Starting phenix.real_space_refine on Tue Jan 21 04:16:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n4u_24178/01_2025/7n4u_24178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4u_24178/01_2025/7n4u_24178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n4u_24178/01_2025/7n4u_24178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4u_24178/01_2025/7n4u_24178.map" model { file = "/net/cci-nas-00/data/ceres_data/7n4u_24178/01_2025/7n4u_24178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4u_24178/01_2025/7n4u_24178.cif" } resolution = 3.34 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= 0.005 sd= 0.043 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 90 5.16 5 C 10068 2.51 5 N 2434 2.21 5 O 2802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15396 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7426 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 50, 'TRANS': 902} Chain: "B" Number of atoms: 7426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 953, 7426 Classifications: {'peptide': 953} Link IDs: {'PTRANS': 50, 'TRANS': 902} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 188 Unusual residues: {'CLR': 2, 'NAG': 4, 'POV': 1, 'VIV': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 188 Unusual residues: {'CLR': 2, 'NAG': 4, 'POV': 1, 'VIV': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.52, per 1000 atoms: 0.62 Number of scatterers: 15396 At special positions: 0 Unit cell: (134.113, 89.131, 136.612, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 2 15.00 O 2802 8.00 N 2434 7.00 C 10068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 525 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A 966 " - pdb=" SG CYS A1024 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 993 " distance=2.03 Simple disulfide: pdb=" SG CYS A 980 " - pdb=" SG CYS A 989 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 525 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B 966 " - pdb=" SG CYS B1024 " distance=2.03 Simple disulfide: pdb=" SG CYS B 967 " - pdb=" SG CYS B 993 " distance=2.03 Simple disulfide: pdb=" SG CYS B 980 " - pdb=" SG CYS B 989 " distance=2.03 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 Atom "HETATM15032 O5 NAG A1401 .*. O " rejected from bonding due to valence issues. Atom "HETATM15265 O5 NAG B1602 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1401 " - " ASN A 431 " " NAG A1402 " - " ASN A 464 " " NAG A1403 " - " ASN A1075 " " NAG A1404 " - " ASN A 506 " " NAG B1602 " - " ASN B 431 " " NAG B1603 " - " ASN B 464 " " NAG B1604 " - " ASN B1075 " " NAG B1605 " - " ASN B 506 " " NAG C 1 " - " ASN A 497 " " NAG D 1 " - " ASN A 909 " " NAG E 1 " - " ASN A1037 " " NAG F 1 " - " ASN B 497 " " NAG G 1 " - " ASN B 909 " " NAG H 1 " - " ASN B1037 " Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 1.9 seconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 14 sheets defined 62.6% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 333 through 349 Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.552A pdb=" N ILE A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.642A pdb=" N LEU A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 491 through 493 No H-bonds generated for 'chain 'A' and resid 491 through 493' Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 517 through 528 removed outlier: 4.012A pdb=" N HIS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 555 removed outlier: 3.742A pdb=" N ALA A 555 " --> pdb=" O PHE A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 551 through 555' Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'A' and resid 583 through 607 removed outlier: 4.039A pdb=" N ALA A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.721A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 removed outlier: 4.066A pdb=" N GLU A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.635A pdb=" N PHE A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 652 removed outlier: 4.019A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 664 Processing helix chain 'A' and resid 665 through 690 Processing helix chain 'A' and resid 695 through 710 removed outlier: 3.602A pdb=" N LEU A 699 " --> pdb=" O SER A 695 " (cutoff:3.500A) Proline residue: A 703 - end of helix removed outlier: 3.612A pdb=" N LEU A 707 " --> pdb=" O PRO A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 724 Processing helix chain 'A' and resid 731 through 762 Proline residue: A 745 - end of helix Processing helix chain 'A' and resid 766 through 804 removed outlier: 3.751A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL A 792 " --> pdb=" O MET A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 835 Processing helix chain 'A' and resid 835 through 841 Processing helix chain 'A' and resid 842 through 864 removed outlier: 4.419A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 848 " --> pdb=" O ILE A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 882 through 894 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.758A pdb=" N MET A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 938 Processing helix chain 'A' and resid 952 through 961 Processing helix chain 'A' and resid 986 through 990 removed outlier: 4.184A pdb=" N CYS A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1017 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1058 through 1081 