Starting phenix.real_space_refine on Tue Dec 31 15:39:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n4v_24179/12_2024/7n4v_24179.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n4v_24179/12_2024/7n4v_24179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n4v_24179/12_2024/7n4v_24179.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n4v_24179/12_2024/7n4v_24179.map" model { file = "/net/cci-nas-00/data/ceres_data/7n4v_24179/12_2024/7n4v_24179.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n4v_24179/12_2024/7n4v_24179.cif" } resolution = 3.58 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= 0.045 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 10064 2.51 5 N 2434 2.21 5 O 2800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15390 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: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 185 Unusual residues: {'CLR': 3, 'NAG': 4, 'POV': 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: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 185 Unusual residues: {'CLR': 3, 'NAG': 4, 'POV': 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: 10.01, per 1000 atoms: 0.65 Number of scatterers: 15390 At special positions: 0 Unit cell: (109.956, 133.28, 134.946, 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 2800 8.00 N 2434 7.00 C 10064 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=2.04 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=2.04 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=2.91 Simple disulfide: pdb=" SG CYS B 980 " - pdb=" SG CYS B 989 " distance=2.09 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 4.14 Conformation dependent library (CDL) restraints added in 2.0 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: 84 helices and 16 sheets defined 62.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 333 through 349 Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.594A 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 removed outlier: 3.603A pdb=" N THR A 373 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 388 through 402 removed outlier: 3.569A pdb=" N GLY A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 436 Processing helix chain 'A' and resid 437 through 453 removed outlier: 3.614A pdb=" N LEU A 441 " --> pdb=" O ASP A 437 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 removed outlier: 4.157A pdb=" N ILE A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 495 removed outlier: 3.745A pdb=" N TYR A 493 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.822A pdb=" N HIS A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN A 527 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 528 " --> pdb=" O TYR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 Processing helix chain 'A' and resid 583 through 607 removed outlier: 3.803A pdb=" N ALA A 587 " --> pdb=" O ASP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 626 removed outlier: 3.573A pdb=" N ASN A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 632 removed outlier: 3.863A pdb=" N GLU A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 652 removed outlier: 3.978A pdb=" N PHE A 636 " --> pdb=" O ASP A 632 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.961A 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 removed outlier: 3.687A pdb=" N GLY A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 701 through 711 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: 3.715A pdb=" N SER A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE A 791 " --> pdb=" O GLN A 787 " (cutoff:3.500A) removed outlier: 4.593A 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: 3.634A pdb=" N ARG A 846 " --> pdb=" O HIS A 842 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 894 removed outlier: 4.157A pdb=" N ASP A 885 " --> pdb=" O SER A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 Processing helix chain 'A' and resid 929 through 938 Processing helix chain 'A' and resid 952 through 961 removed outlier: 3.833A pdb=" N ASP A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1016 Proline residue: A1013 - end of helix Processing helix chain 'A' and resid 1028 through 1033 removed outlier: 3.930A pdb=" N SER A1033 " --> pdb=" O LEU A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1081 removed outlier: 3.659A pdb=" N TYR A1062 " --> pdb=" O ASN A1058 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A1079 " --> pdb=" O ASN A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1100 removed outlier: 3.886A pdb=" N ASN A1099 " --> pdb=" O THR A1096 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL A1100 " --> pdb=" O ILE A1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1096 through 1100' Processing helix chain 'A' and resid 1103 through 1106 Processing helix chain 'A' and resid 1107 through 1131 removed outlier: 4.050A pdb=" N GLU A1111 " --> pdb=" O THR A1107 " (cutoff:3.500A) Proline residue: A1122 - end of helix removed outlier: 3.593A pdb=" N LEU A1129 " --> pdb=" O ALA A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1160 removed outlier: 4.146A pdb=" N LEU A1140 " --> pdb=" O ARG A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1191 removed outlier: 4.236A pdb=" N VAL A1179 " --> pdb=" O VAL A1175 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU A1180 " --> pdb=" O GLY A1176 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A1181 " --> pdb=" O MET A1177 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS A1184 " --> pdb=" O GLU A1180 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1228 removed outlier: 4.147A pdb=" N MET A1218 " --> pdb=" O ALA A1214 " (cutoff:3.500A) Proline residue: A1222 - end of helix removed outlier: 4.330A pdb=" N VAL A1226 " --> pdb=" O PRO A1222 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A1227 " --> pdb=" O GLY A1223 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A1228 " --> pdb=" O ILE A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1239 Processing helix chain 'A' and resid 1239 through 