Starting phenix.real_space_refine on Mon Aug 25 14:00:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hkk_34853/08_2025/8hkk_34853.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hkk_34853/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8hkk_34853/08_2025/8hkk_34853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hkk_34853/08_2025/8hkk_34853.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hkk_34853/08_2025/8hkk_34853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hkk_34853/08_2025/8hkk_34853.map" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.044 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 1} 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: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 1} 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: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 1} 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: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 1} 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: 7.66, per 1000 atoms: 0.27 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: 2.68 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.27 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: 6.45 Time building geometry restraints manager: 3.59 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 1301 or resid 1303 through 1305)) selection = (chain 'B' and (resid 110 through 1301 or resid 1303 through 1305)) selection = (chain 'C' and (resid 110 through 1301 or resid 1303 through 1305)) selection = (chain 'D' and (resid 110 through 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: 1.060 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: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 33.130 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.910 ------------------------------------------------------------------------------- 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 : 12.42 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG A 398 TYR 0.023 0.001 TYR A 317 PHE 0.043 0.001 PHE D 235 TRP 0.042 0.002 TRP A 177 HIS 0.014 0.001 HIS C1159 Details of bonding type rmsd covalent geometry : bond 0.01184 (29328) covalent geometry : angle 1.18741 (39796) hydrogen bonds : bond 0.20708 ( 1393) hydrogen bonds : angle 6.93007 ( 3903) metal coordination : bond 0.00197 ( 16) metal coordination : angle 0.37298 ( 12) *********************** 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 : 1.139 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: 0.7223 time to fit residues: 450.1212 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 : 1.123 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 490 GLN A 505 HIS A 535 HIS A 603 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.131243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.098190 restraints weight = 53958.902| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.07 r_work: 0.3201 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 29344 Z= 0.170 Angle : 0.638 16.557 39808 Z= 0.320 Chirality : 0.043 0.299 4548 Planarity : 0.006 0.153 4992 Dihedral : 4.858 56.747 3926 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.69 % Favored : 97.20 % Rotamer: Outliers : 4.04 % Allowed : 19.88 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.14), residues: 3532 helix: 0.57 (0.12), residues: 1716 sheet: -0.56 (0.25), residues: 356 loop : -0.07 (0.16), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 232 TYR 0.023 0.002 TYR A 351 PHE 0.022 0.002 PHE A 188 TRP 0.017 0.002 TRP A 177 HIS 0.012 0.002 HIS D 291 Details of bonding type rmsd covalent geometry : bond 0.00435 (29328) covalent geometry : angle 0.63837 (39796) hydrogen bonds : bond 0.05111 ( 1393) hydrogen bonds : angle 4.94583 ( 3903) metal coordination : bond 0.00247 ( 16) metal coordination : angle 0.92933 ( 12) *********************** 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 608 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 481 time to evaluate : 1.223 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: 0.6441 (t60) cc_final: 0.5953 (t60) REVERT: A 228 TRP cc_start: 0.6648 (m100) cc_final: 0.5660 (m-10) REVERT: A 241 ASN cc_start: 0.8303 (t0) cc_final: 0.7994 (t0) REVERT: A 252 MET cc_start: 0.6697 (tmt) cc_final: 0.5830 (mpt) REVERT: A 267 MET cc_start: 0.7346 (tmm) cc_final: 0.6270 (pmt) REVERT: A 540 GLN cc_start: 0.8222 (mt0) cc_final: 0.7952 (mm-40) REVERT: A 770 LEU cc_start: 0.8287 (mt) cc_final: 0.8037 (mt) REVERT: A 959 MET cc_start: 0.8710 (ttp) cc_final: 0.8473 (ttm) REVERT: A 1140 LEU cc_start: 0.8211 (tp) cc_final: 0.7933 (tp) REVERT: B 239 PHE cc_start: 0.7462 (p90) cc_final: 0.7253 (p90) REVERT: B 372 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7913 (mmtp) REVERT: B 976 ASP cc_start: 0.8117 (m-30) cc_final: 0.7880 (m-30) REVERT: C 174 MET cc_start: 0.7121 (ptp) cc_final: 0.6781 (pmm) REVERT: C 177 TRP cc_start: 0.7469 (t60) cc_final: 0.6966 (t60) REVERT: C 182 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8226 (pp) REVERT: C 188 PHE cc_start: 0.7664 (t80) cc_final: 0.6999 (t80) REVERT: C 252 MET cc_start: 0.6813 (ttt) cc_final: 0.6419 (tmt) REVERT: C 293 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7522 (mt-10) REVERT: C 354 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7485 (ppp) REVERT: D 182 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7885 (tp) REVERT: D 200 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6802 (tppt) REVERT: D 204 TRP cc_start: 0.6026 (OUTLIER) cc_final: 0.5406 (t60) REVERT: D 278 LEU cc_start: 0.8821 (tt) cc_final: 0.8592 (mt) REVERT: D 293 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7640 (mt-10) REVERT: D 944 LYS cc_start: 0.8392 (mtmm) cc_final: 0.7982 (mmtm) outliers start: 127 outliers final: 44 residues processed: 542 average time/residue: 0.7102 time to fit residues: 449.3701 Evaluate side-chains 507 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 457 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 747 VAL 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 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 747 VAL Chi-restraints excluded: chain B residue 919 THR Chi-restraints excluded: chain B residue 937 SER 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 354 MET Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 747 VAL 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 346 PHE Chi-restraints excluded: chain D residue 426 SER 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 215 optimal weight: 0.9990 chunk 288 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 339 optimal weight: 7.9990 chunk 59 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 306 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN 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 