Starting phenix.real_space_refine on Wed Jun 25 07:51:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hir_34827/06_2025/8hir_34827.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hir_34827/06_2025/8hir_34827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hir_34827/06_2025/8hir_34827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hir_34827/06_2025/8hir_34827.map" model { file = "/net/cci-nas-00/data/ceres_data/8hir_34827/06_2025/8hir_34827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hir_34827/06_2025/8hir_34827.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.133 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 4 8.98 5 Zn 4 6.06 5 S 208 5.16 5 Na 4 4.78 5 C 18908 2.51 5 N 4848 2.21 5 O 5192 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.48s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 29168 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "B" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "C" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "D" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 918, 7278 Classifications: {'peptide': 918} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 41, 'TRANS': 876} Chain breaks: 4 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 125 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 17 Unusual residues: {' K': 4, ' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 13 Unusual residues: {' NA': 1, ' ZN': 1, '6OU': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'6OU:plan-2': 1, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4558 SG CYS A 777 82.687 95.289 12.517 1.00113.91 S ATOM 4564 SG CYS A 778 85.660 98.570 12.340 1.00115.70 S ATOM 4618 SG CYS A 785 86.098 95.282 10.992 1.00138.43 S ATOM 11836 SG CYS B 777 95.308 67.082 12.496 1.00113.48 S ATOM 11842 SG CYS B 778 98.582 64.093 12.329 1.00117.04 S ATOM 11896 SG CYS B 785 95.296 63.676 10.963 1.00136.80 S ATOM 19114 SG CYS C 777 67.051 54.450 12.490 1.00112.86 S ATOM 19120 SG CYS C 778 64.079 51.170 12.324 1.00115.83 S ATOM 19174 SG CYS C 785 63.629 54.465 10.977 1.00137.33 S ATOM 26392 SG CYS D 777 54.468 82.685 12.517 1.00116.50 S ATOM 26398 SG CYS D 778 51.170 85.650 12.341 1.00118.42 S ATOM 26452 SG CYS D 785 54.472 86.094 10.989 1.00137.08 S Time building chain proxies: 17.06, per 1000 atoms: 0.58 Number of scatterers: 29168 At special positions: 0 Unit cell: (150.8, 150.8, 139.36, 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 4 19.00 S 208 16.00 Na 4 11.00 O 5192 8.00 N 4848 7.00 C 18908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.64 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1307 " pdb="ZN ZN A1307 " - pdb=" ND1 HIS A 787 " pdb="ZN ZN A1307 " - pdb=" SG CYS A 777 " pdb="ZN ZN A1307 " - pdb=" SG CYS A 785 " pdb="ZN ZN A1307 " - pdb=" SG CYS A 778 " pdb=" ZN B1303 " pdb="ZN ZN B1303 " - pdb=" ND1 HIS B 787 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 785 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 778 " pdb="ZN ZN B1303 " - pdb=" SG CYS B 777 " pdb=" ZN C1303 " pdb="ZN ZN C1303 " - pdb=" ND1 HIS C 787 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 785 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 778 " pdb="ZN ZN C1303 " - pdb=" SG CYS C 777 " pdb=" ZN D1303 " pdb="ZN ZN D1303 " - pdb=" ND1 HIS D 787 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 785 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 778 " pdb="ZN ZN D1303 " - pdb=" SG CYS D 777 " Number of angles added : 12 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7024 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 24 sheets defined 52.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.564A pdb=" N GLU A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 106 Processing helix chain 'A' and resid 108 through 136 removed outlier: 3.790A pdb=" N LEU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 164 through 169 removed outlier: 3.674A pdb=" N LEU A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 198 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 209 through 225 removed outlier: 3.600A pdb=" N GLU A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Proline residue: A 221 - end of helix 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 254 removed outlier: 4.033A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 293 removed outlier: 4.118A pdb=" N ILE A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 324 through 354 Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.682A pdb=" N GLN A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR A 370 " --> pdb=" O HIS A 366 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 394 removed outlier: 3.516A pdb=" N ASN A 391 " --> pdb=" O MET A 387 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 392 " --> pdb=" O ASP A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 400 removed outlier: 3.540A pdb=" N GLN A 400 " --> pdb=" O PRO A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 removed outlier: 4.136A pdb=" N ARG A 418 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 419 " --> pdb=" O GLN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 445 removed outlier: 3.870A pdb=" N ARG A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.646A pdb=" N HIS A 469 " --> pdb=" O THR A 465 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 removed outlier: 4.352A pdb=" N PHE A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 518 removed outlier: 3.590A pdb=" N ALA A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 removed outlier: 3.601A pdb=" N THR A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 557 removed outlier: 3.540A pdb=" N GLY A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.511A pdb=" N LEU A 779 " --> pdb=" O PRO A 775 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG A 780 " --> pdb=" O PHE A 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 775 through 780' Processing helix chain 'A' and resid 792 through 797 Processing helix chain 'A' and resid 811 through 823 removed outlier: 3.614A pdb=" N ASN A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE A 817 " --> pdb=" O GLY A 813 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 818 " --> pdb=" O LEU A 814 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 819 " --> pdb=" O TYR A 815 " (cutoff:3.500A) Proline residue: A 820 - end of helix Processing helix chain 'A' and resid 843 through 851 removed outlier: 3.837A pdb=" N ALA A 849 " --> pdb=" O HIS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 873 removed outlier: 4.225A pdb=" N LEU A 869 " --> pdb=" O ASN A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 4.106A pdb=" N SER A 890 " --> pdb=" O SER A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 898 removed outlier: 3.716A pdb=" N ALA A 897 " --> pdb=" O GLU A 893 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 893 through 898' Processing helix chain 'A' and resid 898 through 912 removed outlier: 3.657A pdb=" N VAL A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 930 removed outlier: 4.100A pdb=" N ARG A 928 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 953 removed outlier: 3.969A pdb=" N ALA A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 944 " --> pdb=" O LEU A 940 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 971 through 975 Processing helix chain 'A' and resid 976 through 985 removed outlier: 3.924A pdb=" N TYR A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 983 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 984 " --> pdb=" O TYR A 980 " (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 1132 through 1142 removed outlier: 3.947A pdb=" N GLN A1136 " --> pdb=" O TRP A1132 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A1138 " --> pdb=" O SER A1134 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A1142 " --> pdb=" O LEU A1138 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1161 Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.571A pdb=" N GLU B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 106 removed outlier: 3.541A pdb=" N LEU B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 136 removed outlier: 3.767A pdb=" N LEU B 113 " --> pdb=" O GLN B 109 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.643A pdb=" N LEU B 168 " --> pdb=" O TRP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 198 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 209 through 225 removed outlier: 3.616A pdb=" N GLU B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Proline residue: B 221 - end of helix 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 254 removed outlier: 4.021A pdb=" N LEU B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 293 removed outlier: 4.040A pdb=" N ILE B 273 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 324 through 354 Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 364 through 372 removed outlier: 3.689A pdb=" N GLN B 369 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 370 " --> pdb=" O HIS B 366 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 394 removed outlier: 3.501A pdb=" N ASN B 391 " --> pdb=" O MET B 387 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU B 392 " --> pdb=" O ASP B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.517A pdb=" N GLN B 400 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 420 removed outlier: 4.121A pdb=" N ARG B 418 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL B 419 " --> pdb=" O GLN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 445 removed outlier: 3.896A pdb=" N ARG B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 removed outlier: 3.633A pdb=" N HIS B 469 " --> pdb=" O THR B 465 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 498 removed outlier: 3.500A pdb=" N ASN B 496 " --> pdb=" O LYS B 493 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N PHE B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 518 removed outlier: 3.591A pdb=" N ALA B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 534 removed outlier: 3.601A pdb=" N THR B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 534 " --> pdb=" O ILE B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 557 removed outlier: 3.529A pdb=" N GLY B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 591 Processing helix chain 'B' and resid 629 through 633 Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.512A pdb=" N LEU B 779 " --> pdb=" O PRO B 775 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG B 780 " --> pdb=" O PHE B 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 775 through 780' Processing helix chain 'B' and resid 792 through 797 Processing helix chain 'B' and resid 811 through 823 removed outlier: 3.635A pdb=" N ASN B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE B 817 " --> pdb=" O GLY B 813 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 819 " --> pdb=" O TYR B 815 " (cutoff:3.500A) Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 843 through 851 removed outlier: 3.830A pdb=" N ALA B 849 " --> pdb=" O HIS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 873 removed outlier: 4.236A pdb=" N LEU B 869 " --> pdb=" O ASN B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 891 removed outlier: 4.106A pdb=" N SER B 890 " --> pdb=" O SER B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 893 through 898 removed outlier: 3.722A pdb=" N ALA B 897 " --> pdb=" O GLU B 893 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 898 " --> pdb=" O ASP B 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 893 through 898' Processing helix chain 'B' and resid 898 through 912 removed outlier: 3.659A pdb=" N VAL B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 930 removed outlier: 4.112A pdb=" N ARG B 928 " --> pdb=" O SER B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 937 through 953 removed outlier: 3.957A pdb=" N ALA B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 944 " --> pdb=" O LEU B 940 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 961 through 966 Processing helix chain 'B' and resid 973 through 975 No H-bonds generated for 'chain 'B' and resid 973 through 975' Processing helix chain 'B' and resid 976 through 985 removed outlier: 3.930A pdb=" N TYR B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 983 " --> pdb=" O LEU B 979 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL B 984 " --> pdb=" O TYR B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 996 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1021 through 1033 Processing helix chain 'B' and resid 1132 through 1142 removed outlier: 3.949A pdb=" N GLN B1136 " --> pdb=" O TRP B1132 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B1138 " --> pdb=" O SER B1134 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B1142 " --> pdb=" O LEU B1138 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1161 Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.585A pdb=" N GLU C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 106 Processing helix chain 'C' and resid 108 through 136 removed outlier: 3.783A pdb=" N LEU C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.637A pdb=" N LEU C 168 " --> pdb=" O TRP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 198 Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 209 through 225 removed outlier: 3.620A pdb=" N GLU C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Proline residue: C 221 - end of helix 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 256 removed outlier: 4.050A pdb=" N LEU C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP C 255 " --> pdb=" O ASN C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 293 removed outlier: 3.981A pdb=" N ILE C 273 " --> pdb=" O ASN C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 313 Processing helix chain 'C' and resid 324 through 354 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.697A pdb=" N GLN C 369 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR C 370 " --> pdb=" O HIS C 366 