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 177 HIS 0.012 0.001 HIS C 844 PHE 0.049 0.001 PHE D 188 TYR 0.022 0.001 TYR B 582 ARG 0.011 0.000 ARG C 948 Details of bonding type rmsd hydrogen bonds : bond 0.03206 ( 1393) hydrogen bonds : angle 4.25269 ( 3903) metal coordination : bond 0.00295 ( 16) metal coordination : angle 0.96909 ( 12) covalent geometry : bond 0.00300 (29328) covalent geometry : angle 0.61861 (39796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25322.05 seconds wall clock time: 435 minutes 11.00 seconds (26111.00 seconds total)