C 865 ASN C1159 HIS D 632 ASN D 904 ASN D1159 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.129657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.096915 restraints weight = 54176.028| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.06 r_work: 0.3185 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 29344 Z= 0.150 Angle : 0.587 10.787 39808 Z= 0.292 Chirality : 0.043 0.291 4548 Planarity : 0.006 0.146 4992 Dihedral : 4.465 45.524 3908 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.55 % Favored : 97.34 % Rotamer: Outliers : 3.98 % Allowed : 20.42 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.14), residues: 3532 helix: 0.87 (0.12), residues: 1704 sheet: -0.63 (0.25), residues: 356 loop : 0.11 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 459 TYR 0.017 0.002 TYR B 403 PHE 0.030 0.002 PHE A 307 TRP 0.015 0.001 TRP D 177 HIS 0.011 0.001 HIS C1159 Details of bonding type rmsd covalent geometry : bond 0.00377 (29328) covalent geometry : angle 0.58672 (39796) hydrogen bonds : bond 0.03968 ( 1393) hydrogen bonds : angle 4.60970 ( 3903) metal coordination : bond 0.00286 ( 16) metal coordination : angle 0.98170 ( 12) *********************** 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 605 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 480 time to evaluate : 1.231 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: 0.6686 (t60) cc_final: 0.6292 (t60) REVERT: A 228 TRP cc_start: 0.6669 (m100) cc_final: 0.5669 (m-10) REVERT: A 241 ASN cc_start: 0.8252 (t0) cc_final: 0.7733 (t0) REVERT: A 252 MET cc_start: 0.6500 (tmt) cc_final: 0.5789 (mpt) REVERT: A 267 MET cc_start: 0.7165 (tmm) cc_final: 0.6286 (pmt) REVERT: A 323 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8151 (mmtm) REVERT: A 334 MET cc_start: 0.6529 (tmm) cc_final: 0.6252 (tmm) REVERT: A 490 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8192 (mt0) REVERT: A 540 GLN cc_start: 0.8260 (mt0) cc_final: 0.7994 (mm-40) REVERT: A 829 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8333 (ptmm) REVERT: A 940 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.7004 (mt) REVERT: B 334 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6685 (tmm) REVERT: B 347 GLU cc_start: 0.7911 (pp20) cc_final: 0.7559 (mm-30) REVERT: B 372 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7738 (mttt) REVERT: B 976 ASP cc_start: 0.8163 (m-30) cc_final: 0.7948 (m-30) REVERT: B 1011 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8281 (tptt) REVERT: B 1194 ASP cc_start: 0.7492 (m-30) cc_final: 0.7197 (m-30) REVERT: C 168 LEU cc_start: 0.8339 (tm) cc_final: 0.7716 (mt) REVERT: C 174 MET cc_start: 0.7200 (ptp) cc_final: 0.6747 (pmm) REVERT: C 182 ILE cc_start: 0.8494 (OUTLIER) cc_final: 0.8228 (pp) REVERT: C 235 PHE cc_start: 0.8285 (t80) cc_final: 0.7906 (t80) REVERT: C 291 HIS cc_start: 0.7788 (t-90) cc_final: 0.7367 (t-90) REVERT: C 293 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7502 (mt-10) REVERT: C 354 MET cc_start: 0.7807 (mtm) cc_final: 0.7456 (ppp) REVERT: C 940 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7113 (mt) REVERT: D 182 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7956 (tp) REVERT: D 200 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6757 (tppt) REVERT: D 204 TRP cc_start: 0.6162 (OUTLIER) cc_final: 0.5489 (t60) REVERT: D 235 PHE cc_start: 0.8231 (t80) cc_final: 0.7971 (t80) REVERT: D 250 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8492 (tm-30) REVERT: D 293 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7716 (mt-10) REVERT: D 548 GLN cc_start: 0.8355 (tp40) cc_final: 0.8062 (tp40) REVERT: D 782 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7586 (m-30) REVERT: D 944 LYS cc_start: 0.8435 (mtmm) cc_final: 0.8050 (mmtm) outliers start: 125 outliers final: 52 residues processed: 543 average time/residue: 0.6996 time to fit residues: 443.8288 Evaluate side-chains 515 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 451 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 490 GLN Chi-restraints excluded: chain A residue 491 ILE 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 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 192 MET Chi-restraints excluded: chain B residue 242 CYS 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 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 204 TRP Chi-restraints excluded: chain C residue 242 CYS Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 747 VAL 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 940 LEU 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 491 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 250 optimal weight: 7.9990 chunk 159 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 88 optimal weight: 20.0000 chunk 291 optimal weight: 2.9990 chunk 172 optimal weight: 0.3980 chunk 44 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 297 optimal weight: 0.4980 chunk 89 optimal weight: 40.0000 chunk 347 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 ASN C1159 HIS D 490 GLN D 632 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.132106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.099305 restraints weight = 53646.832| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.16 r_work: 0.3205 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2190 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= 0.115 Angle : 0.566 10.080 39808 Z= 0.278 Chirality : 0.041 0.276 4548 Planarity : 0.005 0.140 4992 Dihedral : 4.286 46.949 3908 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.49 % Favored : 97.40 % Rotamer: Outliers : 4.13 % Allowed : 21.34 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.14), residues: 3532 helix: 1.20 (0.13), residues: 1676 sheet: -0.54 (0.26), residues: 356 loop : 0.31 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 417 TYR 0.018 0.001 TYR A 553 PHE 0.028 0.001 PHE A 307 TRP 0.015 0.001 TRP D 177 HIS 0.010 0.001 HIS C1159 Details of bonding type rmsd covalent geometry : bond 0.00285 (29328) covalent geometry : angle 0.56597 (39796) hydrogen bonds : bond 0.03437 ( 1393) hydrogen bonds : angle 4.42305 ( 3903) metal coordination : bond 0.00343 ( 16) metal coordination : angle 0.96115 ( 12) *********************** 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 597 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 467 time to evaluate : 1.093 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: 0.6581 (t60) cc_final: 0.6236 (t60) REVERT: A 228 TRP cc_start: 0.6613 (m100) cc_final: 0.5631 (m-10) REVERT: A 241 ASN cc_start: 0.8213 (t0) cc_final: 0.7633 (t0) REVERT: A 267 MET cc_start: 0.7212 (tmm) cc_final: 0.6393 (pmt) REVERT: A 334 MET cc_start: 0.6610 (tmm) cc_final: 0.6349 (tmm) REVERT: A 372 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7922 (mttm) REVERT: A 829 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8332 (ptmm) REVERT: B 204 TRP cc_start: 0.6050 (OUTLIER) cc_final: 0.5396 (t60) REVERT: B 334 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6764 (tmm) REVERT: B 354 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6965 (ttm) REVERT: B 372 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7702 (mttt) REVERT: B 447 MET cc_start: 0.8674 (tpt) cc_final: 0.8453 (tpt) REVERT: B 867 ASP cc_start: 0.8019 (m-30) cc_final: 0.7655 (m-30) REVERT: B 950 ARG cc_start: 0.7726 (ttp80) cc_final: 0.7425 (mtm180) REVERT: B 976 ASP cc_start: 0.8123 (m-30) cc_final: 0.7857 (m-30) REVERT: B 1140 LEU cc_start: 0.8164 (tp) cc_final: 0.7878 (tp) REVERT: C 169 TRP cc_start: 0.7903 (m100) cc_final: 0.7480 (m-10) REVERT: C 174 MET cc_start: 0.7118 (ptp) cc_final: 0.6651 (pmm) REVERT: C 182 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8335 (pp) REVERT: C 234 LEU cc_start: 0.8771 (tm) cc_final: 0.8547 (tp) REVERT: C 235 PHE cc_start: 0.8343 (t80) cc_final: 0.8071 (t80) REVERT: C 293 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7519 (mt-10) REVERT: C 354 MET cc_start: 0.7773 (mtm) cc_final: 0.7412 (ppp) REVERT: C 1017 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8385 (mt) REVERT: D 182 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7961 (tp) REVERT: D 200 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6716 (tppt) REVERT: D 204 TRP cc_start: 0.6162 (OUTLIER) cc_final: 0.5441 (t60) REVERT: D 235 PHE cc_start: 0.8209 (t80) cc_final: 0.7985 (t80) REVERT: D 281 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8950 (tt) REVERT: D 293 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7663 (mt-10) REVERT: D 447 MET cc_start: 0.8799 (tpt) cc_final: 0.8521 (tpt) REVERT: D 490 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8260 (mt0) REVERT: D 566 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7935 (ttp) REVERT: D 782 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: D 940 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6863 (mt) REVERT: D 944 LYS cc_start: 0.8436 (mtmm) cc_final: 0.8021 (mmtm) outliers start: 130 outliers final: 48 residues processed: 533 average time/residue: 0.6836 time to fit residues: 427.3155 Evaluate side-chains 511 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 447 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 372 LYS 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 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 192 MET Chi-restraints excluded: chain B residue 204 TRP 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 354 MET Chi-restraints excluded: chain B residue 372 LYS Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 947 LYS Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 859 MET 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 301 LEU Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 490 GLN 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 829 LYS Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 940 LEU 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 186 optimal weight: 9.9990 chunk 289 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 97 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 305 optimal weight: 2.9990 chunk 136 optimal weight: 0.1980 chunk 16 optimal weight: 10.0000 chunk 222 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 GLN 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 180 GLN C 241 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.129505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.095959 restraints weight = 54265.229| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.36 r_work: 0.3145 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 29344 Z= 0.182 Angle : 0.603 10.182 39808 Z= 0.295 Chirality : 0.043 0.269 4548 Planarity : 0.005 0.136 4992 Dihedral : 4.400 51.390 3906 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.66 % Favored : 97.23 % Rotamer: Outliers : 4.77 % Allowed : 21.18 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.14), residues: 3532 helix: 1.14 (0.12), residues: 1704 sheet: -0.68 (0.26), residues: 356 loop : 0.25 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 428 TYR 0.020 0.002 TYR B 582 PHE 0.030 0.002 PHE A 307 TRP 0.019 0.001 TRP C 177 HIS 0.011 0.002 HIS A 844 Details of bonding type rmsd covalent geometry : bond 0.00463 (29328) covalent geometry : angle 0.60290 (39796) hydrogen bonds : bond 0.03707 ( 1393) hydrogen bonds : angle 4.46265 ( 3903) metal coordination : bond 0.00206 ( 16) metal coordination : angle 0.72549 ( 12) *********************** 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 614 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 464 time to evaluate : 1.208 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 177 TRP cc_start: 0.6623 (t60) cc_final: 0.6297 (t60) REVERT: A 228 TRP cc_start: 0.6716 (m100) cc_final: 0.5715 (m-10) REVERT: A 241 ASN cc_start: 0.8300 (t0) cc_final: 0.7778 (t0) REVERT: A 267 MET cc_start: 0.7206 (tmm) cc_final: 0.6455 (pmt) REVERT: A 334 MET cc_start: 0.6615 (tmm) cc_final: 0.6302 (tmm) REVERT: A 355 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: A 585 PHE cc_start: 0.7856 (t80) cc_final: 0.7640 (t80) REVERT: A 829 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8330 (ptmm) REVERT: B 193 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6731 (pp) REVERT: B 204 TRP cc_start: 0.5997 (OUTLIER) cc_final: 0.5327 (t60) REVERT: B 334 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6837 (tmm) REVERT: B 372 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7826 (mttt) REVERT: B 976 ASP cc_start: 0.8238 (m-30) cc_final: 0.7998 (m-30) REVERT: B 1194 ASP cc_start: 0.7513 (m-30) cc_final: 0.7259 (m-30) REVERT: C 168 LEU cc_start: 0.8313 (tm) cc_final: 0.7632 (mt) REVERT: C 182 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8419 (pp) REVERT: C 293 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7450 (mt-10) REVERT: C 354 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7377 (ppp) REVERT: C 631 GLU cc_start: 0.8355 (mp0) cc_final: 0.8022 (mp0) REVERT: C 1140 LEU cc_start: 0.8257 (tp) cc_final: 0.7968 (tp) REVERT: D 182 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7991 (tp) REVERT: D 193 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6703 (mt) REVERT: D 200 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6738 (tppt) REVERT: D 204 TRP cc_start: 0.6015 (OUTLIER) cc_final: 0.5278 (t60) REVERT: D 293 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7779 (mt-10) REVERT: D 490 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8425 (mt0) REVERT: D 548 GLN cc_start: 0.8239 (tp40) cc_final: 0.8016 (tp40) REVERT: D 566 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.7855 (tmt) REVERT: D 782 