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS C 372 " --> pdb=" O ALA C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 394 removed outlier: 3.591A pdb=" N ASN C 391 " --> pdb=" O MET C 387 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU C 392 " --> pdb=" O ASP C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 400 removed outlier: 3.515A pdb=" N GLN C 400 " --> pdb=" O PRO C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 420 removed outlier: 4.104A pdb=" N ARG C 418 " --> pdb=" O VAL C 414 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL C 419 " --> pdb=" O GLN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 445 removed outlier: 3.888A pdb=" N ARG C 444 " --> pdb=" O GLN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 482 removed outlier: 3.628A pdb=" N HIS C 469 " --> pdb=" O THR C 465 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR C 471 " --> pdb=" O ALA C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 498 removed outlier: 3.511A pdb=" N ASN C 496 " --> pdb=" O LYS C 493 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 518 removed outlier: 3.591A pdb=" N ALA C 515 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 534 removed outlier: 3.618A pdb=" N THR C 531 " --> pdb=" O SER C 527 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 534 " --> pdb=" O ILE C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 557 removed outlier: 3.535A pdb=" N GLY C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 591 Processing helix chain 'C' and resid 629 through 633 Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.507A pdb=" N LEU C 779 " --> pdb=" O PRO C 775 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG C 780 " --> pdb=" O PHE C 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 775 through 780' Processing helix chain 'C' and resid 792 through 797 Processing helix chain 'C' and resid 811 through 823 removed outlier: 3.636A pdb=" N ASN C 816 " --> pdb=" O ASN C 812 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE C 817 " --> pdb=" O GLY C 813 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE C 818 " --> pdb=" O LEU C 814 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 819 " --> pdb=" O TYR C 815 " (cutoff:3.500A) Proline residue: C 820 - end of helix Processing helix chain 'C' and resid 843 through 851 removed outlier: 3.832A pdb=" N ALA C 849 " --> pdb=" O HIS C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 873 removed outlier: 4.252A pdb=" N LEU C 869 " --> pdb=" O ASN C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.107A pdb=" N SER C 890 " --> pdb=" O SER C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 898 removed outlier: 3.731A pdb=" N ALA C 897 " --> pdb=" O GLU C 893 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASP C 898 " --> pdb=" O ASP C 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 893 through 898' Processing helix chain 'C' and resid 898 through 912 removed outlier: 3.664A pdb=" N VAL C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 910 " --> pdb=" O GLN C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 930 removed outlier: 4.094A pdb=" N ARG C 928 " --> pdb=" O SER C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 953 removed outlier: 3.969A pdb=" N ALA C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS C 944 " --> pdb=" O LEU C 940 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 961 through 966 Processing helix chain 'C' and resid 973 through 975 No H-bonds generated for 'chain 'C' and resid 973 through 975' Processing helix chain 'C' and resid 976 through 985 removed outlier: 3.926A pdb=" N TYR C 980 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 983 " --> pdb=" O LEU C 979 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL C 984 " --> pdb=" O TYR C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 996 Processing helix chain 'C' and resid 1013 through 1017 Processing helix chain 'C' and resid 1021 through 1033 Processing helix chain 'C' and resid 1132 through 1142 removed outlier: 3.946A pdb=" N GLN C1136 " --> pdb=" O TRP C1132 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C1138 " --> pdb=" O SER C1134 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C1142 " --> pdb=" O LEU C1138 " (cutoff:3.500A) Processing helix chain 'C' and resid 1144 through 1161 Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.578A pdb=" N GLU D 94 " --> pdb=" O PHE D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 106 removed outlier: 3.517A pdb=" N LEU D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 136 removed outlier: 3.760A pdb=" N LEU D 113 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 142 Processing helix chain 'D' and resid 164 through 169 removed outlier: 3.670A pdb=" N LEU D 168 " --> pdb=" O TRP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 198 removed outlier: 3.531A pdb=" N ALA D 178 " --> pdb=" O MET D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 209 through 225 removed outlier: 3.598A pdb=" N GLU D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Proline residue: D 221 - end of helix Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 240 through 254 removed outlier: 4.086A pdb=" N LEU D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 293 removed outlier: 4.119A pdb=" N ILE D 273 " --> pdb=" O ASN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 324 through 354 Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 364 through 369 removed outlier: 3.709A pdb=" N GLN D 369 " --> pdb=" O ARG D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 394 removed outlier: 3.520A pdb=" N ASN D 391 " --> pdb=" O MET D 387 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU D 392 " --> pdb=" O ASP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 400 removed outlier: 3.541A pdb=" N GLN D 400 " --> pdb=" O PRO D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 420 removed outlier: 4.133A pdb=" N ARG D 418 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL D 419 " --> pdb=" O GLN D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 445 removed outlier: 3.876A pdb=" N ARG D 444 " --> pdb=" O GLN D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 482 removed outlier: 3.636A pdb=" N HIS D 469 " --> pdb=" O THR D 465 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR D 471 " --> pdb=" O ALA D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 498 removed outlier: 3.504A pdb=" N ASN D 496 " --> pdb=" O LYS D 493 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 518 removed outlier: 3.589A pdb=" N ALA D 515 " --> pdb=" O GLU D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 534 removed outlier: 3.602A pdb=" N THR D 531 " --> pdb=" O SER D 527 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 534 " --> pdb=" O ILE D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 557 removed outlier: 3.567A pdb=" N GLY D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 591 Processing helix chain 'D' and resid 629 through 633 Processing helix chain 'D' and resid 775 through 780 removed outlier: 3.510A pdb=" N LEU D 779 " --> pdb=" O PRO D 775 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 780 " --> pdb=" O PHE D 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 775 through 780' Processing helix chain 'D' and resid 792 through 797 Processing helix chain 'D' and resid 811 through 823 removed outlier: 3.612A pdb=" N ASN D 816 " --> pdb=" O ASN D 812 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE D 817 " --> pdb=" O GLY D 813 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 818 " --> pdb=" O LEU D 814 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL D 819 " --> pdb=" O TYR D 815 " (cutoff:3.500A) Proline residue: D 820 - end of helix Processing helix chain 'D' and resid 843 through 851 removed outlier: 3.838A pdb=" N ALA D 849 " --> pdb=" O HIS D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 873 removed outlier: 4.219A pdb=" N LEU D 869 " --> pdb=" O ASN D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 891 removed outlier: 4.102A pdb=" N SER D 890 " --> pdb=" O SER D 887 " (cutoff:3.500A) Processing helix chain 'D' and resid 893 through 898 removed outlier: 3.733A pdb=" N ALA D 897 " --> pdb=" O GLU D 893 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP D 898 " --> pdb=" O ASP D 894 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 893 through 898' Processing helix chain 'D' and resid 898 through 912 removed outlier: 3.686A pdb=" N VAL D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG D 910 " --> pdb=" O GLN D 906 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 930 removed outlier: 4.108A pdb=" N ARG D 928 " --> pdb=" O SER D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 937 through 953 removed outlier: 3.969A pdb=" N ALA D 941 " --> pdb=" O SER D 937 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS D 944 " --> pdb=" O LEU D 940 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU D 946 " --> pdb=" O LEU D 942 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 948 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 961 through 966 Processing helix chain 'D' and resid 971 through 975 Processing helix chain 'D' and resid 976 through 985 removed outlier: 3.921A pdb=" N TYR D 980 " --> pdb=" O ASP D 976 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 983 " --> pdb=" O LEU D 979 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL D 984 " --> pdb=" O TYR D 980 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 996 Processing helix chain 'D' and resid 1013 through 1017 Processing helix chain 'D' and resid 1021 through 1033 Processing helix chain 'D' and resid 1132 through 1142 removed outlier: 3.941A pdb=" N GLN D1136 " --> pdb=" O TRP D1132 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D1138 " --> pdb=" O SER D1134 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D1142 " --> pdb=" O LEU D1138 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1161 Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 433 removed outlier: 6.227A pdb=" N VAL A 404 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU A 432 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ILE A 406 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL A 374 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU A 407 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU A 376 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 456 " --> pdb=" O CYS A 377 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 487 " --> pdb=" O HIS A 505 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N VAL A 507 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 489 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 560 through 565 removed outlier: 6.832A pdb=" N ILE A 625 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU A 595 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 750 through 752 Processing sheet with id=AA5, first strand: chain 'A' and resid 856 through 860 removed outlier: 6.297A pdb=" N ILE A 834 " --> pdb=" O TYR A 857 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N MET A 859 " --> pdb=" O ILE A 834 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU A 836 " --> pdb=" O MET A 859 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ILE A 803 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 837 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 805 " --> pdb=" O LEU A 837 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU A 802 " --> pdb=" O ASN A 879 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N VAL A 881 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 804 " --> pdb=" O VAL A 881 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 916 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1006 through 1012 removed outlier: 4.094A pdb=" N ASP A1194 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A1039 " --> pdb=" O TYR A1197 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE A1199 " --> pdb=" O PRO A1037 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 143 through 144 Processing sheet with id=AA8, first strand: chain 'B' and resid 429 through 433 removed outlier: 6.234A pdb=" N VAL B 404 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU B 432 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE B 406 " --> pdb=" O LEU B 432 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL B 374 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU B 407 " --> pdb=" O VAL B 374 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 376 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 456 " --> pdb=" O CYS B 377 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 487 " --> pdb=" O HIS B 505 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N VAL B 507 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 489 " --> pdb=" O VAL B 507 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 560 through 565 removed outlier: 6.866A pdb=" N ILE B 625 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU B 595 " --> pdb=" O ILE B 625 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 750 through 752 Processing sheet with id=AB2, first strand: chain 'B' and resid 856 through 860 removed outlier: 6.275A pdb=" N ILE B 834 " --> pdb=" O TYR B 857 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N MET B 859 " --> pdb=" O ILE B 834 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LEU B 836 " --> pdb=" O MET B 859 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE B 803 " --> pdb=" O VAL B 835 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU B 837 " --> pdb=" O ILE B 803 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 805 " --> pdb=" O LEU B 837 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU B 802 " --> pdb=" O ALA B 877 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN B 879 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER B 916 " --> pdb=" O ASP B 878 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE B 970 " --> pdb=" O ILE B 917 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 