removed outlier: 3.552A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1106 Processing helix chain 'A' and resid 1107 through 1131 removed outlier: 4.015A pdb=" N GLU A1111 " --> pdb=" O THR A1107 " (cutoff:3.500A) Proline residue: A1122 - end of helix removed outlier: 3.720A pdb=" N LEU A1129 " --> pdb=" O ALA A1125 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A1131 " --> pdb=" O SER A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1160 Processing helix chain 'A' and resid 1164 through 1178 Processing helix chain 'A' and resid 1178 through 1191 removed outlier: 5.076A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1226 removed outlier: 3.967A pdb=" N SER A1210 " --> pdb=" O ILE A1206 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA A1211 " --> pdb=" O SER A1207 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Proline residue: A1222 - end of helix removed outlier: 3.880A pdb=" N VAL A1226 " --> pdb=" O PRO A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1230 Processing helix chain 'A' and resid 1232 through 1239 Processing helix chain 'A' and resid 1239 through 1266 removed outlier: 5.318A pdb=" N LEU A1258 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1270 through 1274 removed outlier: 3.511A pdb=" N LEU A1273 " --> pdb=" O ASN A1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 349 Processing helix chain 'B' and resid 351 through 368 removed outlier: 3.554A pdb=" N ILE B 355 " --> pdb=" O TRP B 351 " (cutoff:3.500A) Proline residue: B 362 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 388 through 402 Processing helix chain 'B' and resid 437 through 453 removed outlier: 3.643A pdb=" N LEU B 441 " --> pdb=" O ASP B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 517 through 528 removed outlier: 4.013A pdb=" N HIS B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 555 removed outlier: 3.743A pdb=" N ALA B 555 " --> pdb=" O PHE B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 555' Processing helix chain 'B' and resid 563 through 567 Processing helix chain 'B' and resid 583 through 607 removed outlier: 4.039A pdb=" N ALA B 587 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.721A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 removed outlier: 4.066A pdb=" N GLU B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.638A pdb=" N PHE B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 652 removed outlier: 4.019A pdb=" N ILE B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 664 Processing helix chain 'B' and resid 665 through 690 Processing helix chain 'B' and resid 695 through 710 removed outlier: 3.602A pdb=" N LEU B 699 " --> pdb=" O SER B 695 " (cutoff:3.500A) Proline residue: B 703 - end of helix removed outlier: 3.611A pdb=" N LEU B 707 " --> pdb=" O PRO B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 724 Processing helix chain 'B' and resid 731 through 762 Proline residue: B 745 - end of helix Processing helix chain 'B' and resid 766 through 804 removed outlier: 3.749A pdb=" N SER B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE B 791 " --> pdb=" O GLN B 787 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 792 " --> pdb=" O MET B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 835 Processing helix chain 'B' and resid 835 through 841 Processing helix chain 'B' and resid 842 through 864 removed outlier: 4.420A pdb=" N GLY B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 848 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 877 Processing helix chain 'B' and resid 882 through 894 Processing helix chain 'B' and resid 912 through 918 removed outlier: 3.757A pdb=" N MET B 916 " --> pdb=" O SER B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 938 Processing helix chain 'B' and resid 952 through 961 Processing helix chain 'B' and resid 986 through 990 removed outlier: 4.185A pdb=" N CYS B 989 " --> pdb=" O SER B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1017 Proline residue: B1013 - end of helix Processing helix chain 'B' and resid 1058 through 1081 removed outlier: 3.553A pdb=" N ASP B1079 " --> pdb=" O ASN B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1106 Processing helix chain 'B' and resid 1107 through 1131 removed outlier: 4.012A pdb=" N GLU B1111 " --> pdb=" O THR B1107 " (cutoff:3.500A) Proline residue: B1122 - end of helix removed outlier: 3.718A pdb=" N LEU B1129 " --> pdb=" O ALA B1125 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B1131 " --> pdb=" O SER B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1160 Processing helix chain 'B' and resid 1164 through 1178 Processing helix chain 'B' and resid 1178 through 1191 removed outlier: 5.076A pdb=" N HIS B1184 " --> pdb=" O GLU B1180 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE B1185 " --> pdb=" O PHE B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1196 through 1226 removed outlier: 3.968A pdb=" N SER B1210 " --> pdb=" O ILE B1206 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA B1211 " --> pdb=" O SER B1207 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET B1218 " --> pdb=" O ALA B1214 " (cutoff:3.500A) Proline residue: B1222 - end of helix removed outlier: 3.878A pdb=" N VAL B1226 " --> pdb=" O PRO B1222 " (cutoff:3.500A) Processing helix chain 'B' and resid 1227 through 1230 Processing helix chain 'B' and resid 1232 through 1239 Processing