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7632 (m-30) REVERT: D 944 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8011 (mmtm) outliers start: 150 outliers final: 69 residues processed: 546 average time/residue: 0.6721 time to fit residues: 431.8802 Evaluate side-chains 534 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 450 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 176 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 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 193 LEU Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 240 LEU 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 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 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 204 TRP 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 523 CYS 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 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 1138 LEU 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 292 LEU Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 426 SER Chi-restraints excluded: chain D residue 490 GLN 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 829 LYS Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 937 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 345 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 chunk 340 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 312 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 147 optimal weight: 4.9990 chunk 331 optimal weight: 7.9990 chunk 190 optimal weight: 9.9990 chunk 289 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 396 HIS A 603 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 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 ASN C 845 HIS C 865 ASN C1159 HIS D 470 GLN D 632 ASN D1159 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.095513 restraints weight = 53518.949| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.53 r_work: 0.3084 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 29344 Z= 0.333 Angle : 0.711 9.965 39808 Z= 0.346 Chirality : 0.049 0.263 4548 Planarity : 0.006 0.133 4992 Dihedral : 4.760 53.864 3906 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.46 % Rotamer: Outliers : 4.58 % Allowed : 21.34 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.14), residues: 3532 helix: 1.02 (0.12), residues: 1680 sheet: -1.29 (0.25), residues: 400 loop : 0.23 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 961 TYR 0.022 0.002 TYR D1022 PHE 0.033 0.003 PHE C 307 TRP 0.017 0.002 TRP D 177 HIS 0.011 0.002 HIS C 844 Details of bonding type rmsd covalent geometry : bond 0.00846 (29328) covalent geometry : angle 0.71096 (39796) hydrogen bonds : bond 0.04314 ( 1393) hydrogen bonds : angle 4.62997 ( 3903) metal coordination : bond 0.00374 ( 16) metal coordination : angle 0.61678 ( 12) *********************** 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 602 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 458 time to evaluate : 1.125 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 177 TRP cc_start: 0.6651 (t60) cc_final: 0.6204 (t60) REVERT: A 193 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5369 (mt) REVERT: A 228 TRP cc_start: 0.6891 (m100) cc_final: 0.5770 (m-10) REVERT: A 241 ASN cc_start: 0.8314 (t0) cc_final: 0.7728 (t0) REVERT: A 267 MET cc_start: 0.6792 (tmm) cc_final: 0.6313 (pmt) REVERT: A 323 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8295 (mmtm) REVERT: A 334 MET cc_start: 0.6898 (tmm) cc_final: 0.6463 (tmm) REVERT: A 355 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: A 411 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7743 (mt-10) REVERT: A 576 GLU cc_start: 0.7232 (tp30) cc_final: 0.6848 (mm-30) REVERT: A 585 PHE cc_start: 0.8039 (t80) cc_final: 0.7821 (t80) REVERT: A 829 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8329 (ptmm) REVERT: A 876 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7513 (p90) REVERT: B 192 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7466 (mtp) REVERT: B 204 TRP cc_start: 0.6199 (OUTLIER) cc_final: 0.5534 (t60) REVERT: B 334 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6662 (tmm) REVERT: B 372 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7972 (mttt) REVERT: B 413 ASP cc_start: 0.7008 (t0) cc_final: 0.6750 (t0) REVERT: B 876 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.7497 (p90) REVERT: B 969 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8755 (p) REVERT: C 168 LEU cc_start: 0.8325 (tm) cc_final: 0.7599 (mt) REVERT: C 174 MET cc_start: 0.7788 (tpp) cc_final: 0.7263 (pmm) REVERT: C 182 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8313 (pp) REVERT: C 354 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7447 (ppp) REVERT: C 631 GLU cc_start: 0.8368 (mp0) cc_final: 0.8122 (mp0) REVERT: C 876 TYR cc_start: 0.8110 (p90) cc_final: 0.7384 (p90) REVERT: C 1140 LEU cc_start: 0.8198 (tp) cc_final: 0.7962 (tp) REVERT: D 182 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8100 (tp) REVERT: D 193 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6735 (mt) REVERT: D 200 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6692 (tppt) REVERT: D 204 TRP cc_start: 0.6080 (OUTLIER) cc_final: 0.5515 (t60) REVERT: D 278 LEU cc_start: 0.8990 (tt) cc_final: 0.8775 (mt) REVERT: D 293 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7873 (mt-10) REVERT: D 415 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: D 566 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.7792 (tmt) REVERT: D 576 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7087 (mm-30) REVERT: D 782 ASP cc_start: 0.8085 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: D 944 LYS cc_start: 0.8475 (mtmm) cc_final: 0.7938 (mmtm) REVERT: D 950 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7649 (ttp80) REVERT: D 974 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8095 (tmm) outliers start: 144 outliers final: 81 residues processed: 536 average time/residue: 0.6810 time to fit residues: 431.1673 Evaluate side-chains 547 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 445 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 176 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 299 LEU 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 766 LEU 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 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 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 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 419 VAL 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 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 204 TRP Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 242 CYS 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 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 772 VAL 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 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 131 ILE 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 292 LEU 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 419 VAL 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 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 829 LYS Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 937 SER Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 950 ARG Chi-restraints excluded: chain D residue 969 VAL Chi-restraints excluded: chain D residue 972 ILE Chi-restraints excluded: chain D residue 974 MET 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 230 optimal weight: 10.0000 chunk 347 optimal weight: 0.1980 chunk 198 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 56 optimal weight: 8.9990 chunk 342 optimal weight: 0.