919 " --> pdb=" O PHE B 970 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 1006 through 1012 removed outlier: 4.129A pdb=" N ASP B1194 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY B1039 " --> pdb=" O TYR B1197 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B1199 " --> pdb=" O PRO B1037 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB5, first strand: chain 'C' and resid 429 through 433 removed outlier: 6.226A pdb=" N VAL C 404 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N LEU C 432 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ILE C 406 " --> pdb=" O LEU C 432 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 374 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N LEU C 407 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU C 376 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU C 487 " --> pdb=" O HIS C 505 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N VAL C 507 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL C 489 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 560 through 565 removed outlier: 6.861A pdb=" N ILE C 625 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LEU C 595 " --> pdb=" O ILE C 625 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 750 through 752 Processing sheet with id=AB8, first strand: chain 'C' and resid 856 through 860 removed outlier: 6.271A pdb=" N ILE C 834 " --> pdb=" O TYR C 857 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET C 859 " --> pdb=" O ILE C 834 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU C 836 " --> pdb=" O MET C 859 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE C 803 " --> pdb=" O VAL C 835 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU C 837 " --> pdb=" O ILE C 803 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL C 805 " --> pdb=" O LEU C 837 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU C 802 " --> pdb=" O ALA C 877 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN C 879 " --> pdb=" O LEU C 802 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 916 " --> pdb=" O ASP C 878 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N PHE C 970 " --> pdb=" O ILE C 917 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR C 919 " --> pdb=" O PHE C 970 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 1006 through 1012 removed outlier: 4.112A pdb=" N ASP C1194 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY C1039 " --> pdb=" O TYR C1197 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE C1199 " --> pdb=" O PRO C1037 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 143 through 144 Processing sheet with id=AC2, first strand: chain 'D' and resid 429 through 433 removed outlier: 6.216A pdb=" N VAL D 404 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LEU D 432 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ILE D 406 " --> pdb=" O LEU D 432 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL D 374 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU D 407 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU D 376 " --> pdb=" O LEU D 407 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU D 487 " --> pdb=" O HIS D 505 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N VAL D 507 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL D 489 " --> pdb=" O VAL D 507 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 560 through 565 removed outlier: 6.840A pdb=" N ILE D 625 " --> pdb=" O LEU D 595 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU D 595 " --> pdb=" O ILE D 625 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 750 through 752 Processing sheet with id=AC5, first strand: chain 'D' and resid 856 through 860 removed outlier: 6.291A pdb=" N ILE D 834 " --> pdb=" O TYR D 857 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N MET D 859 " --> pdb=" O ILE D 834 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU D 836 " --> pdb=" O MET D 859 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE D 803 " --> pdb=" O VAL D 835 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LEU D 837 " --> pdb=" O ILE D 803 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL D 805 " --> pdb=" O LEU D 837 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 802 " --> pdb=" O ASN D 879 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N VAL D 881 " --> pdb=" O LEU D 802 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE D 804 " --> pdb=" O VAL D 881 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER D 916 " --> pdb=" O ASP D 878 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1006 through 1012 removed outlier: 4.104A pdb=" N ASP D1194 " --> pdb=" O ILE D1012 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY D1039 " --> pdb=" O TYR D1197 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE D1199 " --> pdb=" O PRO D1037 " (cutoff:3.500A) 1217 hydrogen bonds defined for protein. 3384 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: 12.21 Time building geometry restraints manager: 7.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9201 1.34 - 1.46: 6777 1.46 - 1.58: 13562 1.58 - 1.70: 0 1.70 - 1.81: 304 Bond restraints: 29844 Sorted by residual: bond pdb=" CB PRO C 230 " pdb=" CG PRO C 230 " ideal model delta sigma weight residual 1.492 1.390 0.102 5.00e-02 4.00e+02 4.14e+00 bond pdb=" CA PRO C 229 " pdb=" C PRO C 229 " ideal model delta sigma weight residual 1.517 1.536 -0.019 9.30e-03 1.16e+04 4.13e+00 bond pdb=" CA ILE C 203 " pdb=" CB ILE C 203 " ideal model delta sigma weight residual 1.540 1.563 -0.023 1.36e-02 5.41e+03 2.88e+00 bond pdb=" CA ILE B 203 " pdb=" CB ILE B 203 " ideal model delta sigma weight residual 1.540 1.562 -0.022 1.36e-02 5.41e+03 2.61e+00 bond pdb=" CA ILE D 203 " pdb=" CB ILE D 203 " ideal model delta sigma weight residual 1.540 1.562 -0.022 1.36e-02 5.41e+03 2.61e+00 ... (remaining 29839 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.37: 40406 5.37 - 10.74: 73 10.74 - 16.10: 9 16.10 - 21.47: 8 21.47 - 26.84: 4 Bond angle restraints: 40500 Sorted by residual: angle pdb=" N ARG D 172 " pdb=" CA ARG D 172 " pdb=" C ARG D 172 " ideal model delta sigma weight residual 109.79 82.95 26.84 1.56e+00 4.11e-01 2.96e+02 angle pdb=" N ARG A 172 " pdb=" CA ARG A 172 " pdb=" C ARG A 172 " ideal model delta sigma weight residual 109.79 83.15 26.64 1.56e+00 4.11e-01 2.92e+02 angle pdb=" N ARG B 172 " pdb=" CA ARG B 172 " pdb=" C ARG B 172 " ideal model delta sigma weight residual 109.79 83.30 26.49 1.56e+00 4.11e-01 2.88e+02 angle pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" C ARG C 172 " ideal model delta sigma weight residual 109.79 83.31 26.48 1.56e+00 4.11e-01 2.88e+02 angle pdb=" N LYS C 173 " pdb=" CA LYS C 173 " pdb=" CB LYS C 173 " ideal model delta sigma weight residual 110.39 91.56 18.83 1.59e+00 3.96e-01 1.40e+02 ... (remaining 40495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15553 17.94 - 35.89: 1825 35.89 - 53.83: 393 53.83 - 71.77: 65 71.77 - 89.71: 16 Dihedral angle restraints: 17852 sinusoidal: 7008 harmonic: 10844 Sorted by residual: dihedral pdb=" C ARG A 172 " pdb=" N ARG A 172 " pdb=" CA ARG A 172 " pdb=" CB ARG A 172 " ideal model delta harmonic sigma weight residual -122.60 -106.79 -15.81 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" C ARG B 172 " pdb=" N ARG B 172 " pdb=" CA ARG B 172 " pdb=" CB ARG B 172 " ideal model delta harmonic sigma weight residual -122.60 -106.79 -15.81 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" C ARG C 172 " pdb=" N ARG C 172 " pdb=" CA ARG C 172 " pdb=" CB ARG C 172 " ideal model delta harmonic sigma weight residual -122.60 -106.87 -15.73 0 2.50e+00 1.60e-01 3.96e+01 ... (remaining 17849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 4522 0.115 - 0.229: 73 0.229 - 0.344: 5 0.344 - 0.458: 6 0.458 - 0.573: 6 Chirality restraints: 4612 Sorted by residual: chirality pdb=" CA ILE B 203 " pdb=" N ILE B 203 " pdb=" C ILE B 203 " pdb=" CB ILE B 203 " both_signs ideal model delta sigma weight residual False 2.43 3.01 -0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" CA ARG A 172 " pdb=" N ARG A 172 " pdb=" C ARG A 172 " pdb=" CB ARG A 172 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" CA ARG B 172 " pdb=" N ARG B 172 " pdb=" C ARG B 172 " pdb=" CB ARG B 172 " both_signs ideal model delta sigma weight residual False 2.51 3.06 -0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 4609 not shown) Planarity restraints: 5088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 228 " 0.076 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO C 229 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 229 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 229 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B1191 " 0.035 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO B1192 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B1192 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B1192 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C1191 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C1192 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO C1192 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C1192 " -0.029 5.00e-02 4.00e+02 ... (remaining 5085 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.63: 385 2.63 - 3.26: 30062 3.26 - 3.88: 55919 3.88 - 4.51: 77382 4.51 - 5.14: 123735 Nonbonded interactions: 287483 Sorted by model distance: nonbonded pdb=" N ARG D 172 " pdb=" O ARG D 172 " model vdw 2.000 2.496 nonbonded pdb=" N ARG A 172 " pdb=" O ARG A 172 " model vdw 2.005 2.496 nonbonded pdb=" N ARG C 172 " pdb=" O ARG C 172 " model vdw 2.006 2.496 nonbonded pdb=" N ARG B 172 " pdb=" O ARG B 172 " model vdw 2.008 2.496 nonbonded pdb=" OD2 ASP C 468 " pdb=" ND2 ASN C 496 " model vdw 2.055 3.120 ... (remaining 287478 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 85 through 1205) selection = (chain 'B' and resid 85 through 1205) selection = (chain 'C' and resid 85 through 1205) selection = (chain 'D' and resid 85 through 1205) } 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.530 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 71.290 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.130 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 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 : 0.006 0.542 29860 Z= 0.198 Angle : 0.800 26.841 40512 Z= 0.430 Chirality : 0.049 0.573 4612 Planarity : 0.004 0.106 5088 Dihedral : 15.768 89.714 10828 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.09 % Allowed : 22.31 % Favored : 77.59 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.13), residues: 3632 helix: -1.67 (0.12), residues: 1636 sheet: -1.42 (0.26), residues: 396 loop : -0.45 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 177 HIS 0.004 0.001 HIS C 586 PHE 0.025 0.001 PHE D 932 TYR 0.025 0.001 TYR A 130 ARG 0.009 0.001 ARG A 828 Details of bonding type rmsd hydrogen bonds : bond 0.25453 ( 1217) hydrogen bonds : angle 8.45967 ( 3384) metal coordination : bond 0.23209 ( 16) metal coordination : angle 13.10564 ( 12) covalent geometry : bond 0.00286 (29844) covalent geometry : angle 0.76756 (40500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 560 time to evaluate : 3.112 Fit side-chains revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8099 (m110) cc_final: 0.7328 (p0) REVERT: A 232 ARG cc_start: 0.6242 (mtt90) cc_final: 0.5994 (mmt90) REVERT: A 426 SER cc_start: 0.8059 (t) cc_final: 0.7592 (m) REVERT: A 576 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7714 (tp30) REVERT: A 876 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.5526 (p90) REVERT: A 909 PHE cc_start: 0.8291 (t80) cc_final: 0.7337 (m-80) REVERT: A 1020 ARG cc_start: 0.7803 (mtm110) cc_final: 0.7218 (ptp-170) REVERT: B 388 ASP cc_start: 0.7727 (m-30) cc_final: 0.7445 (m-30) REVERT: B 909 PHE cc_start: 0.8233 (t80) cc_final: 0.7294 (m-80) REVERT: B 1020 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7512 (mtm110) REVERT: C 163 ASN cc_start: 0.7807 (m-40) cc_final: 0.7182 (p0) REVERT: C 176 LEU cc_start: 0.8163 (mt) cc_final: 0.7960 (mm) REVERT: C 426 SER cc_start: 0.8031 (t) cc_final: 0.7560 (m) REVERT: C 576 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7730 (tp30) REVERT: C 792 ASP cc_start: 0.7633 (p0) cc_final: 0.7214 (p0) REVERT: C 909 PHE cc_start: 0.8238 (t80) cc_final: 0.7332 (m-10) REVERT: C 1020 ARG cc_start: 0.7806 (mtm110) cc_final: 0.7481 (mtm110) REVERT: D 174 MET cc_start: 0.7954 (pmm) cc_final: 0.6515 (mpp) REVERT: D 177 TRP cc_start: 0.8388 (t60) cc_final: 0.8081 (t60) REVERT: D 426 SER cc_start: 0.8076 (t) cc_final: 0.7610 (m) REVERT: D 794 LYS cc_start: 0.7652 (tptt) cc_final: 0.7450 (tptt) REVERT: D 909 PHE cc_start: 0.8040 (t80) cc_final: 0.7490 (m-80) REVERT: D 1020 ARG cc_start: 0.7807 (mtm110) cc_final: 0.7484 (mtm110) outliers start: 3 outliers final: 1 residues processed: 561 average time/residue: 0.4651 time to fit residues: 403.2840 Evaluate side-chains 525 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 523 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 1045 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 0.2980 chunk 275 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 285 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 212 optimal weight: 0.1980 chunk 330 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN A 151 GLN A 241 ASN A 369 GLN A 490 GLN A 499 HIS A 505 HIS A 844 HIS A 871 GLN A 879 ASN A 923 HIS A1147 GLN B 119 ASN B 151 GLN B 241 ASN B 369 GLN ** B 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 490 GLN B 499 HIS B 505 HIS B 844 HIS B 871 GLN B 879 ASN B1147 GLN C 119 ASN C 151 GLN C 241 ASN C 369 GLN ** C 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 499 HIS C 505 HIS C 844 HIS C 871 GLN C 879 ASN C1147 GLN D 119 ASN D 151 GLN D 241 ASN D 369 GLN D 490 GLN D 499 HIS D 505 HIS D 844 HIS D 871 GLN D 879 ASN D1147 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.162237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.117335 restraints weight = 35163.816| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.38 r_work: 0.3211 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29860 Z= 0.144 Angle : 0.629 13.159 40512 Z= 0.315 Chirality : 0.044 0.236 4612 Planarity : 0.004 0.042 5088 Dihedral : 4.639 36.791 4023 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.90 % Allowed : 21.58 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 3632 helix: -0.62 (0.12), residues: 1660 sheet: -1.71 (0.25), residues: 396 loop : -0.43 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 177 HIS 0.005 0.001 HIS D 586 PHE 0.017 0.001 PHE D 932 TYR 0.016 0.001 TYR A 130 ARG 0.005 0.000 ARG D 828 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 1217) hydrogen bonds : angle 5.05467 ( 3384) metal coordination : bond 0.01599 ( 16) metal coordination : angle 4.64676 ( 12) covalent geometry : bond 0.00321 (29844) covalent geometry : angle 0.62405 (40500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 595 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8262 (m110) cc_final: 0.7365 (p0) REVERT: A 180 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8333 (mm-40) REVERT: A 222 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7437 (t80) REVERT: A 232 ARG cc_start: 0.6127 (mtt90) cc_final: 0.5904 (mmt90) REVERT: A 354 MET cc_start: 0.6771 (ppp) cc_final: 0.5903 (mtt) REVERT: A 388 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6934 (m-30) REVERT: A 426 SER cc_start: 0.8096 (t) cc_final: 0.7669 (m) REVERT: A 491 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8358 (tp) REVERT: A 576 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7814 (tp30) REVERT: A 792 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7241 (p0) REVERT: A 909 PHE cc_start: 0.8389 (t80) cc_final: 0.7360 (m-80) REVERT: B 174 MET cc_start: 0.8094 (pmm) cc_final: 0.6739 (mpp) REVERT: B 177 TRP cc_start: 0.8409 (t60) cc_final: 0.8118 (t60) REVERT: B 180 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8421 (mm-40) REVERT: B 275 PHE cc_start: 0.7633 (t80) cc_final: 0.7406 (t80) REVERT: B 388 ASP cc_start: 0.7500 (m-30) cc_final: 0.7114 (m-30) REVERT: B 491 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8272 (tp) REVERT: B 570 LYS cc_start: 0.8906 (mmmm) cc_final: 0.8542 (mtmt) REVERT: B 576 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7813 (tp30) REVERT: B 909 PHE cc_start: 0.8356 (t80) cc_final: 0.7366 (m-80) REVERT: C 163 ASN cc_start: 0.7869 (m-40) cc_final: 0.7034 (p0) REVERT: C 177 TRP cc_start: 0.8363 (t60) cc_final: 0.8032 (t60) REVERT: C 180 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8555 (mm-40) REVERT: C 190 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8255 (tm-30) REVERT: C 275 PHE cc_start: 0.7625 (t80) cc_final: 0.7395 (t80) REVERT: C 491 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8257 (tp) REVERT: C 576 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7892 (tp30) REVERT: C 631 GLU cc_start: 0.8064 (mp0) cc_final: 0.7757 (mp0) REVERT: C 787 HIS cc_start: 0.7570 (m90) cc_final: 0.7272 (m90) REVERT: C 792 ASP cc_start: 0.7641 (p0) cc_final: 0.7217 (p0) REVERT: C 909 PHE cc_start: 0.8355 (t80) cc_final: 0.7323 (m-80) REVERT: C 1167 TYR cc_start: 0.7509 (t80) cc_final: 0.7238 (t80) REVERT: D 174 MET cc_start: 0.7894 (pmm) cc_final: 0.6508 (mpp) REVERT: D 177 TRP cc_start: 0.8254 (t60) cc_final: 0.8010 (t60) REVERT: D 180 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8453 (mm-40) REVERT: D 222 PHE cc_start: 0.7852 (OUTLIER) cc_final: 0.7315 (t80) REVERT: D 232 ARG cc_start: 0.6110 (mtt90) cc_final: 0.5899 (mtt-85) REVERT: D 388 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7029 (m-30) REVERT: D 631 GLU cc_start: 0.7799 (mp0) cc_final: 0.7408 (tp30) REVERT: D 843 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7955 (m-30) REVERT: D 909 PHE cc_start: 0.8383 (t80) cc_final: 0.7330 (m-10) REVERT: D 1167 TYR cc_start: 0.7520 (t80) cc_final: 0.7241 (t80) outliers start: 60 outliers final: 26 residues processed: 639 average time/residue: 0.5484 time to fit residues: 546.7978 Evaluate side-chains 566 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 531 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 951 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 59 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 122 optimal weight: 4.9990 chunk 352 optimal weight: 0.9990 chunk 204 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 ASN A1046 HIS D 550 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114351 restraints weight = 35781.350| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.38 r_work: 0.3173 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 29860 Z= 0.194 Angle : 0.611 13.276 40512 Z= 0.305 Chirality : 0.045 0.214 4612 Planarity : 0.004 0.047 5088 Dihedral : 4.595 37.327 4020 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.16 % Allowed : 20.98 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 3632 helix: -0.37 (0.12), residues: 1652 sheet: -1.86 (0.24), residues: 396 loop : -0.44 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.006 0.001 HIS A 586 PHE 0.035 0.002 PHE A 97 TYR 0.014 0.002 TYR A 987 ARG 0.005 0.000 ARG D1020 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 1217) hydrogen bonds : angle 4.76227 ( 3384) metal coordination : bond 0.01309 ( 16) metal coordination : angle 2.96801 ( 12) covalent geometry : bond 0.00469 (29844) covalent geometry : angle 0.60846 (40500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 577 time to evaluate : 3.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.5252 (tttt) cc_final: 0.4886 (ttpt) REVERT: A 153 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.5642 (m-10) REVERT: A 163 ASN cc_start: 0.8282 (m110) cc_final: 0.7568 (t0) REVERT: A 174 MET cc_start: 0.8095 (pmm) cc_final: 0.7142 (tpp) REVERT: A 180 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8200 (mm-40) REVERT: A 222 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7609 (t80) REVERT: A 354 MET cc_start: 0.6902 (ppp) cc_final: 0.5951 (mtt) REVERT: A 426 SER cc_start: 0.8058 (t) cc_final: 0.7621 (m) REVERT: A 576 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7833 (tp30) REVERT: A 792 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7293 (p0) REVERT: A 908 MET cc_start: 0.8722 (mmp) cc_final: 0.8251 (mmt) REVERT: A 909 PHE cc_start: 0.8410 (t80) cc_final: 0.7327 (m-10) REVERT: A 1167 TYR cc_start: 0.7285 (t80) cc_final: 0.7044 (t80) REVERT: B 153 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.5047 (m-10) REVERT: B 174 MET cc_start: 0.8097 (pmm) cc_final: 0.7068 (tpp) REVERT: B 177 TRP cc_start: 0.8387 (t60) cc_final: 0.8168 (t60) REVERT: B 180 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8188 (mm-40) REVERT: B 388 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: B 570 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8340 (pttp) REVERT: B 576 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7919 (tp30) REVERT: B 787 HIS cc_start: 0.7783 (m90) cc_final: 0.7447 (m90) REVERT: B 792 ASP cc_start: 0.7635 (p0) cc_final: 0.7196 (p0) REVERT: B 908 MET cc_start: 0.8697 (mmp) cc_final: 0.8208 (mmt) REVERT: B 909 PHE cc_start: 0.8403 (t80) cc_final: 0.7305 (m-10) REVERT: B 920 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: C 153 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.4667 (m-10) REVERT: C 163 ASN cc_start: 0.7914 (m-40) cc_final: 0.7041 (p0) REVERT: C 180 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8370 (mm-40) REVERT: C 190 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8198 (tm-30) REVERT: C 570 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8335 (pttp) REVERT: C 576 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7938 (tp30) REVERT: C 787 HIS cc_start: 0.7704 (m90) cc_final: 0.7365 (m90) REVERT: C 792 ASP cc_start: 0.7655 (p0) cc_final: 0.7205 (p0) REVERT: C 908 MET cc_start: 0.8741 (mmp) cc_final: 0.8278 (mmt) REVERT: C 909 PHE cc_start: 0.8382 (t80) cc_final: 0.7290 (m-80) REVERT: C 920 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: C 1136 GLN cc_start: 0.5736 (OUTLIER) cc_final: 0.4576 (tm-30) REVERT: C 1167 TYR cc_start: 0.7443 (t80) cc_final: 0.7210 (t80) REVERT: D 153 TYR cc_start: 0.6719 (OUTLIER) cc_final: 0.5648 (m-10) REVERT: D 163 ASN cc_start: 0.8075 (m110) cc_final: 0.7337 (t0) REVERT: D 174 MET cc_start: 0.7912 (pmm) cc_final: 0.6420 (mpp) REVERT: D 177 TRP cc_start: 0.8294 (t60) cc_final: 0.8031 (t60) REVERT: D 180 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8377 (mm-40) REVERT: D 222 PHE cc_start: 0.8072 (OUTLIER) cc_final: 0.7472 (t80) REVERT: D 576 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7931 (tp30) REVERT: D 631 GLU cc_start: 0.7898 (mp0) cc_final: 0.7529 (mp0) REVERT: D 787 HIS cc_start: 0.7623 (m90) cc_final: 0.7288 (m90) REVERT: D 843 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7969 (m-30) REVERT: D 876 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.6093 (p90) REVERT: D 908 MET cc_start: 0.8699 (mmp) cc_final: 0.8237 (mmt) REVERT: D 909 PHE cc_start: 0.8413 (t80) cc_final: 0.7315 (m-10) REVERT: D 1136 GLN cc_start: 0.5763 (OUTLIER) cc_final: 0.4593 (tm-30) REVERT: D 1167 TYR cc_start: 0.7425 (t80) cc_final: 0.7192 (t80) outliers start: 100 outliers final: 63 residues processed: 638 average time/residue: 0.4637 time to fit residues: 461.6809 Evaluate side-chains 614 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 537 time to evaluate : 4.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 829 LYS Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 781 LEU Chi-restraints excluded: chain B residue 809 THR Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 809 THR Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 1136 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 139 optimal weight: 0.6980 chunk 214 optimal weight: 0.9990 chunk 318 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 161 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.162704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120200 restraints weight = 35905.581| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.53 r_work: 0.3202 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29860 Z= 0.115 Angle : 0.561 13.898 40512 Z= 0.279 Chirality : 0.042 0.221 4612 Planarity : 0.004 0.046 5088 Dihedral : 4.333 32.638 4020 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.88 % Allowed : 21.42 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3632 helix: -0.01 (0.13), residues: 1660 sheet: -1.83 (0.24), residues: 396 loop : -0.19 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.006 0.001 HIS A 586 PHE 0.030 0.001 PHE A 97 TYR 0.013 0.001 TYR A 987 ARG 0.006 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 1217) hydrogen bonds : angle 4.51746 ( 3384) metal coordination : bond 0.00683 ( 16) metal coordination : angle 2.17453 ( 12) covalent geometry : bond 0.00265 (29844) covalent geometry : angle 0.55942 (40500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 605 time to evaluate : 3.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.5384 (tttt) cc_final: 0.5118 (ttpt) REVERT: A 163 ASN cc_start: 0.8273 (m110) cc_final: 0.7440 (p0) REVERT: A 174 MET cc_start: 0.7991 (pmm) cc_final: 0.7144 (tpp) REVERT: A 180 GLN cc_start: 0.8747 (mm-40) cc_final: 0.8219 (mm-40) REVERT: A 222 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7715 (t80) REVERT: A 275 PHE cc_start: 0.7665 (t80) cc_final: 0.7323 (t80) REVERT: A 354 MET cc_start: 0.6831 (ppp) cc_final: 0.5862 (mtt) REVERT: A 366 HIS cc_start: 0.8056 (t-90) cc_final: 0.7742 (t-90) REVERT: A 388 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7331 (m-30) REVERT: A 426 SER cc_start: 0.7990 (t) cc_final: 0.7631 (m) REVERT: A 570 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8611 (mtmt) REVERT: A 576 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7882 (tp30) REVERT: A 780 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7657 (ttp80) REVERT: A 787 HIS cc_start: 0.7855 (m90) cc_final: 0.7506 (m90) REVERT: A 792 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7372 (p0) REVERT: A 876 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.6126 (p90) REVERT: A 908 MET cc_start: 0.8823 (mmp) cc_final: 0.8456 (mmt) REVERT: A 909 PHE cc_start: 0.8510 (t80) cc_final: 0.7525 (m-10) REVERT: A 920 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8302 (tt0) REVERT: A 1136 GLN cc_start: 0.5892 (OUTLIER) cc_final: 0.4827 (tm-30) REVERT: B 174 MET cc_start: 0.8020 (pmm) cc_final: 0.7132 (tpp) REVERT: B 177 TRP cc_start: 0.8470 (t60) cc_final: 0.8206 (t60) REVERT: B 275 PHE cc_start: 0.7722 (t80) cc_final: 0.7447 (t80) REVERT: B 388 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: B 426 SER cc_start: 0.8038 (t) cc_final: 0.7675 (m) REVERT: B 570 LYS cc_start: 0.8957 (mmmm) cc_final: 0.8653 (mtmt) REVERT: B 575 TYR cc_start: 0.8348 (m-80) cc_final: 0.8141 (m-80) REVERT: B 576 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7903 (tp30) REVERT: B 787 HIS cc_start: 0.7864 (m90) cc_final: 0.7527 (m90) REVERT: B 792 ASP cc_start: 0.7700 (p0) cc_final: 0.7276 (p0) REVERT: B 909 PHE cc_start: 0.8514 (t80) cc_final: 0.7533 (m-10) REVERT: B 920 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: B 1136 GLN cc_start: 0.5828 (OUTLIER) cc_final: 0.4727 (tm-30) REVERT: B 1167 TYR cc_start: 0.7394 (t80) cc_final: 0.7147 (t80) REVERT: C 163 ASN cc_start: 0.7920 (m-40) cc_final: 0.7138 (p0) REVERT: C 174 MET cc_start: 0.6531 (mpp) cc_final: 0.6037 (tpp) REVERT: C 177 TRP cc_start: 0.8411 (t60) cc_final: 0.8197 (t60) REVERT: C 180 GLN cc_start: 0.8743 (mm-40) cc_final: 0.8281 (mm-40) REVERT: C 190 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8214 (tm-30) REVERT: C 275 PHE cc_start: 0.7711 (t80) cc_final: 0.7455 (t80) REVERT: C 366 HIS cc_start: 0.8125 (t-90) cc_final: 0.7826 (t-90) REVERT: C 388 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7379 (m-30) REVERT: C 418 ARG cc_start: 0.7550 (ptp-110) cc_final: 0.7271 (ptm160) REVERT: C 426 SER cc_start: 0.7994 (t) cc_final: 0.7612 (m) REVERT: C 570 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8654 (mtmt) REVERT: C 576 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7945 (tp30) REVERT: C 780 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7618 (ttp80) REVERT: C 787 HIS cc_start: 0.7785 (m90) cc_final: 0.7468 (m90) REVERT: C 792 ASP cc_start: 0.7679 (p0) cc_final: 0.7252 (p0) REVERT: C 860 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8514 (mt-10) REVERT: C 909 PHE cc_start: 0.8495 (t80) cc_final: 0.7521 (m-80) REVERT: C 920 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: C 1136 GLN cc_start: 0.5878 (OUTLIER) cc_final: 0.4809 (tm-30) REVERT: D 98 LYS cc_start: 0.5110 (tttt) cc_final: 0.4594 (ttpt) REVERT: D 153 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.5499 (m-10) REVERT: D 163 ASN cc_start: 0.8030 (m110) cc_final: 0.7360 (t0) REVERT: D 174 MET cc_start: 0.7980 (pmm) cc_final: 0.6417 (mtt) REVERT: D 177 TRP cc_start: 0.8423 (t60) cc_final: 0.8171 (t60) REVERT: D 180 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8302 (mm-40) REVERT: D 222 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7646 (t80) REVERT: D 354 MET cc_start: 0.6851 (ppp) cc_final: 0.5980 (mtt) REVERT: D 426 SER cc_start: 0.7961 (t) cc_final: 0.7602 (m) REVERT: D 576 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7955 (tp30) REVERT: D 631 GLU cc_start: 0.7989 (mp0) cc_final: 0.7590 (mp0) REVERT: D 787 HIS cc_start: 0.7857 (m90) cc_final: 0.7512 (m90) REVERT: D 792 ASP cc_start: 0.7819 (p0) cc_final: 0.7407 (p0) REVERT: D 843 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: D 876 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.6164 (p90) REVERT: D 908 MET cc_start: 0.8792 (mmp) cc_final: 0.8441 (mmt) REVERT: D 909 PHE cc_start: 0.8464 (t80) cc_final: 0.7505 (m-10) REVERT: D 920 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: D 1136 GLN cc_start: 0.5897 (OUTLIER) cc_final: 0.4830 (tm-30) outliers start: 91 outliers final: 51 residues processed: 664 average time/residue: 0.4670 time to fit residues: 490.7621 Evaluate side-chains 620 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 551 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 920 GLU Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 1136 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 306 optimal weight: 0.0770 chunk 22 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 318 optimal weight: 8.9990 chunk 301 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 400 GLN B 586 HIS B1046 HIS D 614 HIS D1046 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.161989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118339 restraints weight = 35736.203| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.48 r_work: 0.3212 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29860 Z= 0.135 Angle : 0.570 14.331 40512 Z= 0.282 Chirality : 0.043 0.229 4612 Planarity : 0.004 0.051 5088 Dihedral : 4.287 31.869 4020 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.07 % Allowed : 21.90 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3632 helix: 0.11 (0.13), residues: 1660 sheet: -1.81 (0.24), residues: 396 loop : -0.16 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 177 HIS 0.006 0.001 HIS B 586 PHE 0.029 0.001 PHE A 97 TYR 0.015 0.001 TYR D1167 ARG 0.006 0.000 ARG A1020 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 1217) hydrogen bonds : angle 4.45108 ( 3384) metal coordination : bond 0.00658 ( 16) metal coordination : angle 1.88643 ( 12) covalent geometry : bond 0.00323 (29844) covalent geometry : angle 0.56935 (40500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 577 time to evaluate : 3.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LYS cc_start: 0.5326 (tttt) cc_final: 0.5115 (ttpt) REVERT: A 113 LEU cc_start: 0.6632 (OUTLIER) cc_final: 0.6390 (mt) REVERT: A 153 TYR cc_start: 0.6734 (OUTLIER) cc_final: 0.5534 (m-10) REVERT: A 163 ASN cc_start: 0.8276 (m110) cc_final: 0.7607 (t0) REVERT: A 174 MET cc_start: 0.7983 (pmm) cc_final: 0.7189 (tpp) REVERT: A 180 GLN cc_start: 0.8757 (mm-40) cc_final: 0.8220 (mm-40) REVERT: A 209 ARG cc_start: 0.5838 (tpt170) cc_final: 0.5478 (tpt90) REVERT: A 222 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7767 (t80) REVERT: A 275 PHE cc_start: 0.7698 (t80) cc_final: 0.7339 (t80) REVERT: A 354 MET cc_start: 0.6894 (ppp) cc_final: 0.5982 (mtt) REVERT: A 366 HIS cc_start: 0.8086 (t-90) cc_final: 0.7775 (t-90) REVERT: A 388 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: A 426 SER cc_start: 0.7988 (t) cc_final: 0.7615 (m) REVERT: A 570 LYS cc_start: 0.8951 (mmmm) cc_final: 0.8436 (pttp) REVERT: A 576 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7860 (tp30) REVERT: A 780 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7667 (ttp80) REVERT: A 787 HIS cc_start: 0.7825 (m90) cc_final: 0.7484 (m90) REVERT: A 792 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7376 (p0) REVERT: A 876 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.6114 (p90) REVERT: A 908 MET cc_start: 0.8805 (mmp) cc_final: 0.8476 (mmt) REVERT: A 909 PHE cc_start: 0.8486 (t80) cc_final: 0.7509 (m-80) REVERT: A 920 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: A 1136 GLN cc_start: 0.5876 (OUTLIER) cc_final: 0.4848 (tm-30) REVERT: B 174 MET cc_start: 0.8085 (pmm) cc_final: 0.7154 (tpp) REVERT: B 177 TRP cc_start: 0.8448 (t60) cc_final: 0.8107 (t60) REVERT: B 180 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8444 (mm-40) REVERT: B 209 ARG cc_start: 0.5870 (tpt170) cc_final: 0.5488 (tpt90) REVERT: B 275 PHE cc_start: 0.7740 (t80) cc_final: 0.7414 (t80) REVERT: B 388 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: B 400 GLN cc_start: 0.7840 (mm-40) cc_final: 0.7588 (mm110) REVERT: B 426 SER cc_start: 0.7977 (t) cc_final: 0.7620 (m) REVERT: B 570 LYS cc_start: 0.8956 (mmmm) cc_final: 0.8438 (pttp) REVERT: B 575 TYR cc_start: 0.8336 (m-80) cc_final: 0.8050 (m-80) REVERT: B 576 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7917 (tp30) REVERT: B 787 HIS cc_start: 0.7827 (m90) cc_final: 0.7495 (m90) REVERT: B 792 ASP cc_start: 0.7627 (p0) cc_final: 0.7209 (p0) REVERT: B 909 PHE cc_start: 0.8502 (t80) cc_final: 0.7529 (m-80) REVERT: B 920 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: B 951 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6956 (pp20) REVERT: B 1136 GLN cc_start: 0.6084 (OUTLIER) cc_final: 0.5009 (tm-30) REVERT: B 1167 TYR cc_start: 0.7437 (t80) cc_final: 0.7233 (t80) REVERT: C 153 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.4498 (m-10) REVERT: C 163 ASN cc_start: 0.7918 (m-40) cc_final: 0.7108 (p0) REVERT: C 174 MET cc_start: 0.6532 (mpp) cc_final: 0.6025 (tpp) REVERT: C 177 TRP cc_start: 0.8389 (t60) cc_final: 0.8137 (t60) REVERT: C 180 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8239 (mm-40) REVERT: C 190 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8184 (tm-30) REVERT: C 209 ARG cc_start: 0.5786 (tpt170) cc_final: 0.5371 (tpt90) REVERT: C 275 PHE cc_start: 0.7714 (t80) cc_final: 0.7392 (t80) REVERT: C 387 MET cc_start: 0.8466 (mmt) cc_final: 0.8162 (mmm) REVERT: C 388 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: C 418 ARG cc_start: 0.7561 (ptp-110) cc_final: 0.7249 (ptm160) REVERT: C 426 SER cc_start: 0.7933 (t) cc_final: 0.7555 (m) REVERT: C 566 MET cc_start: 0.8078 (ttp) cc_final: 0.7637 (tmm) REVERT: C 570 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8656 (mtmt) REVERT: C 576 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7910 (tp30) REVERT: C 780 ARG cc_start: 0.8163 (ttp80) cc_final: 0.7608 (ttp80) REVERT: C 787 HIS cc_start: 0.7821 (m90) cc_final: 0.7499 (m90) REVERT: C 792 ASP cc_start: 0.7668 (p0) cc_final: 0.7267 (p0) REVERT: C 908 MET cc_start: 0.8767 (mmt) cc_final: 0.8441 (mmt) REVERT: C 909 PHE cc_start: 0.8485 (t80) cc_final: 0.7505 (m-80) REVERT: C 958 PHE cc_start: 0.8591 (p90) cc_final: 0.8277 (p90) REVERT: C 1136 GLN cc_start: 0.5860 (OUTLIER) cc_final: 0.4826 (tm-30) REVERT: D 98 LYS cc_start: 0.5051 (tttt) cc_final: 0.4545 (ttpt) REVERT: D 153 TYR cc_start: 0.6732 (OUTLIER) cc_final: 0.5548 (m-10) REVERT: D 163 ASN cc_start: 0.8027 (m110) cc_final: 0.7358 (t0) REVERT: D 174 MET cc_start: 0.7996 (pmm) cc_final: 0.6511 (mtt) REVERT: D 177 TRP cc_start: 0.8400 (t60) cc_final: 0.8168 (t60) REVERT: D 180 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8284 (mm-40) REVERT: D 195 ILE cc_start: 0.8541 (mm) cc_final: 0.8278 (mt) REVERT: D 222 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7661 (t80) REVERT: D 354 MET cc_start: 0.6862 (ppp) cc_final: 0.5995 (mtt) REVERT: D 426 SER cc_start: 0.7950 (t) cc_final: 0.7588 (m) REVERT: D 566 MET cc_start: 0.8073 (ttp) cc_final: 0.7636 (tmm) REVERT: D 576 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7941 (tp30) REVERT: D 631 GLU cc_start: 0.7992 (mp0) cc_final: 0.7573 (mp0) REVERT: D 780 ARG cc_start: 0.8377 (ttt-90) cc_final: 0.7813 (ttt-90) REVERT: D 783 LYS cc_start: 0.7963 (tttt) cc_final: 0.7594 (tptm) REVERT: D 787 HIS cc_start: 0.7842 (m90) cc_final: 0.7503 (m90) REVERT: D 792 ASP cc_start: 0.7813 (p0) cc_final: 0.7395 (p0) REVERT: D 843 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: D 876 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.6151 (p90) REVERT: D 908 MET cc_start: 0.8759 (mmp) cc_final: 0.8428 (mmt) REVERT: D 909 PHE cc_start: 0.8428 (t80) cc_final: 0.7434 (m-10) REVERT: D 920 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: D 1136 GLN cc_start: 0.5931 (OUTLIER) cc_final: 0.4864 (tm-30) outliers start: 97 outliers final: 59 residues processed: 642 average time/residue: 0.4550 time to fit residues: 460.3014 Evaluate side-chains 629 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 549 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 1136 GLN Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 341 optimal weight: 1.9990 chunk 293 optimal weight: 0.9990 chunk 278 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 243 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 56 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS C 586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.163659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120327 restraints weight = 35933.978| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.48 r_work: 0.3239 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29860 Z= 0.109 Angle : 0.563 14.737 40512 Z= 0.277 Chirality : 0.042 0.237 4612 Planarity : 0.004 0.049 5088 Dihedral : 4.160 28.382 4020 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.13 % Allowed : 22.50 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3632 helix: 0.29 (0.13), residues: 1656 sheet: -1.72 (0.24), residues: 404 loop : -0.12 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 353 HIS 0.005 0.001 HIS D 586 PHE 0.025 0.001 PHE A 97 TYR 0.015 0.001 TYR D1167 ARG 0.008 0.000 ARG D1020 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 1217) hydrogen bonds : angle 4.38275 ( 3384) metal coordination : bond 0.00441 ( 16) metal coordination : angle 1.69810 ( 12) covalent geometry : bond 0.00252 (29844) covalent geometry : angle 0.56263 (40500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 595 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8221 (m110) cc_final: 0.7293 (p0) REVERT: A 174 MET cc_start: 0.8041 (pmm) cc_final: 0.7166 (tpp) REVERT: A 180 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8245 (mm-40) REVERT: A 209 ARG cc_start: 0.5587 (tpt170) cc_final: 0.5236 (tpt90) REVERT: A 222 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7637 (t80) REVERT: A 275 PHE cc_start: 0.7500 (t80) cc_final: 0.7027 (t80) REVERT: A 354 MET cc_start: 0.6856 (ppp) cc_final: 0.6017 (mtt) REVERT: A 388 ASP cc_start: 0.7596 (m-30) cc_final: 0.7310 (m-30) REVERT: A 400 GLN cc_start: 0.7701 (mm-40) cc_final: 0.7065 (mp10) REVERT: A 426 SER cc_start: 0.7941 (t) cc_final: 0.7539 (m) REVERT: A 570 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8391 (pttp) REVERT: A 575 TYR cc_start: 0.8217 (m-80) cc_final: 0.7947 (m-80) REVERT: A 576 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7907 (tp30) REVERT: A 780 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7459 (ttp80) REVERT: A 787 HIS cc_start: 0.7841 (m90) cc_final: 0.7479 (m90) REVERT: A 792 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7047 (p0) REVERT: A 876 TYR cc_start: 0.7786 (OUTLIER) cc_final: 0.5974 (p90) REVERT: A 908 MET cc_start: 0.8666 (mmp) cc_final: 0.8299 (mmt) REVERT: A 909 PHE cc_start: 0.8306 (t80) cc_final: 0.7240 (m-80) REVERT: A 920 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: A 951 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6851 (pp20) REVERT: A 958 PHE cc_start: 0.8490 (p90) cc_final: 0.8194 (p90) REVERT: A 1136 GLN cc_start: 0.5602 (OUTLIER) cc_final: 0.4733 (tm-30) REVERT: B 174 MET cc_start: 0.8039 (pmm) cc_final: 0.7102 (tpp) REVERT: B 177 TRP cc_start: 0.8362 (t60) cc_final: 0.7979 (t60) REVERT: B 180 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8495 (mm-40) REVERT: B 209 ARG cc_start: 0.5614 (tpt170) cc_final: 0.5238 (tpt90) REVERT: B 275 PHE cc_start: 0.7606 (t80) cc_final: 0.7322 (t80) REVERT: B 388 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7391 (m-30) REVERT: B 418 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6953 (ptp-110) REVERT: B 426 SER cc_start: 0.7926 (t) cc_final: 0.7515 (m) REVERT: B 570 LYS cc_start: 0.8873 (mmmm) cc_final: 0.8328 (pttp) REVERT: B 575 TYR cc_start: 0.8231 (m-80) cc_final: 0.7972 (m-80) REVERT: B 576 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7927 (tp30) REVERT: B 631 GLU cc_start: 0.8051 (mp0) cc_final: 0.7492 (tt0) REVERT: B 787 HIS cc_start: 0.7812 (m90) cc_final: 0.7493 (m90) REVERT: B 792 ASP cc_start: 0.7701 (p0) cc_final: 0.7274 (p0) REVERT: B 908 MET cc_start: 0.8620 (mmp) cc_final: 0.8337 (mmt) REVERT: B 909 PHE cc_start: 0.8309 (t80) cc_final: 0.7256 (m-80) REVERT: B 951 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6894 (pp20) REVERT: B 958 PHE cc_start: 0.8525 (p90) cc_final: 0.8135 (p90) REVERT: C 113 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.6190 (mt) REVERT: C 163 ASN cc_start: 0.7867 (m-40) cc_final: 0.6992 (p0) REVERT: C 174 MET cc_start: 0.6480 (mpp) cc_final: 0.5934 (tpp) REVERT: C 177 TRP cc_start: 0.8270 (t60) cc_final: 0.8021 (t60) REVERT: C 180 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8241 (mm-40) REVERT: C 190 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8136 (tm-30) REVERT: C 192 MET cc_start: 0.8027 (mmt) cc_final: 0.7623 (mmm) REVERT: C 199 TYR cc_start: 0.7886 (t80) cc_final: 0.7643 (t80) REVERT: C 209 ARG cc_start: 0.5595 (tpt170) cc_final: 0.5227 (tpt90) REVERT: C 275 PHE cc_start: 0.7567 (t80) cc_final: 0.7264 (t80) REVERT: C 388 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7315 (m-30) REVERT: C 418 ARG cc_start: 0.7406 (ptp-110) cc_final: 0.6722 (ptp90) REVERT: C 426 SER cc_start: 0.7889 (t) cc_final: 0.7464 (m) REVERT: C 566 MET cc_start: 0.7993 (ttp) cc_final: 0.7451 (tmm) REVERT: C 570 LYS cc_start: 0.8817 (mmmm) cc_final: 0.8393 (pttp) REVERT: C 575 TYR cc_start: 0.8265 (m-80) cc_final: 0.8018 (m-80) REVERT: C 576 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7871 (tp30) REVERT: C 780 ARG cc_start: 0.8009 (ttp80) cc_final: 0.7409 (ttp80) REVERT: C 787 HIS cc_start: 0.7756 (m90) cc_final: 0.7447 (m90) REVERT: C 792 ASP cc_start: 0.7609 (p0) cc_final: 0.7188 (p0) REVERT: C 830 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7670 (pt0) REVERT: C 860 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8479 (mt-10) REVERT: C 908 MET cc_start: 0.8654 (mmt) cc_final: 0.8285 (mmt) REVERT: C 909 PHE cc_start: 0.8290 (t80) cc_final: 0.7215 (m-80) REVERT: C 958 PHE cc_start: 0.8473 (p90) cc_final: 0.8097 (p90) REVERT: C 1136 GLN cc_start: 0.5857 (OUTLIER) cc_final: 0.4962 (tm-30) REVERT: D 98 LYS cc_start: 0.4799 (tttt) cc_final: 0.4328 (ttpt) REVERT: D 174 MET cc_start: 0.8024 (pmm) cc_final: 0.6555 (mtt) REVERT: D 177 TRP cc_start: 0.8298 (t60) cc_final: 0.8045 (t60) REVERT: D 180 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8293 (mm-40) REVERT: D 195 ILE cc_start: 0.8362 (mm) cc_final: 0.8134 (mt) REVERT: D 209 ARG cc_start: 0.5558 (tpt170) cc_final: 0.5183 (tpt90) REVERT: D 222 PHE cc_start: 0.8113 (OUTLIER) cc_final: 0.7627 (t80) REVERT: D 354 MET cc_start: 0.7005 (ppp) cc_final: 0.6112 (mtt) REVERT: D 388 ASP cc_start: 0.7591 (m-30) cc_final: 0.7351 (m-30) REVERT: D 400 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7195 (mp10) REVERT: D 426 SER cc_start: 0.7911 (t) cc_final: 0.7506 (m) REVERT: D 566 MET cc_start: 0.7980 (ttp) cc_final: 0.7445 (tmm) REVERT: D 575 TYR cc_start: 0.8223 (m-80) cc_final: 0.7947 (m-80) REVERT: D 576 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7847 (tp30) REVERT: D 631 GLU cc_start: 0.7984 (mp0) cc_final: 0.7483 (mp0) REVERT: D 787 HIS cc_start: 0.7748 (m90) cc_final: 0.7428 (m90) REVERT: D 792 ASP cc_start: 0.7759 (p0) cc_final: 0.7380 (p0) REVERT: D 876 TYR cc_start: 0.7876 (OUTLIER) cc_final: 0.6037 (p90) REVERT: D 908 MET cc_start: 0.8639 (mmp) cc_final: 0.8281 (mmt) REVERT: D 909 PHE cc_start: 0.8250 (t80) cc_final: 0.7165 (m-10) REVERT: D 920 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8212 (tt0) REVERT: D 1136 GLN cc_start: 0.5730 (OUTLIER) cc_final: 0.4854 (tm-30) outliers start: 99 outliers final: 56 residues processed: 654 average time/residue: 0.4257 time to fit residues: 435.6110 Evaluate side-chains 633 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 561 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain B residue 1138 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 1136 GLN Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 144 optimal weight: 6.9990 chunk 285 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 356 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 327 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 131 optimal weight: 0.9980 chunk 148 optimal weight: 0.2980 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS A 586 HIS D 923 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.163064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118367 restraints weight = 35940.729| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.55 r_work: 0.3205 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29860 Z= 0.150 Angle : 0.583 14.808 40512 Z= 0.287 Chirality : 0.044 0.242 4612 Planarity : 0.004 0.050 5088 Dihedral : 4.194 29.190 4020 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.39 % Allowed : 22.44 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3632 helix: 0.30 (0.13), residues: 1660 sheet: -1.76 (0.25), residues: 412 loop : -0.09 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.012 0.001 HIS A 366 PHE 0.020 0.001 PHE B 932 TYR 0.017 0.001 TYR B1167 ARG 0.006 0.000 ARG D1020 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 1217) hydrogen bonds : angle 4.39688 ( 3384) metal coordination : bond 0.00577 ( 16) metal coordination : angle 1.60611 ( 12) covalent geometry : bond 0.00364 (29844) covalent geometry : angle 0.58251 (40500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 570 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 TYR cc_start: 0.6751 (OUTLIER) cc_final: 0.4715 (m-10) REVERT: A 163 ASN cc_start: 0.8267 (m110) cc_final: 0.7389 (p0) REVERT: A 174 MET cc_start: 0.7986 (pmm) cc_final: 0.7134 (tpp) REVERT: A 180 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8194 (mm-40) REVERT: A 195 ILE cc_start: 0.8570 (mm) cc_final: 0.8317 (mt) REVERT: A 199 TYR cc_start: 0.7873 (t80) cc_final: 0.7670 (t80) REVERT: A 209 ARG cc_start: 0.5691 (tpt170) cc_final: 0.5320 (tpt90) REVERT: A 222 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7762 (t80) REVERT: A 275 PHE cc_start: 0.7852 (t80) cc_final: 0.7539 (t80) REVERT: A 354 MET cc_start: 0.6914 (ppp) cc_final: 0.6085 (mtt) REVERT: A 388 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: A 400 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7204 (mp10) REVERT: A 426 SER cc_start: 0.7961 (t) cc_final: 0.7612 (m) REVERT: A 566 MET cc_start: 0.7387 (ppp) cc_final: 0.7146 (tmm) REVERT: A 570 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8486 (pttp) REVERT: A 575 TYR cc_start: 0.8307 (m-80) cc_final: 0.8008 (m-80) REVERT: A 576 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7931 (tp30) REVERT: A 780 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7679 (ttp80) REVERT: A 787 HIS cc_start: 0.7953 (m90) cc_final: 0.7564 (m90) REVERT: A 792 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7111 (p0) REVERT: A 843 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8072 (m-30) REVERT: A 876 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.6114 (p90) REVERT: A 908 MET cc_start: 0.8791 (mmp) cc_final: 0.8463 (mmt) REVERT: A 909 PHE cc_start: 0.8459 (t80) cc_final: 0.7507 (m-80) REVERT: A 920 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: A 951 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6860 (pp20) REVERT: A 958 PHE cc_start: 0.8561 (p90) cc_final: 0.8214 (p90) REVERT: A 1136 GLN cc_start: 0.5939 (OUTLIER) cc_final: 0.4951 (tm-30) REVERT: B 163 ASN cc_start: 0.7126 (p0) cc_final: 0.6880 (p0) REVERT: B 174 MET cc_start: 0.8029 (pmm) cc_final: 0.7125 (tpp) REVERT: B 177 TRP cc_start: 0.8451 (t60) cc_final: 0.8073 (t60) REVERT: B 180 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8469 (mm-40) REVERT: B 209 ARG cc_start: 0.5717 (tpt170) cc_final: 0.5320 (tpp-160) REVERT: B 275 PHE cc_start: 0.7899 (t80) cc_final: 0.7633 (t80) REVERT: B 388 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: B 418 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7055 (ptp-110) REVERT: B 426 SER cc_start: 0.7960 (t) cc_final: 0.7616 (m) REVERT: B 566 MET cc_start: 0.7491 (ppp) cc_final: 0.7234 (tmm) REVERT: B 570 LYS cc_start: 0.8932 (mmmm) cc_final: 0.8426 (pttp) REVERT: B 575 TYR cc_start: 0.8314 (m-80) cc_final: 0.8032 (m-80) REVERT: B 576 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7907 (tp30) REVERT: B 787 HIS cc_start: 0.7863 (m90) cc_final: 0.7523 (m90) REVERT: B 792 ASP cc_start: 0.7708 (p0) cc_final: 0.7303 (p0) REVERT: B 876 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.6229 (p90) REVERT: B 908 MET cc_start: 0.8758 (mmp) cc_final: 0.8491 (mmt) REVERT: B 909 PHE cc_start: 0.8466 (t80) cc_final: 0.7535 (m-10) REVERT: B 920 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: B 951 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6899 (pp20) REVERT: B 958 PHE cc_start: 0.8545 (p90) cc_final: 0.8245 (p90) REVERT: B 1136 GLN cc_start: 0.6088 (OUTLIER) cc_final: 0.5062 (tm-30) REVERT: C 153 TYR cc_start: 0.6731 (OUTLIER) cc_final: 0.4579 (m-10) REVERT: C 163 ASN cc_start: 0.7911 (m-40) cc_final: 0.7108 (p0) REVERT: C 174 MET cc_start: 0.6435 (mpp) cc_final: 0.5925 (tpp) REVERT: C 177 TRP cc_start: 0.8391 (t60) cc_final: 0.8126 (t60) REVERT: C 180 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8199 (mm-40) REVERT: C 190 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8198 (tm-30) REVERT: C 199 TYR cc_start: 0.7961 (t80) cc_final: 0.7691 (t80) REVERT: C 209 ARG cc_start: 0.5640 (tpt170) cc_final: 0.5258 (tpt90) REVERT: C 275 PHE cc_start: 0.7863 (t80) cc_final: 0.7552 (t80) REVERT: C 418 ARG cc_start: 0.7554 (ptp-110) cc_final: 0.6951 (ptp-170) REVERT: C 426 SER cc_start: 0.7922 (t) cc_final: 0.7552 (m) REVERT: C 566 MET cc_start: 0.8136 (ttp) cc_final: 0.7647 (tmm) REVERT: C 570 LYS cc_start: 0.8867 (mmmm) cc_final: 0.8484 (pttp) REVERT: C 575 TYR cc_start: 0.8350 (m-80) cc_final: 0.8071 (m-80) REVERT: C 576 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7927 (tp30) REVERT: C 780 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7658 (ttp80) REVERT: C 787 HIS cc_start: 0.7846 (m90) cc_final: 0.7519 (m90) REVERT: C 792 ASP cc_start: 0.7704 (p0) cc_final: 0.6969 (p0) REVERT: C 830 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7893 (pt0) REVERT: C 908 MET cc_start: 0.8766 (mmt) cc_final: 0.8444 (mmt) REVERT: C 909 PHE cc_start: 0.8455 (t80) cc_final: 0.7495 (m-80) REVERT: C 958 PHE cc_start: 0.8575 (p90) cc_final: 0.8289 (p90) REVERT: C 1136 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.5044 (tm-30) REVERT: D 98 LYS cc_start: 0.4989 (tttt) cc_final: 0.4475 (ttpt) REVERT: D 153 TYR cc_start: 0.6771 (OUTLIER) cc_final: 0.5625 (m-10) REVERT: D 163 ASN cc_start: 0.8078 (m110) cc_final: 0.7389 (t0) REVERT: D 177 TRP cc_start: 0.8392 (t60) cc_final: 0.8148 (t60) REVERT: D 180 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8283 (mm-40) REVERT: D 195 ILE cc_start: 0.8470 (mm) cc_final: 0.8254 (mt) REVERT: D 209 ARG cc_start: 0.5836 (tpt170) cc_final: 0.5428 (tpt90) REVERT: D 222 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7744 (t80) REVERT: D 354 MET cc_start: 0.6985 (ppp) cc_final: 0.6124 (mtt) REVERT: D 418 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7124 (ptp-110) REVERT: D 426 SER cc_start: 0.7982 (t) cc_final: 0.7639 (m) REVERT: D 566 MET cc_start: 0.8153 (ttp) cc_final: 0.7613 (tmm) REVERT: D 575 TYR cc_start: 0.8332 (m-80) cc_final: 0.8042 (m-80) REVERT: D 576 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7943 (tp30) REVERT: D 631 GLU cc_start: 0.8043 (mp0) cc_final: 0.7572 (mp0) REVERT: D 780 ARG cc_start: 0.8350 (ttt180) cc_final: 0.7937 (ttt-90) REVERT: D 787 HIS cc_start: 0.7850 (m90) cc_final: 0.7510 (m90) REVERT: D 792 ASP cc_start: 0.7805 (p0) cc_final: 0.7425 (p0) REVERT: D 843 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: D 876 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.6164 (p90) REVERT: D 908 MET cc_start: 0.8764 (mmp) cc_final: 0.8458 (mmt) REVERT: D 909 PHE cc_start: 0.8405 (t80) cc_final: 0.7438 (m-10) REVERT: D 920 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: D 951 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6869 (pp20) REVERT: D 1136 GLN cc_start: 0.6037 (OUTLIER) cc_final: 0.5080 (tm-30) outliers start: 107 outliers final: 64 residues processed: 639 average time/residue: 0.4303 time to fit residues: 430.2389 Evaluate side-chains 647 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 558 time to evaluate : 3.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 TYR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 498 PHE Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 972 ILE Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 153 TYR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 153 TYR Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 1136 GLN Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 329 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 248 optimal weight: 0.0040 chunk 170 optimal weight: 1.9990 chunk 269 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 332 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 chunk 356 optimal weight: 1.9990 chunk 339 optimal weight: 0.0870 overall best weight: 0.7174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS C 366 HIS C 614 HIS C 923 HIS D 586 HIS D 812 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.164389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.121851 restraints weight = 36095.472| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.57 r_work: 0.3227 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29860 Z= 0.107 Angle : 0.571 15.666 40512 Z= 0.279 Chirality : 0.042 0.253 4612 Planarity : 0.004 0.051 5088 Dihedral : 4.082 25.415 4020 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.78 % Allowed : 23.54 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3632 helix: 0.50 (0.13), residues: 1656 sheet: -1.60 (0.25), residues: 404 loop : -0.08 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 204 HIS 0.012 0.001 HIS A 366 PHE 0.026 0.001 PHE D 275 TYR 0.025 0.001 TYR C 582 ARG 0.007 0.000 ARG A1020 Details of bonding type rmsd hydrogen bonds : bond 0.03251 ( 1217) hydrogen bonds : angle 4.35554 ( 3384) metal coordination : bond 0.00383 ( 16) metal coordination : angle 1.54516 ( 12) covalent geometry : bond 0.00248 (29844) covalent geometry : angle 0.57043 (40500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 584 time to evaluate : 4.