helix chain 'B' and resid 1239 through 1266 removed outlier: 5.323A pdb=" N LEU B1258 " --> pdb=" O GLY B1254 " (cutoff:3.500A) Proline residue: B1259 - end of helix Processing helix chain 'B' and resid 1270 through 1274 removed outlier: 3.512A pdb=" N LEU B1273 " --> pdb=" O ASN B1270 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 489 Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 423 Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 509 Processing sheet with id=AA5, first strand: chain 'A' and resid 948 through 951 removed outlier: 5.155A pdb=" N TYR A1052 " --> pdb=" O PRO A 949 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET A1050 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 979 through 980 removed outlier: 4.144A pdb=" N ARG A 968 " --> pdb=" O CYS A 980 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A 991 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.762A pdb=" N THR A1046 " --> pdb=" O ASN A1037 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 487 through 489 Processing sheet with id=AA9, first strand: chain 'B' and resid 487 through 489 Processing sheet with id=AB1, first strand: chain 'B' and resid 419 through 423 Processing sheet with id=AB2, first strand: chain 'B' and resid 505 through 509 Processing sheet with id=AB3, first strand: chain 'B' and resid 948 through 951 removed outlier: 5.154A pdb=" N TYR B1052 " --> pdb=" O PRO B 949 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET B1050 " --> pdb=" O SER B 951 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 979 through 980 removed outlier: 4.144A pdb=" N ARG B 968 " --> pdb=" O CYS B 980 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B 991 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.762A pdb=" N THR B1046 " --> pdb=" O ASN B1037 " (cutoff:3.500A) 811 hydrogen bonds defined for protein. 2337 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: 5.64 Time building geometry restraints manager: 4.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2384 1.31 - 1.44: 4270 1.44 - 1.57: 8980 1.57 - 1.69: 4 1.69 - 1.82: 138 Bond restraints: 15776 Sorted by residual: bond pdb=" C4 VIV B1608 " pdb=" O1 VIV B1608 " ideal model delta sigma weight residual 1.358 1.463 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C4 VIV A1407 " pdb=" O1 VIV A1407 " ideal model delta sigma weight residual 1.358 1.463 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" N VAL A 662 " pdb=" CA VAL A 662 " ideal model delta sigma weight residual 1.456 1.500 -0.043 9.50e-03 1.11e+04 2.09e+01 bond pdb=" N VAL B 662 " pdb=" CA VAL B 662 " ideal model delta sigma weight residual 1.456 1.500 -0.043 9.50e-03 1.11e+04 2.07e+01 bond pdb=" N TYR B 579 " pdb=" CA TYR B 579 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.69e+01 ... (remaining 15771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 17246 2.36 - 4.72: 4015 4.72 - 7.09: 217 7.09 - 9.45: 16 9.45 - 11.81: 6 Bond angle restraints: 21500 Sorted by residual: angle pdb=" C GLY B 671 " pdb=" N GLY B 672 " pdb=" CA GLY B 672 " ideal model delta sigma weight residual 119.94 125.32 -5.38 1.11e+00 8.12e-01 2.35e+01 angle pdb=" C GLY A 671 " pdb=" N GLY A 672 " pdb=" CA GLY A 672 " ideal model delta sigma weight residual 119.94 125.30 -5.36 1.11e+00 8.12e-01 2.33e+01 angle pdb=" C GLN A 342 " pdb=" N GLY A 343 " pdb=" CA GLY A 343 " ideal model delta sigma weight residual 119.94 125.09 -5.15 1.11e+00 8.12e-01 2.16e+01 angle pdb=" C GLN B 342 " pdb=" N GLY B 343 " pdb=" CA GLY B 343 " ideal model delta sigma weight residual 119.94 125.08 -5.14 1.11e+00 8.12e-01 2.15e+01 angle pdb=" C ALA A 914 " pdb=" N GLY A 915 " pdb=" CA GLY A 915 " ideal model delta sigma weight residual 119.94 125.04 -5.10 1.11e+00 8.12e-01 2.11e+01 ... (remaining 21495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.97: 9440 31.97 - 63.95: 334 63.95 - 95.92: 54 95.92 - 127.89: 22 127.89 - 159.87: 2 Dihedral angle restraints: 9852 sinusoidal: 4300 harmonic: 5552 Sorted by residual: dihedral pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 159.81 -66.81 1 1.00e+01 1.00e-02 5.82e+01 dihedral pdb=" CB CYS B 525 " pdb=" SG CYS B 525 " pdb=" SG CYS B 542 " pdb=" CB CYS B 542 " ideal model delta sinusoidal sigma weight residual 93.00 159.76 -66.76 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS B 966 " pdb=" SG CYS B 966 " pdb=" SG CYS B1024 " pdb=" CB CYS B1024 " ideal model delta sinusoidal sigma weight residual 93.00 143.82 -50.82 1 1.00e+01 1.00e-02 3.54e+01 ... (remaining 9849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.948: 2526 0.948 - 1.896: 2 1.896 - 2.844: 2 2.844 - 3.792: 2 3.792 - 4.740: 8 Chirality restraints: 2540 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-02 2.50e+03 5.48e+04 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 2.28 -4.68 2.00e-02 2.50e+03 5.48e+04 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 2.27 -4.67 2.00e-02 2.50e+03 5.45e+04 ... (remaining 2537 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG D 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.147 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " -0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG G 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1602 " 0.218 2.00e-02 2.50e+03 1.86e-01 4.31e+02 pdb=" C7 NAG B1602 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B1602 " -0.038 