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 241 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS B1159 HIS C 632 ASN C 845 HIS C1159 HIS 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 = 0.3936 r_free = 0.3936 target = 0.129398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095840 restraints weight = 53876.417| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.41 r_work: 0.3133 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 29344 Z= 0.154 Angle : 0.617 11.908 39808 Z= 0.301 Chirality : 0.043 0.258 4548 Planarity : 0.005 0.130 4992 Dihedral : 4.530 57.227 3906 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.75 % Favored : 97.14 % Rotamer: Outliers : 3.94 % Allowed : 22.49 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.14), residues: 3532 helix: 1.13 (0.13), residues: 1704 sheet: -1.00 (0.26), residues: 356 loop : 0.31 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 133 TYR 0.018 0.002 TYR C 938 PHE 0.031 0.002 PHE C 307 TRP 0.017 0.001 TRP D 177 HIS 0.010 0.001 HIS C 844 Details of bonding type rmsd covalent geometry : bond 0.00381 (29328) covalent geometry : angle 0.61672 (39796) hydrogen bonds : bond 0.03574 ( 1393) hydrogen bonds : angle 4.46322 ( 3903) metal coordination : bond 0.00195 ( 16) metal coordination : angle 0.85256 ( 12) *********************** 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 577 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 453 time to evaluate : 0.834 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: 0.6614 (t60) cc_final: 0.6206 (t60) REVERT: A 193 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5373 (mt) REVERT: A 228 TRP cc_start: 0.6817 (m100) cc_final: 0.5762 (m-10) REVERT: A 241 ASN cc_start: 0.8260 (t0) cc_final: 0.7570 (t0) REVERT: A 252 MET cc_start: 0.6274 (tmt) cc_final: 0.5361 (mmt) REVERT: A 267 MET cc_start: 0.6641 (tmm) cc_final: 0.6211 (pmt) REVERT: A 334 MET cc_start: 0.6889 (tmm) cc_final: 0.6435 (tmm) REVERT: A 355 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: A 411 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7736 (mt-10) REVERT: A 576 GLU cc_start: 0.7092 (tp30) cc_final: 0.6708 (mm-30) REVERT: A 585 PHE cc_start: 0.8046 (t80) cc_final: 0.7824 (t80) REVERT: A 829 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8294 (ptmm) REVERT: A 959 MET cc_start: 0.8692 (ttp) cc_final: 0.8479 (ttm) REVERT: B 192 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7368 (mtp) REVERT: B 204 TRP cc_start: 0.6141 (OUTLIER) cc_final: 0.5465 (t60) REVERT: B 334 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6843 (tmm) REVERT: B 372 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7827 (mttt) REVERT: B 413 ASP cc_start: 0.6978 (t0) cc_final: 0.6760 (t0) REVERT: B 585 PHE cc_start: 0.8090 (t80) cc_final: 0.7854 (t80) REVERT: B 876 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.7366 (p90) REVERT: C 168 LEU cc_start: 0.8321 (tm) cc_final: 0.7601 (mt) REVERT: C 174 MET cc_start: 0.7920 (tpp) cc_final: 0.7356 (pmm) REVERT: C 182 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8343 (pp) REVERT: C 293 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7530 (mt-10) REVERT: C 354 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7395 (ppp) REVERT: C 631 GLU cc_start: 0.8291 (mp0) cc_final: 0.7990 (mp0) REVERT: C 876 TYR cc_start: 0.8053 (p90) cc_final: 0.7188 (p90) REVERT: D 182 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8055 (tp) REVERT: D 193 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6659 (mt) REVERT: D 200 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6741 (tppt) REVERT: D 204 TRP cc_start: 0.5992 (OUTLIER) cc_final: 0.5398 (t60) REVERT: D 241 ASN cc_start: 0.8135 (t0) cc_final: 0.7622 (t0) REVERT: D 278 LEU cc_start: 0.8964 (tt) cc_final: 0.8741 (mt) REVERT: D 293 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7843 (mt-10) REVERT: D 415 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: D 426 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8573 (m) REVERT: D 566 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7591 (tmt) REVERT: D 576 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6931 (mm-30) REVERT: D 782 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: D 944 LYS cc_start: 0.8526 (mtmm) cc_final: 0.8011 (mmtm) REVERT: D 950 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7559 (ttp80) REVERT: D 969 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8677 (p) outliers start: 124 outliers final: 64 residues processed: 521 average time/residue: 0.6778 time to fit residues: 411.5927 Evaluate side-chains 526 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 442 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 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 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 192 MET Chi-restraints excluded: chain B residue 204 TRP Chi-restraints excluded: chain B residue 240 LEU 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 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 794 LYS Chi-restraints excluded: chain B residue 876 TYR 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 1010 MET Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 204 TRP 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 523 CYS 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 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 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 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 491 ILE 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 829 LYS Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 950 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 217 optimal weight: 0.0970 chunk 83 optimal weight: 0.9990 chunk 349 optimal weight: 7.9990 chunk 325 optimal weight: 4.9990 chunk 233 optimal weight: 0.9990 chunk 342 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 845 HIS A1159 HIS B 241 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 