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8219 (m110) cc_final: 0.7395 (p0) REVERT: A 174 MET cc_start: 0.8065 (pmm) cc_final: 0.7203 (tpp) REVERT: A 180 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8189 (mm-40) REVERT: A 195 ILE cc_start: 0.8405 (mm) cc_final: 0.8189 (mt) REVERT: A 209 ARG cc_start: 0.5638 (tpt170) cc_final: 0.5207 (tpp-160) REVERT: A 222 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7649 (t80) REVERT: A 275 PHE cc_start: 0.7645 (t80) cc_final: 0.7239 (t80) REVERT: A 279 LEU cc_start: 0.8560 (mt) cc_final: 0.8351 (mt) REVERT: A 354 MET cc_start: 0.6946 (ppp) cc_final: 0.6096 (mtt) REVERT: A 388 ASP cc_start: 0.7658 (m-30) cc_final: 0.7388 (m-30) REVERT: A 400 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7070 (mp10) REVERT: A 426 SER cc_start: 0.7966 (t) cc_final: 0.7583 (m) REVERT: A 566 MET cc_start: 0.7413 (ppp) cc_final: 0.7101 (tmm) REVERT: A 570 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8372 (pttp) REVERT: A 575 TYR cc_start: 0.8182 (m-80) cc_final: 0.7881 (m-80) REVERT: A 576 GLU cc_start: 0.8413 (tm-30) cc_final: 0.7860 (tp30) REVERT: A 600 ARG cc_start: 0.6512 (mtp180) cc_final: 0.6229 (mtt-85) REVERT: A 780 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7430 (ttp80) REVERT: A 787 HIS cc_start: 0.7846 (m90) cc_final: 0.7477 (m90) REVERT: A 792 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7043 (p0) REVERT: A 843 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7990 (m-30) REVERT: A 876 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.6037 (p90) REVERT: A 909 PHE cc_start: 0.8255 (t80) cc_final: 0.7139 (m-80) REVERT: A 920 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7824 (tt0) REVERT: A 951 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6863 (pp20) REVERT: A 958 PHE cc_start: 0.8449 (p90) cc_final: 0.8101 (p90) REVERT: A 1020 ARG cc_start: 0.8039 (mtm110) cc_final: 0.7461 (ptp-170) REVERT: A 1136 GLN cc_start: 0.5703 (OUTLIER) cc_final: 0.4922 (tm-30) REVERT: B 174 MET cc_start: 0.8062 (pmm) cc_final: 0.7160 (tpp) REVERT: B 177 TRP cc_start: 0.8338 (t60) cc_final: 0.7949 (t60) REVERT: B 180 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8535 (mm-40) REVERT: B 209 ARG cc_start: 0.5734 (tpt170) cc_final: 0.5353 (tpp-160) REVERT: B 275 PHE cc_start: 0.7717 (t80) cc_final: 0.7424 (t80) REVERT: B 388 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: B 400 GLN cc_start: 0.7874 (mm110) cc_final: 0.7275 (mp10) REVERT: B 418 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6796 (ptm-80) REVERT: B 426 SER cc_start: 0.7930 (t) cc_final: 0.7532 (m) REVERT: B 566 MET cc_start: 0.7454 (ppp) cc_final: 0.7153 (tmm) REVERT: B 570 LYS cc_start: 0.8788 (mmmm) cc_final: 0.8355 (pttp) REVERT: B 575 TYR cc_start: 0.8215 (m-80) cc_final: 0.7922 (m-80) REVERT: B 576 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7820 (tp30) REVERT: B 631 GLU cc_start: 0.8112 (mp0) cc_final: 0.7543 (tt0) REVERT: B 787 HIS cc_start: 0.7781 (m90) cc_final: 0.7466 (m90) REVERT: B 792 ASP cc_start: 0.7681 (p0) cc_final: 0.7280 (p0) REVERT: B 908 MET cc_start: 0.8597 (mmp) cc_final: 0.8310 (mmt) REVERT: B 909 PHE cc_start: 0.8265 (t80) cc_final: 0.7178 (m-10) REVERT: B 920 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: B 951 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7009 (pp20) REVERT: B 958 PHE cc_start: 0.8457 (p90) cc_final: 0.8092 (p90) REVERT: C 163 ASN cc_start: 0.7854 (m-40) cc_final: 0.7101 (p0) REVERT: C 174 MET cc_start: 0.6445 (mpp) cc_final: 0.5936 (tpp) REVERT: C 180 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8211 (mm-40) REVERT: C 190 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8103 (tm-30) REVERT: C 199 TYR cc_start: 0.7851 (t80) cc_final: 0.7580 (t80) REVERT: C 209 ARG cc_start: 0.5437 (tpt170) cc_final: 0.5081 (tpp-160) REVERT: C 275 PHE cc_start: 0.7628 (t80) cc_final: 0.7354 (t80) REVERT: C 388 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7467 (m-30) REVERT: C 418 ARG cc_start: 0.7382 (ptp-110) cc_final: 0.6755 (ptp-170) REVERT: C 426 SER cc_start: 0.7912 (t) cc_final: 0.7507 (m) REVERT: C 566 MET cc_start: 0.8000 (ttp) cc_final: 0.7540 (tmm) REVERT: C 570 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8382 (pttp) REVERT: C 575 TYR cc_start: 0.8226 (m-80) cc_final: 0.7991 (m-80) REVERT: C 576 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7853 (tp30) REVERT: C 780 ARG cc_start: 0.8167 (ttp80) cc_final: 0.7544 (ttp80) REVERT: C 787 HIS cc_start: 0.7789 (m90) cc_final: 0.7474 (m90) REVERT: C 792 ASP cc_start: 0.7534 (p0) cc_final: 0.6787 (p0) REVERT: C 830 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7753 (pt0) REVERT: C 908 MET cc_start: 0.8690 (mmt) cc_final: 0.8331 (mmt) REVERT: C 909 PHE cc_start: 0.8238 (t80) cc_final: 0.7144 (m-80) REVERT: C 930 MET cc_start: 0.9043 (mmm) cc_final: 0.8828 (mmm) REVERT: C 951 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6400 (pp20) REVERT: C 958 PHE cc_start: 0.8369 (p90) cc_final: 0.8026 (p90) REVERT: C 1136 GLN cc_start: 0.5731 (OUTLIER) cc_final: 0.4948 (tm-30) REVERT: D 98 LYS cc_start: 0.4830 (tttt) cc_final: 0.4366 (ttpt) REVERT: D 174 MET cc_start: 0.8003 (pmm) cc_final: 0.6592 (mtt) REVERT: D 177 TRP cc_start: 0.8295 (t60) cc_final: 0.7994 (t60) REVERT: D 180 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8291 (mm-40) REVERT: D 199 TYR cc_start: 0.7864 (t80) cc_final: 0.7616 (t80) REVERT: D 209 ARG cc_start: 0.5606 (tpt170) cc_final: 0.5177 (tpp-160) REVERT: D 222 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7651 (t80) REVERT: D 354 MET cc_start: 0.7014 (ppp) cc_final: 0.6071 (mtt) REVERT: D 366 HIS cc_start: 0.7971 (t-90) cc_final: 0.7644 (t-90) REVERT: D 388 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: D 400 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7162 (mp10) REVERT: D 426 SER cc_start: 0.7941 (t) cc_final: 0.7564 (m) REVERT: D 566 MET cc_start: 0.8008 (ttp) cc_final: 0.7488 (tmm) REVERT: D 575 TYR cc_start: 0.8220 (m-80) cc_final: 0.7921 (m-80) REVERT: D 576 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7864 (tp30) REVERT: D 631 GLU cc_start: 0.8023 (mp0) cc_final: 0.7500 (mp0) REVERT: D 780 ARG cc_start: 0.8116 (ttt180) cc_final: 0.7715 (ttp80) REVERT: D 787 HIS cc_start: 0.7765 (m90) cc_final: 0.7444 (m90) REVERT: D 792 ASP cc_start: 0.7742 (p0) cc_final: 0.7340 (p0) REVERT: D 876 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.6008 (p90) REVERT: D 908 MET cc_start: 0.8664 (mmp) cc_final: 0.8326 (mmt) REVERT: D 909 PHE cc_start: 0.8232 (t80) cc_final: 0.7124 (m-10) REVERT: D 920 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: D 951 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6849 (pp20) REVERT: D 958 PHE cc_start: 0.8443 (p90) cc_final: 0.8092 (p90) REVERT: D 1136 GLN cc_start: 0.5748 (OUTLIER) cc_final: 0.4959 (tm-30) outliers start: 88 outliers final: 56 residues processed: 640 average time/residue: 0.6094 time to fit residues: 616.8158 Evaluate side-chains 644 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 568 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 388 ASP Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 878 ASP Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 388 ASP Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 1136 GLN Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 326 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 271 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 292 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 ASN B 366 HIS C 366 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.163968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118682 restraints weight = 36042.983| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.42 r_work: 0.3228 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29860 Z= 0.121 Angle : 0.582 15.795 40512 Z= 0.283 Chirality : 0.043 0.259 4612 Planarity : 0.004 0.047 5088 Dihedral : 4.066 24.769 4020 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.10 % Allowed : 23.23 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3632 helix: 0.52 (0.13), residues: 1672 sheet: -1.56 (0.25), residues: 404 loop : -0.06 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 353 HIS 0.013 0.001 HIS C 366 PHE 0.018 0.001 PHE D 222 TYR 0.026 0.001 TYR D 582 ARG 0.007 0.000 ARG D1020 Details of bonding type rmsd hydrogen bonds : bond 0.03265 ( 1217) hydrogen bonds : angle 4.34409 ( 3384) metal coordination : bond 0.00408 ( 16) metal coordination : angle 1.46731 ( 12) covalent geometry : bond 0.00285 (29844) covalent geometry : angle 0.58135 (40500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 574 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8255 (m110) cc_final: 0.7424 (p0) REVERT: A 174 MET cc_start: 0.8061 (pmm) cc_final: 0.7208 (tpp) REVERT: A 180 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8189 (mm-40) REVERT: A 195 ILE cc_start: 0.8379 (mm) cc_final: 0.8175 (mt) REVERT: A 209 ARG cc_start: 0.5841 (tpt170) cc_final: 0.5468 (tpp-160) REVERT: A 222 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7640 (t80) REVERT: A 275 PHE cc_start: 0.7674 (t80) cc_final: 0.7269 (t80) REVERT: A 279 LEU cc_start: 0.8579 (mt) cc_final: 0.8348 (mt) REVERT: A 354 MET cc_start: 0.6835 (ppp) cc_final: 0.6162 (mtt) REVERT: A 388 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7411 (m-30) REVERT: A 400 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7030 (mp10) REVERT: A 426 SER cc_start: 0.7966 (t) cc_final: 0.7587 (m) REVERT: A 566 MET cc_start: 0.7557 (ppp) cc_final: 0.7211 (tmm) REVERT: A 570 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8375 (pttp) REVERT: A 575 TYR cc_start: 0.8089 (m-80) cc_final: 0.7753 (m-80) REVERT: A 576 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7862 (tp30) REVERT: A 600 ARG cc_start: 0.6552 (mtp180) cc_final: 0.6282 (mtt-85) REVERT: A 780 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7507 (ttp80) REVERT: A 787 HIS cc_start: 0.7852 (m90) cc_final: 0.7482 (m90) REVERT: A 792 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7041 (p0) REVERT: A 843 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7994 (m-30) REVERT: A 876 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.5986 (p90) REVERT: A 908 MET cc_start: 0.8656 (mmp) cc_final: 0.8365 (mmt) REVERT: A 909 PHE cc_start: 0.8229 (t80) cc_final: 0.7161 (m-10) REVERT: A 920 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: A 951 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6893 (pp20) REVERT: A 958 PHE cc_start: 0.8439 (p90) cc_final: 0.8045 (p90) REVERT: A 1136 GLN cc_start: 0.5693 (OUTLIER) cc_final: 0.4940 (tm-30) REVERT: B 163 ASN cc_start: 0.7124 (p0) cc_final: 0.6853 (p0) REVERT: B 174 MET cc_start: 0.8084 (pmm) cc_final: 0.7173 (tpp) REVERT: B 177 TRP cc_start: 0.8326 (t60) cc_final: 0.7845 (t60) REVERT: B 180 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8510 (mm-40) REVERT: B 209 ARG cc_start: 0.5897 (tpt170) cc_final: 0.5376 (tpt90) REVERT: B 275 PHE cc_start: 0.7644 (t80) cc_final: 0.7434 (t80) REVERT: B 388 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: B 400 GLN cc_start: 0.7864 (mm110) cc_final: 0.7270 (mp10) REVERT: B 418 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6910 (ptm-80) REVERT: B 426 SER cc_start: 0.7926 (t) cc_final: 0.7532 (m) REVERT: B 566 MET cc_start: 0.7619 (ppp) cc_final: 0.7279 (tmm) REVERT: B 570 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8368 (pttp) REVERT: B 575 TYR cc_start: 0.8156 (m-80) cc_final: 0.7840 (m-80) REVERT: B 576 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7830 (tp30) REVERT: B 631 GLU cc_start: 0.8124 (mp0) cc_final: 0.7536 (tt0) REVERT: B 787 HIS cc_start: 0.7829 (m90) cc_final: 0.7515 (m90) REVERT: B 792 ASP cc_start: 0.7622 (p0) cc_final: 0.7191 (p0) REVERT: B 876 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.6084 (p90) REVERT: B 908 MET cc_start: 0.8589 (mmp) cc_final: 0.8285 (mmt) REVERT: B 909 PHE cc_start: 0.8245 (t80) cc_final: 0.7186 (m-10) REVERT: B 920 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7760 (tt0) REVERT: B 951 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.7032 (pp20) REVERT: B 958 PHE cc_start: 0.8428 (p90) cc_final: 0.8038 (p90) REVERT: B 1136 GLN cc_start: 0.5868 (OUTLIER) cc_final: 0.5044 (tm-30) REVERT: C 163 ASN cc_start: 0.7849 (m-40) cc_final: 0.7105 (p0) REVERT: C 174 MET cc_start: 0.6419 (mpp) cc_final: 0.5908 (tpp) REVERT: C 180 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8221 (mm-40) REVERT: C 190 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8124 (tm-30) REVERT: C 199 TYR cc_start: 0.7823 (t80) cc_final: 0.7512 (t80) REVERT: C 209 ARG cc_start: 0.5665 (tpt170) cc_final: 0.5305 (tpp-160) REVERT: C 275 PHE cc_start: 0.7650 (t80) cc_final: 0.7346 (t80) REVERT: C 418 ARG cc_start: 0.7420 (ptp-110) cc_final: 0.6846 (ptp-170) REVERT: C 426 SER cc_start: 0.7907 (t) cc_final: 0.7520 (m) REVERT: C 566 MET cc_start: 0.7998 (ttp) cc_final: 0.7416 (tmm) REVERT: C 570 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8412 (pttp) REVERT: C 575 TYR cc_start: 0.8225 (m-80) cc_final: 0.7935 (m-80) REVERT: C 576 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7874 (tp30) REVERT: C 780 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7571 (ttp80) REVERT: C 787 HIS cc_start: 0.7735 (m90) cc_final: 0.7418 (m90) REVERT: C 792 ASP cc_start: 0.7467 (p0) cc_final: 0.6756 (p0) REVERT: C 830 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7779 (pt0) REVERT: C 909 PHE cc_start: 0.8218 (t80) cc_final: 0.7169 (m-80) REVERT: C 930 MET cc_start: 0.9058 (mmm) cc_final: 0.8818 (mmm) REVERT: C 951 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6514 (pp20) REVERT: C 958 PHE cc_start: 0.8382 (p90) cc_final: 0.8035 (p90) REVERT: C 1136 GLN cc_start: 0.5705 (OUTLIER) cc_final: 0.4944 (tm-30) REVERT: D 98 LYS cc_start: 0.4853 (tttt) cc_final: 0.4384 (ttpt) REVERT: D 174 MET cc_start: 0.7999 (pmm) cc_final: 0.6575 (mtt) REVERT: D 177 TRP cc_start: 0.8309 (t60) cc_final: 0.7994 (t60) REVERT: D 180 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8309 (mm-40) REVERT: D 199 TYR cc_start: 0.7885 (t80) cc_final: 0.7630 (t80) REVERT: D 209 ARG cc_start: 0.5641 (tpt170) cc_final: 0.5211 (tpp-160) REVERT: D 222 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7630 (t80) REVERT: D 354 MET cc_start: 0.7043 (ppp) cc_final: 0.6148 (mtt) REVERT: D 366 HIS cc_start: 0.8053 (t-90) cc_final: 0.7724 (t-90) REVERT: D 400 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7089 (mp10) REVERT: D 418 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6849 (ptm-80) REVERT: D 426 SER cc_start: 0.7941 (t) cc_final: 0.7572 (m) REVERT: D 566 MET cc_start: 0.8039 (ttp) cc_final: 0.7501 (tmm) REVERT: D 575 TYR cc_start: 0.8193 (m-80) cc_final: 0.7886 (m-80) REVERT: D 576 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7870 (tp30) REVERT: D 631 GLU cc_start: 0.8036 (mp0) cc_final: 0.7513 (mp0) REVERT: D 780 ARG cc_start: 0.8159 (ttt180) cc_final: 0.7777 (ttp80) REVERT: D 787 HIS cc_start: 0.7762 (m90) cc_final: 0.7438 (m90) REVERT: D 792 ASP cc_start: 0.7735 (p0) cc_final: 0.7010 (p0) REVERT: D 843 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: D 876 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.6006 (p90) REVERT: D 908 MET cc_start: 0.8675 (mmp) cc_final: 0.8346 (mmt) REVERT: D 909 PHE cc_start: 0.8236 (t80) cc_final: 0.7159 (m-10) REVERT: D 920 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8249 (tt0) REVERT: D 951 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6968 (pp20) REVERT: D 1136 GLN cc_start: 0.5724 (OUTLIER) cc_final: 0.4966 (tm-30) outliers start: 98 outliers final: 60 residues processed: 639 average time/residue: 0.4300 time to fit residues: 429.8988 Evaluate side-chains 649 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 566 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 418 ARG Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 876 TYR Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 843 ASP Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 975 LEU Chi-restraints excluded: chain D residue 1136 GLN Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 172 optimal weight: 10.0000 chunk 128 optimal weight: 0.1980 chunk 294 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 332 optimal weight: 0.6980 chunk 279 optimal weight: 9.9990 chunk 257 optimal weight: 7.9990 chunk 357 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 270 optimal weight: 0.0670 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 HIS B 923 HIS C 366 HIS C1046 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.165299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.120487 restraints weight = 35954.681| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.41 r_work: 0.3254 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29860 Z= 0.105 Angle : 0.577 15.442 40512 Z= 0.279 Chirality : 0.042 0.280 4612 Planarity : 0.004 0.046 5088 Dihedral : 3.972 21.653 4020 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.53 % Allowed : 23.61 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3632 helix: 0.66 (0.13), residues: 1668 sheet: -1.65 (0.25), residues: 380 loop : -0.03 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 204 HIS 0.014 0.001 HIS C 366 PHE 0.027 0.001 PHE D 275 TYR 0.018 0.001 TYR D1167 ARG 0.008 0.000 ARG C1020 Details of bonding type rmsd hydrogen bonds : bond 0.03148 ( 1217) hydrogen bonds : angle 4.31031 ( 3384) metal coordination : bond 0.00288 ( 16) metal coordination : angle 1.42897 ( 12) covalent geometry : bond 0.00240 (29844) covalent geometry : angle 0.57624 (40500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7264 Ramachandran restraints generated. 3632 Oldfield, 0 Emsley, 3632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 581 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASN cc_start: 0.8233 (m110) cc_final: 0.7411 (p0) REVERT: A 174 MET cc_start: 0.8020 (pmm) cc_final: 0.7201 (tpp) REVERT: A 180 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8142 (mm-40) REVERT: A 209 ARG cc_start: 0.5926 (tpt170) cc_final: 0.5416 (tpt90) REVERT: A 222 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7581 (t80) REVERT: A 275 PHE cc_start: 0.7661 (t80) cc_final: 0.7262 (t80) REVERT: A 279 LEU cc_start: 0.8580 (mt) cc_final: 0.8357 (mt) REVERT: A 354 MET cc_start: 0.6700 (ppp) cc_final: 0.5997 (mtt) REVERT: A 366 HIS cc_start: 0.7839 (t-90) cc_final: 0.7570 (t-170) REVERT: A 388 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: A 400 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7056 (mp10) REVERT: A 418 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.7128 (ptp-110) REVERT: A 426 SER cc_start: 0.7911 (t) cc_final: 0.7548 (m) REVERT: A 566 MET cc_start: 0.7641 (ppp) cc_final: 0.7288 (tmm) REVERT: A 570 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8352 (pttp) REVERT: A 575 TYR cc_start: 0.8106 (m-80) cc_final: 0.7855 (m-80) REVERT: A 576 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7834 (tp30) REVERT: A 600 ARG cc_start: 0.6501 (mtp180) cc_final: 0.6232 (mtt-85) REVERT: A 780 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7450 (ttp80) REVERT: A 787 HIS cc_start: 0.7844 (m90) cc_final: 0.7490 (m90) REVERT: A 792 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.7040 (p0) REVERT: A 876 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.5994 (p90) REVERT: A 908 MET cc_start: 0.8635 (mmp) cc_final: 0.8342 (mmt) REVERT: A 909 PHE cc_start: 0.8197 (t80) cc_final: 0.7127 (m-10) REVERT: A 920 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: A 951 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6992 (pp20) REVERT: A 958 PHE cc_start: 0.8370 (p90) cc_final: 0.8020 (p90) REVERT: B 163 ASN cc_start: 0.7113 (p0) cc_final: 0.6839 (p0) REVERT: B 174 MET cc_start: 0.8044 (pmm) cc_final: 0.7168 (tpp) REVERT: B 177 TRP cc_start: 0.8308 (t60) cc_final: 0.7894 (t60) REVERT: B 180 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8509 (mm-40) REVERT: B 199 TYR cc_start: 0.7743 (t80) cc_final: 0.7236 (t80) REVERT: B 209 ARG cc_start: 0.5896 (tpt170) cc_final: 0.5632 (tpt90) REVERT: B 275 PHE cc_start: 0.7667 (t80) cc_final: 0.7391 (t80) REVERT: B 388 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: B 400 GLN cc_start: 0.7819 (mm110) cc_final: 0.7202 (mp10) REVERT: B 418 ARG cc_start: 0.7505 (ptp-110) cc_final: 0.7047 (ptm-80) REVERT: B 426 SER cc_start: 0.7949 (t) cc_final: 0.7571 (m) REVERT: B 566 MET cc_start: 0.7698 (ppp) cc_final: 0.7346 (tmm) REVERT: B 570 LYS cc_start: 0.8772 (mmmm) cc_final: 0.8354 (pttp) REVERT: B 575 TYR cc_start: 0.8120 (m-80) cc_final: 0.7875 (m-80) REVERT: B 576 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7820 (tp30) REVERT: B 631 GLU cc_start: 0.8118 (mp0) cc_final: 0.7457 (tt0) REVERT: B 787 HIS cc_start: 0.7819 (m90) cc_final: 0.7508 (m90) REVERT: B 792 ASP cc_start: 0.7581 (p0) cc_final: 0.7161 (p0) REVERT: B 908 MET cc_start: 0.8584 (mmp) cc_final: 0.8289 (mmt) REVERT: B 909 PHE cc_start: 0.8189 (t80) cc_final: 0.7177 (m-10) REVERT: B 920 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: B 951 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.7020 (pp20) REVERT: B 958 PHE cc_start: 0.8383 (p90) cc_final: 0.8056 (p90) REVERT: C 163 ASN cc_start: 0.7762 (m-40) cc_final: 0.7067 (p0) REVERT: C 174 MET cc_start: 0.6425 (mpp) cc_final: 0.5916 (tpp) REVERT: C 180 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8165 (mm-40) REVERT: C 190 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8097 (tm-30) REVERT: C 199 TYR cc_start: 0.7729 (t80) cc_final: 0.7378 (t80) REVERT: C 209 ARG cc_start: 0.5745 (tpt170) cc_final: 0.5267 (tpt90) REVERT: C 228 TRP cc_start: 0.5700 (m-90) cc_final: 0.5263 (m-90) REVERT: C 275 PHE cc_start: 0.7623 (t80) cc_final: 0.7371 (t80) REVERT: C 388 ASP cc_start: 0.7714 (m-30) cc_final: 0.7474 (m-30) REVERT: C 418 ARG cc_start: 0.7438 (ptp-110) cc_final: 0.6908 (ptp90) REVERT: C 426 SER cc_start: 0.7854 (t) cc_final: 0.7474 (m) REVERT: C 566 MET cc_start: 0.7951 (ttp) cc_final: 0.7465 (tmm) REVERT: C 570 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8415 (pttp) REVERT: C 575 TYR cc_start: 0.8183 (m-80) cc_final: 0.7956 (m-80) REVERT: C 576 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7856 (tp30) REVERT: C 780 ARG cc_start: 0.8142 (ttp80) cc_final: 0.7509 (ttp80) REVERT: C 787 HIS cc_start: 0.7740 (m90) cc_final: 0.7432 (m90) REVERT: C 792 ASP cc_start: 0.7403 (p0) cc_final: 0.6981 (p0) REVERT: C 830 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7810 (pt0) REVERT: C 908 MET cc_start: 0.8657 (mmp) cc_final: 0.8374 (mmt) REVERT: C 909 PHE cc_start: 0.8185 (t80) cc_final: 0.7147 (m-80) REVERT: C 930 MET cc_start: 0.9021 (mmm) cc_final: 0.8778 (mmm) REVERT: C 951 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6495 (pp20) REVERT: C 958 PHE cc_start: 0.8377 (p90) cc_final: 0.8082 (p90) REVERT: C 1136 GLN cc_start: 0.5657 (OUTLIER) cc_final: 0.4973 (tm-30) REVERT: D 98 LYS cc_start: 0.4803 (tttt) cc_final: 0.4338 (ttpt) REVERT: D 174 MET cc_start: 0.7959 (pmm) cc_final: 0.6661 (mpp) REVERT: D 177 TRP cc_start: 0.8278 (t60) cc_final: 0.7968 (t60) REVERT: D 180 GLN cc_start: 0.8735 (mm-40) cc_final: 0.8293 (mm-40) REVERT: D 209 ARG cc_start: 0.5812 (tpt170) cc_final: 0.5426 (tpp-160) REVERT: D 222 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7590 (t80) REVERT: D 354 MET cc_start: 0.6868 (ppp) cc_final: 0.6152 (mtt) REVERT: D 366 HIS cc_start: 0.8048 (t-90) cc_final: 0.7721 (t-90) REVERT: D 388 ASP cc_start: 0.7752 (m-30) cc_final: 0.7484 (m-30) REVERT: D 400 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7136 (mp10) REVERT: D 418 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6988 (ptm-80) REVERT: D 426 SER cc_start: 0.7881 (t) cc_final: 0.7521 (m) REVERT: D 566 MET cc_start: 0.7979 (ttp) cc_final: 0.7458 (tmm) REVERT: D 575 TYR cc_start: 0.8122 (m-80) cc_final: 0.7882 (m-80) REVERT: D 576 GLU cc_start: 0.8427 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 631 GLU cc_start: 0.8021 (mp0) cc_final: 0.7472 (mp0) REVERT: D 780 ARG cc_start: 0.8139 (ttt180) cc_final: 0.7745 (ttp80) REVERT: D 787 HIS cc_start: 0.7808 (m90) cc_final: 0.7492 (m90) REVERT: D 792 ASP cc_start: 0.7708 (p0) cc_final: 0.6996 (p0) REVERT: D 843 ASP cc_start: 0.8187 (t0) cc_final: 0.7970 (m-30) REVERT: D 876 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.6047 (p90) REVERT: D 908 MET cc_start: 0.8660 (mmp) cc_final: 0.8349 (mmt) REVERT: D 909 PHE cc_start: 0.8121 (t80) cc_final: 0.7070 (m-10) REVERT: D 920 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: D 951 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6998 (pp20) REVERT: D 958 PHE cc_start: 0.8380 (p90) cc_final: 0.8056 (p90) REVERT: D 1136 GLN cc_start: 0.5666 (OUTLIER) cc_final: 0.4999 (tm-30) outliers start: 80 outliers final: 54 residues processed: 636 average time/residue: 0.4290 time to fit residues: 428.9434 Evaluate side-chains 632 residues out of total 3312 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 560 time to evaluate : 4.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 374 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 418 ARG Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 763 SER Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain A residue 862 SER Chi-restraints excluded: chain A residue 876 TYR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 951 GLU Chi-restraints excluded: chain A residue 1136 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1187 ASP Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 747 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 862 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 951 GLU Chi-restraints excluded: chain B residue 1136 GLN Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 747 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain C residue 951 GLU Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain D residue 222 PHE Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain D residue 458 SER Chi-restraints excluded: chain D residue 491 ILE Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 747 VAL Chi-restraints excluded: chain D residue 763 SER Chi-restraints excluded: chain D residue 862 SER Chi-restraints excluded: chain D residue 876 TYR Chi-restraints excluded: chain D residue 878 ASP Chi-restraints excluded: chain D residue 920 GLU Chi-restraints excluded: chain D residue 951 GLU Chi-restraints excluded: chain D residue 1136 GLN Chi-restraints excluded: chain D residue 1138 LEU Chi-restraints excluded: chain D residue 1187 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 321 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 282 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 359 optimal weight: 7.9990 chunk 265 optimal weight: 0.2980 chunk 360 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 281 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.163951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.118563 restraints weight = 36001.868| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.41 r_work: 0.3236 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29860 Z= 0.131 Angle : 0.593 15.606 40512 Z= 0.286 Chirality : 0.043 0.274 4612 Planarity : 0.004 0.045 5088 Dihedral : 4.012 22.894 4020 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.66 % Allowed : 23.64 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3632 helix: 0.65 (0.13), residues: 1668 sheet: -1.57 (0.25), residues: 412 loop : 0.00 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.003 0.001 HIS B 291 PHE 0.019 0.001 PHE D 222 TYR 0.018 0.001 TYR D1167 ARG 0.008 0.000 ARG D1020 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 1217) hydrogen bonds : angle 4.31795 ( 3384) metal coordination : bond 0.00389 ( 16) metal coordination : angle 1.39166 ( 12) covalent geometry : bond 0.00315 (29844) covalent geometry : angle 0.59211 (40500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18998.27 seconds wall clock time: 333 minutes 49.12 seconds (20029.12 seconds total)