2.00e-02 2.50e+03 pdb=" N2 NAG B1602 " -0.304 2.00e-02 2.50e+03 pdb=" O7 NAG B1602 " 0.169 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 188 2.66 - 3.22: 13837 3.22 - 3.78: 23853 3.78 - 4.34: 30309 4.34 - 4.90: 53852 Nonbonded interactions: 122039 Sorted by model distance: nonbonded pdb=" O VAL B 660 " pdb=" OD2 ASP B 808 " model vdw 2.102 3.040 nonbonded pdb=" O VAL A 660 " pdb=" OD2 ASP A 808 " model vdw 2.103 3.040 nonbonded pdb=" O VAL B 380 " pdb=" OG SER B 384 " model vdw 2.273 3.040 nonbonded pdb=" O VAL A 380 " pdb=" OG SER A 384 " model vdw 2.274 3.040 nonbonded pdb=" O MET A 661 " pdb=" N ASP A 808 " model vdw 2.360 3.120 ... (remaining 122034 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 333 through 1285 or resid 1402 through 1404 or resid 1406) \ ) selection = (chain 'B' and (resid 333 through 1285 or resid 1602 through 1604 or resid 1606) \ ) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.670 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 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 : 0.014 0.105 15776 Z= 0.927 Angle : 1.795 11.810 21500 Z= 1.328 Chirality : 0.294 4.740 2540 Planarity : 0.011 0.303 2650 Dihedral : 17.763 159.868 6236 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.26 % Favored : 94.53 % Rotamer: Outliers : 1.79 % Allowed : 7.52 % Favored : 90.69 % 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: -2.74 (0.17), residues: 1902 helix: -1.48 (0.13), residues: 1062 sheet: -2.56 (0.40), residues: 126 loop : -1.97 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 518 HIS 0.005 0.002 HIS B 521 PHE 0.040 0.002 PHE A 791 TYR 0.033 0.003 TYR B1062 ARG 0.006 0.001 ARG A1070 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 ASN cc_start: 0.8461 (t0) cc_final: 0.7944 (t0) REVERT: A 524 TYR cc_start: 0.7666 (t80) cc_final: 0.7206 (t80) REVERT: A 566 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7456 (mp0) REVERT: A 818 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7997 (tp) REVERT: A 994 MET cc_start: 0.7523 (ptp) cc_final: 0.7119 (ppp) REVERT: A 998 MET cc_start: 0.7203 (pmm) cc_final: 0.6584 (pmm) REVERT: A 1102 TYR cc_start: 0.8478 (m-10) cc_final: 0.8015 (m-10) REVERT: A 1103 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7291 (pt0) REVERT: A 1198 LEU cc_start: 0.7637 (mt) cc_final: 0.7296 (tt) REVERT: A 1242 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6458 (tt) REVERT: B 476 ASN cc_start: 0.8353 (t0) cc_final: 0.7817 (t0) REVERT: B 524 TYR cc_start: 0.7651 (t80) cc_final: 0.7172 (t80) REVERT: B 566 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7430 (mp0) REVERT: B 818 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8184 (tp) REVERT: B 994 MET cc_start: 0.7248 (ptp) cc_final: 0.6880 (ppp) REVERT: B 998 MET cc_start: 0.7291 (pmm) cc_final: 0.6676 (pmm) REVERT: B 1102 TYR cc_start: 0.8474 (m-10) cc_final: 0.7981 (m-10) REVERT: B 1198 LEU cc_start: 0.7681 (mt) cc_final: 0.7426 (tt) outliers start: 29 outliers final: 11 residues processed: 206 average time/residue: 0.2534 time to fit residues: 80.2688 Evaluate side-chains 135 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 872 ASP Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 1103 GLU Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 818 LEU Chi-restraints excluded: chain B residue 872 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 8.9990 chunk 144 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 172 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 409 GLN A 527 ASN A1184 HIS A1233 GLN A1253 HIS B 339 GLN B 409 GLN B 527 ASN B1184 HIS B1220 ASN B1233 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.121003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.089877 restraints weight = 24666.999| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.92 r_work: 0.3088 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15776 Z= 0.186 Angle : 0.719 12.899 21500 Z= 0.328 Chirality : 0.054 0.986 2540 Planarity : 0.004 0.037 2650 Dihedral : 13.372 132.046 2887 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.79 % Favored : 97.11 % Rotamer: Outliers : 3.33 % Allowed : 11.04 % Favored : 85.64 % 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: -0.33 (0.20), residues: 1902 helix: 0.78 (0.16), residues: 1052 sheet: -1.96 (0.42), residues: 126 loop : -1.33 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 518 HIS 0.005 0.001 HIS B1053 PHE 0.014 0.001 PHE A 704 TYR 0.014 0.001 TYR B 836 ARG 0.008 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 144 time to evaluate : 1.588 Fit side-chains REVERT: A 476 ASN cc_start: 0.8570 (t0) cc_final: 0.8175 (t0) REVERT: A 524 TYR cc_start: 0.7896 (t80) cc_final: 0.7590 (t80) REVERT: A 566 GLU cc_start: 0.8579 (mt-10) cc_final: 0.7826 (mp0) REVERT: A 607 MET cc_start: 0.8280 (mmm) cc_final: 0.7275 (mmm) REVERT: A 818 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8124 (tp) REVERT: A 994 MET cc_start: 0.7547 (OUTLIER) cc_final: 0.7127 (ppp) REVERT: A 998 MET cc_start: 0.7039 (pmm) cc_final: 0.6351 (pmm) REVERT: A 1023 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8408 (mttp) REVERT: A 1102 TYR cc_start: 0.8625 (m-10) cc_final: 0.8248 (m-10) REVERT: A 1198 LEU cc_start: 0.8452 (mt) cc_final: 0.8093 (tt) REVERT: A 1261 ILE cc_start: 0.8409 (tt) cc_final: 0.8134 (tt) REVERT: B 476 ASN cc_start: 0.8453 (t0) cc_final: 0.8018 (t0) REVERT: B 524 TYR cc_start: 0.7954 (t80) cc_final: 0.7650 (t80) REVERT: B 566 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7849 (mp0) REVERT: B 1023 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8471 (mttp) REVERT: B 1102 TYR cc_start: 0.8606 (m-10) cc_final: 0.8216 (m-10) REVERT: B 1103 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8188 (pt0) REVERT: B 1198 LEU cc_start: 0.8454 (mt) cc_final: 0.8211 (tt) outliers start: 54 outliers final: 22 residues processed: 185 average time/residue: 0.2301 time to fit residues: 68.5630 Evaluate side-chains 141 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 807 LEU Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 994 MET Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1103 GLU Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 0.0270 overall best weight: 0.7042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1220 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.090138 restraints weight = 24702.586| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.87 r_work: 0.3090 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15776 Z= 0.171 Angle : 0.620 10.609 21500 Z= 0.288 Chirality : 0.047 0.834 2540 Planarity : 0.003 0.031 2650 Dihedral : 10.795 115.557 2873 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.26 % Favored : 96.64 % Rotamer: Outliers : 3.02 % Allowed : 12.64 % Favored : 84.34 % 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: 0.26 (0.20), residues: 1902 helix: 1.23 (0.16), residues: 1056 sheet: -1.81 (0.48), residues: 102 loop : -1.05 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 518 HIS 0.004 0.001 HIS B1053 PHE 0.014 0.001 PHE B 930 TYR 0.014 0.001 TYR B 646 ARG 0.004 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 1.764 Fit side-chains REVERT: A 398 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: A 476 ASN cc_start: 0.8541 (t0) cc_final: 0.8174 (t0) REVERT: A 524 TYR cc_start: 0.7890 (t80) cc_final: 0.7611 (t80) REVERT: A 566 GLU cc_start: 0.8615 (mt-10) cc_final: 0.7863 (mp0) REVERT: A 607 MET cc_start: 0.8200 (mmm) cc_final: 0.7219 (mmm) REVERT: A 818 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8254 (tp) REVERT: A 836 TYR cc_start: 0.8135 (t80) cc_final: 0.7842 (t80) REVERT: A 998 MET cc_start: 0.7079 (pmm) cc_final: 0.6438 (pmm) REVERT: A 1023 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8367 (mttp) REVERT: A 1050 MET cc_start: 0.8229 (ttt) cc_final: 0.7456 (ttt) REVERT: A 1102 TYR cc_start: 0.8648 (m-10) cc_final: 0.8299 (m-10) REVERT: A 1128 CYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8534 (m) REVERT: A 1198 LEU cc_start: 0.8509 (mt) cc_final: 0.8128 (tt) REVERT: A 1261 ILE cc_start: 0.8435 (tt) cc_final: 0.8198 (tp) REVERT: B 398 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: B 476 ASN cc_start: 0.8448 (t0) cc_final: 0.8021 (t0) REVERT: B 524 TYR cc_start: 0.7947 (t80) cc_final: 0.7600 (t80) REVERT: B 566 GLU cc_start: 0.8514 (mt-10) cc_final: 0.7925 (mp0) REVERT: B 607 MET cc_start: 0.8252 (mmm) cc_final: 0.7099 (mmm) REVERT: B 836 TYR cc_start: 0.8092 (t80) cc_final: 0.7727 (t80) REVERT: B 994 MET cc_start: 0.7588 (ppp) cc_final: 0.7169 (ppp) REVERT: B 1023 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8450 (mttp) REVERT: B 1050 MET cc_start: 0.8221 (ttt) cc_final: 0.7461 (ttt) REVERT: B 1102 TYR cc_start: 0.8642 (m-10) cc_final: 0.8259 (m-10) REVERT: B 1128 CYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8538 (m) REVERT: B 1198 LEU cc_start: 0.8499 (mt) cc_final: 0.8217 (tt) outliers start: 49 outliers final: 32 residues processed: 161 average time/residue: 0.2325 time to fit residues: 61.4458 Evaluate side-chains 153 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 114 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1139 LEU Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 807 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 107 optimal weight: 0.0170 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.117518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.085928 restraints weight = 25294.724| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.15 r_work: 0.3025 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15776 Z= 0.161 Angle : 0.584 10.564 21500 Z= 0.274 Chirality : 0.044 0.712 2540 Planarity : 0.003 0.030 2650 Dihedral : 10.126 108.927 2870 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.21 % Favored : 96.69 % Rotamer: Outliers : 3.27 % Allowed : 12.82 % Favored : 83.91 % 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: 0.46 (0.20), residues: 1902 helix: 1.35 (0.16), residues: 1056 sheet: -1.70 (0.48), residues: 102 loop : -0.89 (0.24), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 518 HIS 0.003 0.001 HIS B1053 PHE 0.014 0.001 PHE A 839 TYR 0.013 0.001 TYR B 646 ARG 0.002 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 120 time to evaluate : 1.614 Fit side-chains REVERT: A 476 ASN cc_start: 0.8551 (t0) cc_final: 0.8124 (t0) REVERT: A 524 TYR cc_start: 0.7807 (t80) cc_final: 0.7400 (t80) REVERT: A 566 GLU cc_start: 0.8561 (mt-10) cc_final: 0.7714 (mp0) REVERT: A 607 MET cc_start: 0.8163 (mmm) cc_final: 0.7276 (mmm) REVERT: A 818 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8322 (tp) REVERT: A 836 TYR cc_start: 0.7992 (t80) cc_final: 0.7700 (t80) REVERT: A 998 MET cc_start: 0.7267 (pmm) cc_final: 0.6653 (pmm) REVERT: A 1023 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8394 (mttp) REVERT: A 1050 MET cc_start: 0.8359 (ttt) cc_final: 0.7508 (ttt) REVERT: A 1102 TYR cc_start: 0.8690 (m-10) cc_final: 0.8260 (m-10) REVERT: A 1128 CYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8440 (m) REVERT: A 1198 LEU cc_start: 0.8358 (mt) cc_final: 0.7985 (tt) REVERT: A 1261 ILE cc_start: 0.8203 (tt) cc_final: 0.7986 (tp) REVERT: B 476 ASN cc_start: 0.8431 (t0) cc_final: 0.7944 (t0) REVERT: B 524 TYR cc_start: 0.7856 (t80) cc_final: 0.7468 (t80) REVERT: B 566 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7751 (mp0) REVERT: B 607 MET cc_start: 0.8094 (mmm) cc_final: 0.7698 (mmm) REVERT: B 836 TYR cc_start: 0.7960 (t80) cc_final: 0.7597 (t80) REVERT: B 994 MET cc_start: 0.7592 (ppp) cc_final: 0.7148 (ppp) REVERT: B 1023 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8480 (mttp) REVERT: B 1102 TYR cc_start: 0.8694 (m-10) cc_final: 0.8328 (m-10) REVERT: B 1128 CYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8483 (m) REVERT: B 1198 LEU cc_start: 0.8331 (mt) cc_final: 0.8058 (tt) outliers start: 53 outliers final: 32 residues processed: 160 average time/residue: 0.2393 time to fit residues: 61.3985 Evaluate side-chains 153 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 116 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1023 LYS Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1247 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 182 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.112007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.082924 restraints weight = 26241.434| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.83 r_work: 0.3071 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15776 Z= 0.300 Angle : 0.643 10.411 21500 Z= 0.303 Chirality : 0.045 0.617 2540 Planarity : 0.004 0.028 2650 Dihedral : 9.861 102.749 2870 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.00 % Favored : 95.90 % Rotamer: Outliers : 3.14 % Allowed : 13.38 % Favored : 83.48 % 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: 0.32 (0.20), residues: 1902 helix: 1.16 (0.16), residues: 1062 sheet: -1.97 (0.47), residues: 102 loop : -0.80 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 592 HIS 0.006 0.001 HIS B1053 PHE 0.020 0.002 PHE B 791 TYR 0.014 0.001 TYR A 546 ARG 0.003 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 118 time to evaluate : 1.541 Fit side-chains REVERT: A 476 ASN cc_start: 0.8605 (t0) cc_final: 0.8246 (t0) REVERT: A 524 TYR cc_start: 0.8083 (t80) cc_final: 0.7750 (t80) REVERT: A 566 GLU cc_start: 0.8779 (mt-10) cc_final: 0.7927 (mp0) REVERT: A 607 MET cc_start: 0.7976 (mmm) cc_final: 0.7656 (mmm) REVERT: A 818 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8311 (tp) REVERT: A 994 MET cc_start: 0.7811 (ppp) cc_final: 0.7539 (ppp) REVERT: A 998 MET cc_start: 0.7137 (pmm) cc_final: 0.6629 (pmm) REVERT: A 1102 TYR cc_start: 0.8870 (m-10) cc_final: 0.8632 (m-10) REVERT: A 1128 CYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8602 (m) REVERT: A 1130 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 1198 LEU cc_start: 0.8511 (mt) cc_final: 0.8197 (tt) REVERT: A 1261 ILE cc_start: 0.8508 (tt) cc_final: 0.8225 (tt) REVERT: B 476 ASN cc_start: 0.8514 (t0) cc_final: 0.8107 (t0) REVERT: B 524 TYR cc_start: 0.8118 (t80) cc_final: 0.7757 (t80) REVERT: B 566 GLU cc_start: 0.8725 (mt-10) cc_final: 0.7977 (mp0) REVERT: B 607 MET cc_start: 0.8025 (mmm) cc_final: 0.7748 (mmm) REVERT: B 836 TYR cc_start: 0.8254 (t80) cc_final: 0.7991 (t80) REVERT: B 894 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7922 (m-80) REVERT: B 994 MET cc_start: 0.7741 (ppp) cc_final: 0.7202 (ppp) REVERT: B 1103 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8104 (pt0) REVERT: B 1128 CYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8594 (m) REVERT: B 1198 LEU cc_start: 0.8514 (mt) cc_final: 0.8266 (tt) outliers start: 51 outliers final: 34 residues processed: 156 average time/residue: 0.2354 time to fit residues: 59.0782 Evaluate side-chains 151 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1103 GLU Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1247 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 67 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.114097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.085073 restraints weight = 25672.627| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.81 r_work: 0.3101 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15776 Z= 0.182 Angle : 0.574 10.340 21500 Z= 0.269 Chirality : 0.042 0.583 2540 Planarity : 0.003 0.027 2650 Dihedral : 9.437 105.616 2870 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.21 % Allowed : 13.81 % Favored : 82.98 % 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: 0.45 (0.20), residues: 1902 helix: 1.25 (0.16), residues: 1062 sheet: -1.86 (0.48), residues: 102 loop : -0.73 (0.25), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 518 HIS 0.003 0.001 HIS A1053 PHE 0.017 0.001 PHE A 839 TYR 0.012 0.001 TYR B 646 ARG 0.002 0.000 ARG B1002 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 116 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 ASN cc_start: 0.8526 (t0) cc_final: 0.8166 (t0) REVERT: A 524 TYR cc_start: 0.8069 (t80) cc_final: 0.7696 (t80) REVERT: A 566 GLU cc_start: 0.8695 (mt-10) cc_final: 