632 ASN B 845 HIS B1159 HIS ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 ASN C 845 HIS C 865 ASN 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 = 0.3942 r_free = 0.3942 target = 0.130804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097345 restraints weight = 54023.830| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.45 r_work: 0.3142 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 29344 Z= 0.145 Angle : 0.627 12.158 39808 Z= 0.304 Chirality : 0.043 0.252 4548 Planarity : 0.005 0.127 4992 Dihedral : 4.452 59.683 3906 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.06 % Favored : 96.83 % Rotamer: Outliers : 4.07 % Allowed : 22.90 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.14), residues: 3532 helix: 1.23 (0.13), residues: 1704 sheet: -0.96 (0.25), residues: 380 loop : 0.39 (0.17), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1143 TYR 0.022 0.002 TYR C 938 PHE 0.032 0.002 PHE C 307 TRP 0.019 0.001 TRP D 177 HIS 0.010 0.001 HIS C 844 Details of bonding type rmsd covalent geometry : bond 0.00363 (29328) covalent geometry : angle 0.62656 (39796) hydrogen bonds : bond 0.03487 ( 1393) hydrogen bonds : angle 4.42948 ( 3903) metal coordination : bond 0.00274 ( 16) metal coordination : angle 0.87758 ( 12) *********************** 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 581 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 453 time to evaluate : 0.815 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: 0.6642 (t60) cc_final: 0.6214 (t60) REVERT: A 193 LEU cc_start: 0.6123 (OUTLIER) cc_final: 0.5351 (mt) REVERT: A 228 TRP cc_start: 0.6839 (m100) cc_final: 0.5738 (m-10) REVERT: A 241 ASN cc_start: 0.8231 (t0) cc_final: 0.7490 (t0) REVERT: A 252 MET cc_start: 0.6438 (tmt) cc_final: 0.5429 (mmt) REVERT: A 267 MET cc_start: 0.6646 (tmm) cc_final: 0.6290 (pmt) REVERT: A 298 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.7615 (m-40) REVERT: A 334 MET cc_start: 0.6864 (tmm) cc_final: 0.6408 (tmm) REVERT: A 355 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: A 576 GLU cc_start: 0.6936 (tp30) cc_final: 0.6638 (mm-30) REVERT: A 829 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8328 (ptmm) REVERT: A 876 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7258 (p90) REVERT: A 959 MET cc_start: 0.8681 (ttp) cc_final: 0.8466 (ttm) REVERT: B 192 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.7317 (mtp) REVERT: B 334 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6935 (tmm) REVERT: B 372 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7821 (mttt) REVERT: B 413 ASP cc_start: 0.6956 (t0) cc_final: 0.6724 (t0) REVERT: B 566 MET cc_start: 0.8363 (ttp) cc_final: 0.7268 (tmt) REVERT: B 585 PHE cc_start: 0.8021 (t80) cc_final: 0.7788 (t80) REVERT: B 876 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7195 (p90) REVERT: C 168 LEU cc_start: 0.8298 (tm) cc_final: 0.7481 (mt) REVERT: C 169 TRP cc_start: 0.7913 (m100) cc_final: 0.7146 (m-10) REVERT: C 170 VAL cc_start: 0.7685 (t) cc_final: 0.7400 (p) REVERT: C 174 MET cc_start: 0.7829 (tpp) cc_final: 0.7363 (pmm) REVERT: C 182 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8327 (pp) REVERT: C 293 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7449 (mt-10) REVERT: C 354 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7445 (ppp) REVERT: C 631 GLU cc_start: 0.8300 (mp0) cc_final: 0.7988 (mp0) REVERT: C 876 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7091 (p90) REVERT: C 1140 LEU cc_start: 0.8334 (tp) cc_final: 0.8079 (tp) REVERT: D 182 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8053 (tp) REVERT: D 200 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6759 (tppt) REVERT: D 204 TRP cc_start: 0.6023 (OUTLIER) cc_final: 0.5390 (t60) REVERT: D 241 ASN cc_start: 0.8105 (t0) cc_final: 0.7512 (t0) REVERT: D 278 LEU cc_start: 0.8984 (tt) cc_final: 0.8774 (mt) REVERT: D 293 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7800 (mt-10) REVERT: D 415 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: D 426 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8579 (m) REVERT: D 566 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7810 (tmt) REVERT: D 782 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: D 944 LYS cc_start: 0.8420 (mtmm) cc_final: 0.7915 (mmtm) REVERT: D 950 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7541 (ttp80) REVERT: D 969 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8691 (p) REVERT: D 1010 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8693 (ptp) outliers start: 128 outliers final: 67 residues processed: 526 average time/residue: 0.5802 time to fit residues: 357.9412 Evaluate side-chains 536 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 447 time to evaluate : 1.023 ------------------------------------------------------------------------------- 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 298 ASN 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 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 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 192 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 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 1010 MET Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 301 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 523 CYS 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 876 TYR 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 984 VAL Chi-restraints excluded: chain C residue 988 MET Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1159 HIS 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 220 LEU Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 324 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 491 ILE 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 829 LYS Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 919 THR Chi-restraints excluded: chain D residue 950 ARG 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 1010 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 146 optimal weight: 0.7980 chunk 270 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 324 optimal weight: 0.9990 chunk 209 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 302 optimal weight: 0.9990 chunk 318 optimal weight: 0.0770 chunk 179 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 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 C1159 HIS D 490 GLN 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 = 0.3952 r_free = 0.3952 target = 0.131886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099184 restraints weight = 53619.309| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.15 r_work: 0.3183 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 29344 Z= 0.125 Angle : 0.626 12.984 39808 Z= 0.305 Chirality : 0.042 0.248 4548 Planarity : 0.005 0.125 4992 Dihedral : 4.358 56.151 3906 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.69 % Favored : 97.20 % Rotamer: Outliers : 3.72 % Allowed : 23.31 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.14), residues: 3532 helix: 1.40 (0.13), residues: 1680 sheet: -0.89 (0.26), residues: 380 loop : 0.32 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 948 TYR 0.022 0.001 TYR C 938 PHE 0.041 0.002 PHE A 188 TRP 0.024 0.001 TRP D 177 HIS 0.028 0.001 HIS C1159 Details of bonding type rmsd covalent geometry : bond 0.00307 (29328) covalent geometry : angle 0.62586 (39796) hydrogen bonds : bond 0.03327 ( 1393) hydrogen bonds : angle 4.36241 ( 3903) metal coordination : bond 0.00314 ( 16) metal coordination : angle 0.97851 ( 12) *********************** 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 571 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 454 time to evaluate : 1.224 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 129 LEU cc_start: 0.9059 (mm) cc_final: 0.8833 (tp) REVERT: A 176 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7838 (tm) REVERT: A 177 TRP cc_start: 0.6523 (t60) cc_final: 0.6138 (t60) REVERT: A 228 TRP cc_start: 0.6694 (m100) cc_final: 0.5682 (m-10) REVERT: A 241 ASN cc_start: 0.8213 (t0) cc_final: 0.7532 (t0) REVERT: A 246 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8086 (ttpt) REVERT: A 252 MET cc_start: 0.6562 (tmt) cc_final: 0.5569 (mmt) REVERT: A 267 MET cc_start: 0.6636 (tmm) cc_final: 0.6224 (pmt) REVERT: A 298 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7713 (m110) REVERT: A 334 MET cc_start: 0.6786 (tmm) cc_final: 0.6393 (tmm) REVERT: A 355 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: A 576 GLU cc_start: 0.6988 (tp30) cc_final: 0.6735 (mm-30) REVERT: A 876 TYR cc_start: 0.7965 (OUTLIER) cc_final: 0.7150 (p90) REVERT: A 1011 LYS cc_start: 0.8759 (mtpt) cc_final: 0.8359 (tptt) REVERT: B 192 MET cc_start: 0.7541 (mtp) cc_final: 0.7291 (mtp) REVERT: B 372 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7714 (mttt) REVERT: B 566 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7613 (tmt) REVERT: B 576 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7049 (mm-30) REVERT: B 867 ASP cc_start: 0.7938 (m-30) cc_final: 0.7612 (m-30) REVERT: C 168 LEU cc_start: 0.8295 (tm) cc_final: 0.7447 (mt) REVERT: C 169 TRP cc_start: 0.7870 (m100) cc_final: 0.7264 (m-10) REVERT: C 174 MET cc_start: 0.7856 (tpp) cc_final: 0.7374 (pmm) REVERT: C 182 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8307 (pp) REVERT: C 293 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7482 (mt-10) REVERT: C 354 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7433 (ppp) REVERT: C 631 GLU cc_start: 0.8245 (mp0) cc_final: 0.7910 (mp0) REVERT: C 782 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: C 876 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7013 (p90) REVERT: C 892 GLU cc_start: 0.6840 (pp20) cc_final: 0.6292 (pp20) REVERT: D 182 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7981 (tp) REVERT: D 193 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6673 (pt) REVERT: D 200 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.6807 (tppt) REVERT: D 204 TRP cc_start: 0.6091 (OUTLIER) cc_final: 0.5416 (t60) REVERT: D 241 ASN cc_start: 0.8167 (t0) cc_final: 0.7571 (t0) REVERT: D 278 LEU cc_start: 0.8987 (tt) cc_final: 0.8759 (mt) REVERT: D 293 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7698 (mt-10) REVERT: D 426 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8605 (m) REVERT: D 747 VAL cc_start: 0.6781 (OUTLIER) cc_final: 0.6354 (m) REVERT: D 782 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7607 (m-30) REVERT: D 944 LYS cc_start: 0.8440 (mtmm) cc_final: 0.7961 (mmtm) REVERT: D 950 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7542 (ttp80) REVERT: D 969 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8667 (p) REVERT: D 1010 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8683 (ptp) outliers start: 117 outliers final: 64 residues processed: 521 average time/residue: 0.7053 time to fit residues: 429.0556 Evaluate side-chains 531 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 446 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 298 ASN 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 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 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 302 LEU 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 566 MET 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 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 1010 MET Chi-restraints excluded: chain B residue 1176 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 204 TRP Chi-restraints excluded: chain C residue 216 MET 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 523 CYS Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain C residue 876 TYR 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 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 220 LEU Chi-restraints excluded: chain D residue 228 TRP Chi-restraints excluded: chain D residue 238 VAL 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 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 829 LYS 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 950 ARG 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 1010 MET Chi-restraints excluded: chain D residue 1021 THR Chi-restraints excluded: chain D residue 1176 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 126 optimal weight: 2.9990 chunk 142 optimal weight: 8.9990 chunk 254 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 33 optimal weight: 0.0570 chunk 290 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 251 optimal weight: 4.9990 chunk 350 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 overall best weight: 1.7904 ------------------------------------------------------------------------------- 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 845 HIS A 931 GLN A1159 HIS B 241 ASN B 270 GLN ** B 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS B 931 GLN B1159 HIS ** C 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 ASN C 845 HIS C 865 ASN C 931 GLN ** C1159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 632 ASN ** D 845 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1159 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.129325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095458 restraints weight = 53896.399| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.36 r_work: 0.3135 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 29344 Z= 0.175 Angle : 0.648 12.892 39808 Z= 0.316 Chirality : 0.044 0.245 4548 Planarity : 0.005 0.123 4992 Dihedral : 4.434 52.027 3906 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 