0.7900 (mp0) REVERT: A 818 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8283 (tp) REVERT: A 994 MET cc_start: 0.7774 (ppp) cc_final: 0.7451 (ppp) REVERT: A 998 MET cc_start: 0.7193 (pmm) cc_final: 0.6719 (pmm) REVERT: A 1050 MET cc_start: 0.8192 (ttt) cc_final: 0.7381 (ttt) REVERT: A 1102 TYR cc_start: 0.8816 (m-10) cc_final: 0.8578 (m-10) REVERT: A 1128 CYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8611 (m) REVERT: A 1198 LEU cc_start: 0.8519 (mt) cc_final: 0.8206 (tt) REVERT: B 476 ASN cc_start: 0.8436 (t0) cc_final: 0.8052 (t0) REVERT: B 524 TYR cc_start: 0.8113 (t80) cc_final: 0.7728 (t80) REVERT: B 566 GLU cc_start: 0.8613 (mt-10) cc_final: 0.7886 (mp0) REVERT: B 607 MET cc_start: 0.7913 (mmm) cc_final: 0.7692 (mmm) REVERT: B 894 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7973 (m-80) REVERT: B 994 MET cc_start: 0.7661 (ppp) cc_final: 0.7133 (ppp) REVERT: B 1023 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8448 (mttp) REVERT: B 1103 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: B 1128 CYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8600 (m) REVERT: B 1198 LEU cc_start: 0.8486 (mt) cc_final: 0.8229 (tt) REVERT: B 1282 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7120 (pm20) outliers start: 52 outliers final: 33 residues processed: 158 average time/residue: 0.2640 time to fit residues: 64.9090 Evaluate side-chains 151 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1103 GLU Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1247 THR Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 166 optimal weight: 5.9990 chunk 142 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 111 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 168 optimal weight: 0.3980 chunk 115 optimal weight: 8.9990 chunk 37 optimal weight: 0.0770 chunk 87 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.116838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.087011 restraints weight = 26361.820| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.95 r_work: 0.3130 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15776 Z= 0.143 Angle : 0.543 10.240 21500 Z= 0.255 Chirality : 0.041 0.536 2540 Planarity : 0.003 0.027 2650 Dihedral : 9.105 105.323 2870 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.08 % Allowed : 14.06 % Favored : 82.86 % 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: 0.68 (0.20), residues: 1902 helix: 1.38 (0.16), residues: 1066 sheet: -1.64 (0.49), residues: 102 loop : -0.55 (0.25), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 518 HIS 0.003 0.001 HIS A1053 PHE 0.017 0.001 PHE B 839 TYR 0.012 0.001 TYR B 646 ARG 0.002 0.000 ARG B1002 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 1.702 Fit side-chains REVERT: A 476 ASN cc_start: 0.8470 (t0) cc_final: 0.8163 (t0) REVERT: A 524 TYR cc_start: 0.8070 (t80) cc_final: 0.7680 (t80) REVERT: A 566 GLU cc_start: 0.8643 (mt-10) cc_final: 0.7866 (mp0) REVERT: A 607 MET cc_start: 0.8058 (mmm) cc_final: 0.7242 (mmm) REVERT: A 994 MET cc_start: 0.7719 (ppp) cc_final: 0.7411 (ppp) REVERT: A 998 MET cc_start: 0.7136 (pmm) cc_final: 0.6706 (pmm) REVERT: A 1050 MET cc_start: 0.8098 (ttt) cc_final: 0.7324 (ttt) REVERT: A 1102 TYR cc_start: 0.8766 (m-10) cc_final: 0.8478 (m-10) REVERT: A 1128 CYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8605 (m) REVERT: A 1139 LEU cc_start: 0.8261 (tp) cc_final: 0.8037 (tp) REVERT: A 1198 LEU cc_start: 0.8523 (mt) cc_final: 0.8216 (tt) REVERT: A 1282 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: B 476 ASN cc_start: 0.8364 (t0) cc_final: 0.8028 (t0) REVERT: B 524 TYR cc_start: 0.8110 (t80) cc_final: 0.7737 (t80) REVERT: B 566 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7876 (mp0) REVERT: B 894 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7987 (m-80) REVERT: B 994 MET cc_start: 0.7635 (ppp) cc_final: 0.7124 (ppp) REVERT: B 998 MET cc_start: 0.6853 (pmm) cc_final: 0.6578 (pmm) REVERT: B 1023 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8399 (mttp) REVERT: B 1128 CYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8581 (m) REVERT: B 1198 LEU cc_start: 0.8518 (mt) cc_final: 0.8242 (tt) outliers start: 50 outliers final: 35 residues processed: 156 average time/residue: 0.2462 time to fit residues: 60.2927 Evaluate side-chains 149 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 975 ASN Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1282 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1046 THR Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 188 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 74 optimal weight: 0.1980 chunk 131 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 0.2980 chunk 155 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.113581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.084860 restraints weight = 25695.801| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.79 r_work: 0.3101 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15776 Z= 0.209 Angle : 0.563 10.198 21500 Z= 0.265 Chirality : 0.042 0.519 2540 Planarity : 0.003 0.028 2650 Dihedral : 9.023 103.984 2868 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.14 % Allowed : 14.36 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.20), residues: 1902 helix: 1.36 (0.16), residues: 1064 sheet: -1.61 (0.50), residues: 102 loop : -0.49 (0.25), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 592 HIS 0.003 0.001 HIS B1053 PHE 0.016 0.001 PHE A 839 TYR 0.013 0.001 TYR B 646 ARG 0.003 0.000 ARG B 406 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 1.557 Fit side-chains REVERT: A 476 ASN cc_start: 0.8470 (t0) cc_final: 0.8138 (t0) REVERT: A 524 TYR cc_start: 0.8103 (t80) cc_final: 0.7685 (t80) REVERT: A 566 GLU cc_start: 0.8720 (mt-10) cc_final: 0.7931 (mp0) REVERT: A 994 MET cc_start: 0.7728 (ppp) cc_final: 0.7381 (ppp) REVERT: A 1102 TYR cc_start: 0.8827 (m-10) cc_final: 0.8577 (m-10) REVERT: A 1128 CYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8636 (m) REVERT: A 1139 LEU cc_start: 0.8158 (tp) cc_final: 0.7939 (tp) REVERT: A 1198 LEU cc_start: 0.8528 (mt) cc_final: 0.8211 (tt) REVERT: A 1282 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7197 (pm20) REVERT: B 476 ASN cc_start: 0.8381 (t0) cc_final: 0.8024 (t0) REVERT: B 524 TYR cc_start: 0.8146 (t80) cc_final: 0.7739 (t80) REVERT: B 566 GLU cc_start: 0.8701 (mt-10) cc_final: 0.7931 (mp0) REVERT: B 607 MET cc_start: 0.8069 (mmm) cc_final: 0.7150 (mmm) REVERT: B 894 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: B 994 MET cc_start: 0.7674 (ppp) cc_final: 0.7098 (ppp) REVERT: B 998 MET cc_start: 0.6858 (pmm) cc_final: 0.6552 (pmm) REVERT: B 1023 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8457 (mttp) REVERT: B 1103 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8236 (pt0) REVERT: B 1128 CYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8581 (m) REVERT: B 1198 LEU cc_start: 0.8522 (mt) cc_final: 0.8256 (tt) REVERT: B 1282 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7097 (pm20) outliers start: 51 outliers final: 42 residues processed: 153 average time/residue: 0.2429 time to fit residues: 59.1124 Evaluate side-chains 159 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 110 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 712 ASP Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 811 CYS Chi-restraints excluded: chain A residue 851 LEU Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1128 CYS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain A residue 1247 THR Chi-restraints excluded: chain A residue 1282 GLU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 496 ASN Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 654 TYR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 690 LEU Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 712 ASP Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 975 ASN Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1023 LYS Chi-restraints excluded: chain B residue 1103 GLU Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1208 MET Chi-restraints excluded: chain B residue 1247 THR Chi-restraints excluded: chain B residue 1282 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.9821 > 50: distance: 84 - 103: 6.827 distance: 88 - 111: 6.343 distance: 94 - 121: 15.457 distance: 97 - 103: 9.534 distance: 98 - 125: 18.345 distance: 103 - 104: 5.822 distance: 104 - 105: 11.304 distance: 104 - 107: 17.836 distance: 105 - 106: 13.119 distance: 105 - 111: 9.984 distance: 106 - 133: 24.831 distance: 107 - 108: 16.196 distance: 108 - 109: 15.554 distance: 108 - 110: 14.929 distance: 111 - 112: 5.012 distance: 112 - 113: 4.177 distance: 112 - 115: 3.708 distance: 113 - 114: 5.309 distance: 113 - 121: 5.887 distance: 114 - 140: 21.933 distance: 115 - 116: 10.307 distance: 116 - 117: 10.469 distance: 116 - 118: 11.882 distance: 117 - 119: 15.871 distance: 118 - 120: 10.314 distance: 119 - 120: 9.538 distance: 121 - 122: 16.978 distance: 122 - 123: 4.464 distance: 123 - 124: 10.589 distance: 123 - 125: 13.902 distance: 125 - 126: 14.400 distance: 126 - 127: 9.741 distance: 126 - 129: 13.438 distance: 127 - 128: 4.338 distance: 127 - 133: 3.689 distance: 129 - 130: 16.113 distance: 130 - 131: 18.525 distance: 130 - 132: 11.104 distance: 133 - 134: 9.368 distance: 134 - 135: 23.552 distance: 134 - 137: 17.974 distance: 135 - 136: 16.139 distance: 135 - 140: 31.116 distance: 137 - 138: 10.424 distance: 137 - 139: 10.264 distance: 140 - 141: 21.478 distance: 141 - 142: 18.298 distance: 141 - 144: 19.569 distance: 142 - 143: 13.040 distance: 142 - 151: 25.652 distance: 144 - 145: 14.153 distance: 145 - 146: 12.552 distance: 145 - 147: 25.308 distance: 146 - 148: 17.031 distance: 147 - 149: 20.530 distance: 148 - 150: 16.086 distance: 149 - 150: 12.342 distance: 151 - 152: 32.997 distance: 152 - 153: 16.660 distance: 152 - 155: 12.611 distance: 153 - 154: 12.260 distance: 153 - 159: 9.452 distance: 154 - 181: 22.355 distance: 155 - 156: 34.767 distance: 156 - 157: 16.358 distance: 156 - 158: 29.670 distance: 159 - 160: 9.721 distance: 159 - 165: 6.200 distance: 160 - 161: 13.426 distance: 160 - 163: 9.518 distance: 161 - 162: 10.722 distance: 161 - 166: 17.595 distance: 162 - 189: 20.428 distance: 163 - 164: 18.101 distance: 164 - 165: 12.381 distance: 166 - 167: 14.318 distance: 167 - 168: 14.464 distance: 167 - 170: 15.749 distance: 168 - 169: 11.486 distance: 168 - 173: 3.006 distance: 170 - 171: 26.183 distance: 170 - 172: 25.007 distance: 173 - 174: 4.187 distance: 174 - 175: 3.272 distance: 174 - 177: 8.246 distance: 175 - 176: 6.245 distance: 175 - 181: 3.320 distance: 176 - 205: 11.180 distance: 177 - 178: 21.040 distance: 177 - 179: 23.335 distance: 178 - 180: 19.824