3.31 % Allowed : 23.66 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.14), residues: 3532 helix: 1.36 (0.13), residues: 1680 sheet: -1.17 (0.25), residues: 424 loop : 0.40 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 948 TYR 0.023 0.002 TYR C 938 PHE 0.046 0.002 PHE A 188 TRP 0.027 0.001 TRP D 177 HIS 0.012 0.002 HIS C 844 Details of bonding type rmsd covalent geometry : bond 0.00440 (29328) covalent geometry : angle 0.64815 (39796) hydrogen bonds : bond 0.03584 ( 1393) hydrogen bonds : angle 4.40830 ( 3903) metal coordination : bond 0.00264 ( 16) metal coordination : angle 0.86774 ( 12) ********************** 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 549 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 445 time to evaluate : 1.216 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 129 LEU cc_start: 0.9119 (mm) cc_final: 0.8903 (tp) REVERT: A 176 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7818 (tm) REVERT: A 177 TRP cc_start: 0.6604 (t60) cc_final: 0.6162 (t60) REVERT: A 228 TRP cc_start: 0.6755 (m100) cc_final: 0.5689 (m-10) REVERT: A 241 ASN cc_start: 0.8278 (t0) cc_final: 0.7533 (t0) REVERT: A 246 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8028 (ttpt) REVERT: A 252 MET cc_start: 0.6545 (tmt) cc_final: 0.5523 (mmt) REVERT: A 267 MET cc_start: 0.6431 (tmm) cc_final: 0.6018 (pmt) REVERT: A 298 ASN cc_start: 0.8088 (t0) cc_final: 0.7822 (m110) REVERT: A 334 MET cc_start: 0.6938 (tmm) cc_final: 0.6500 (tmm) REVERT: A 355 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: A 576 GLU cc_start: 0.7073 (tp30) cc_final: 0.6873 (mm-30) REVERT: A 829 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8357 (ptmm) REVERT: A 876 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7215 (p90) REVERT: A 1011 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8345 (tptt) REVERT: B 192 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7438 (mtp) REVERT: B 372 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7888 (mttt) REVERT: B 566 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7697 (tmt) REVERT: B 876 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7287 (p90) REVERT: C 168 LEU cc_start: 0.8321 (tm) cc_final: 0.7450 (mt) REVERT: C 169 TRP cc_start: 0.7900 (m100) cc_final: 0.7180 (m-10) REVERT: C 174 MET cc_start: 0.7877 (tpp) cc_final: 0.7398 (pmm) REVERT: C 182 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8345 (pp) REVERT: C 293 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7594 (mt-10) REVERT: C 354 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7427 (ppp) REVERT: C 566 MET cc_start: 0.8481 (ttp) cc_final: 0.7493 (tmt) REVERT: C 631 GLU cc_start: 0.8304 (mp0) cc_final: 0.8036 (mp0) REVERT: C 782 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: C 876 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7110 (p90) REVERT: C 892 GLU cc_start: 0.6964 (pp20) cc_final: 0.6406 (pp20) REVERT: D 182 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8069 (tp) REVERT: D 193 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6747 (pt) REVERT: D 200 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6773 (tppt) REVERT: D 204 TRP cc_start: 0.5856 (OUTLIER) cc_final: 0.5168 (t60) REVERT: D 241 ASN cc_start: 0.8126 (t0) cc_final: 0.7505 (t0) REVERT: D 250 GLU cc_start: 0.8731 (tt0) cc_final: 0.8147 (tm-30) REVERT: D 278 LEU cc_start: 0.9011 (tt) cc_final: 0.8797 (mt) REVERT: D 293 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7725 (mt-10) REVERT: D 747 VAL cc_start: 0.6834 (OUTLIER) cc_final: 0.6403 (m) REVERT: D 782 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: D 859 MET cc_start: 0.8667 (ttp) cc_final: 0.8247 (ttt) REVERT: D 944 LYS cc_start: 0.8442 (mtmm) cc_final: 0.7990 (mmtm) REVERT: D 950 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7566 (ttp80) outliers start: 104 outliers final: 65 residues processed: 502 average time/residue: 0.7030 time to fit residues: 412.3088 Evaluate side-chains 522 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 437 time to evaluate : 1.362 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 246 LYS 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 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 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 192 MET Chi-restraints excluded: chain B residue 302 LEU 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 566 MET 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 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 204 TRP Chi-restraints excluded: chain C residue 216 MET 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 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 876 TYR 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 193 LEU Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 204 TRP Chi-restraints excluded: chain D residue 220 LEU 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 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 829 LYS 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 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 Chi-restraints excluded: chain D residue 1176 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 16 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 352 optimal weight: 0.0170 chunk 51 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 319 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 198 optimal weight: 8.9990 chunk 295 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 632 ASN B 845 HIS B1159 HIS C 632 ASN C 845 HIS D 632 ASN D 845 HIS D1159 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.129476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.095946 restraints weight = 54143.467| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.40 r_work: 0.3113 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 29344 Z= 0.199 Angle : 0.669 15.391 39808 Z= 0.324 Chirality : 0.044 0.243 4548 Planarity : 0.005 0.121 4992 Dihedral : 4.479 49.213 3906 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.31 % Favored : 96.57 % Rotamer: Outliers : 3.18 % Allowed : 23.70 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.14), residues: 3532 helix: 1.21 (0.13), residues: 1708 sheet: -1.24 (0.25), residues: 424 loop : 0.46 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 948 TYR 0.024 0.002 TYR C 938 PHE 0.049 0.002 PHE D 188 TRP 0.028 0.001 TRP D 177 HIS 0.012 0.002 HIS B 844 Details of bonding type rmsd covalent geometry : bond 0.00501 (29328) covalent geometry : angle 0.66925 (39796) hydrogen bonds : bond 0.03670 ( 1393) hydrogen bonds : angle 4.43086 ( 3903) metal coordination : bond 0.00252 ( 16) metal coordination : angle 0.81964 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12607.33 seconds wall clock time: 215 minutes 18.94 seconds (12918.94 seconds total)