1266 removed outlier: 4.704A pdb=" N LEU A1258 " --> pdb=" O GLY A1254 " (cutoff:3.500A) Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1277 through 1281 Processing helix chain 'B' and resid 334 through 349 Processing helix chain 'B' and resid 351 through 368 removed outlier: 3.594A 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 removed outlier: 3.602A pdb=" N THR B 373 " --> pdb=" O LEU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 383 Processing helix chain 'B' and resid 388 through 402 removed outlier: 3.568A pdb=" N GLY B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 436 Processing helix chain 'B' and resid 437 through 453 removed outlier: 3.612A pdb=" N LEU B 441 " --> pdb=" O ASP B 437 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 471 removed outlier: 4.157A pdb=" N ILE B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 495 removed outlier: 3.744A pdb=" N TYR B 493 " --> pdb=" O LEU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 Processing helix chain 'B' and resid 517 through 528 removed outlier: 3.822A pdb=" N HIS B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN B 527 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 Processing helix chain 'B' and resid 583 through 607 removed outlier: 3.803A pdb=" N ALA B 587 " --> pdb=" O ASP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 626 removed outlier: 3.572A pdb=" N ASN B 626 " --> pdb=" O GLU B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 632 removed outlier: 3.863A pdb=" N GLU B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 652 removed outlier: 3.979A pdb=" N PHE B 636 " --> pdb=" O ASP B 632 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 641 " --> pdb=" O ALA B 637 " (cutoff:3.500A) removed outlier: 3.962A 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 removed outlier: 3.688A pdb=" N GLY B 669 " --> pdb=" O LYS B 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 700 Processing helix chain 'B' and resid 701 through 711 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: 3.716A pdb=" N SER B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE B 791 " --> pdb=" O GLN B 787 " (cutoff:3.500A) removed outlier: 4.593A 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: 3.635A pdb=" N ARG B 846 " --> pdb=" O HIS B 842 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 894 removed outlier: 4.157A pdb=" N ASP B 885 " --> pdb=" O SER B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 Processing helix chain 'B' and resid 929 through 938 Processing helix chain 'B' and resid 952 through 961 removed outlier: 3.834A pdb=" N ASP B 956 " --> pdb=" O SER B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 1004 through 1016 Proline residue: B1013 - end of helix Processing helix chain 'B' and resid 1028 through 1033 removed outlier: 3.930A pdb=" N SER B1033 " --> pdb=" O LEU B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1081 removed outlier: 3.659A pdb=" N TYR B1062 " --> pdb=" O ASN B1058 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B1079 " --> pdb=" O ASN B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1096 through 1100 removed outlier: 3.884A pdb=" N ASN B1099 " --> pdb=" O THR B1096 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B1100 " --> pdb=" O ILE B1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1096 through 1100' Processing helix chain 'B' and resid 1103 through 1106 Processing helix chain 'B' and resid 1107 through 1131 removed outlier: 4.049A pdb=" N GLU B1111 " --> pdb=" O THR B1107 " (cutoff:3.500A) Proline residue: B1122 - end of helix removed outlier: 3.593A pdb=" N LEU B1129 " --> pdb=" O ALA B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1134 through 1160 removed outlier: 4.150A pdb=" N LEU B1140 " --> pdb=" O ARG B1136 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1191 removed outlier: 4.236A pdb=" N VAL B1179 " --> pdb=" O VAL B1175 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU B1180 " --> pdb=" O GLY B1176 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE B1181 " --> pdb=" O MET B1177 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS B1184 " --> pdb=" O GLU B1180 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B1185 " --> pdb=" O PHE B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1196 through 1228 removed outlier: 4.145A pdb=" N MET B1218 " --> pdb=" O ALA B1214 " (cutoff:3.500A) Proline residue: B1222 - end of helix removed outlier: 4.330A pdb=" N VAL B1226 " --> pdb=" O PRO B1222 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B1227 " --> pdb=" O GLY B1223 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B1228 " --> pdb=" O ILE B1224 " (cutoff:3.500A) Processing helix chain 'B' and resid 1232 through 1239 Processing helix chain 'B' and resid 1239 through 1266 removed outlier: 4.708A pdb=" N LEU B1258 " --> pdb=" O GLY B1254 " (cutoff:3.500A) Proline residue: B1259 - end of helix Processing helix chain 'B' and resid 1277 through 1281 Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 423 removed outlier: 3.570A pdb=" N LYS A 430 " --> pdb=" O TYR A 422 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 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 556 through 557 Processing sheet with id=AA6, first strand: chain 'A' and resid 948 through 951 removed outlier: 5.177A pdb=" N TYR A1052 " --> pdb=" O PRO A 949 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET A1050 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 979 through 980 removed outlier: 3.924A pdb=" N ARG A 968 " --> pdb=" O CYS A 980 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 991 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1036 through 1038 removed outlier: 3.933A pdb=" N THR A1046 " --> pdb=" O ASN A1037 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 410 through 411 Processing sheet with id=AB1, first strand: chain 'B' and resid 420 through 423 removed outlier: 3.569A pdb=" N LYS B 430 " --> pdb=" O TYR B 422 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 487 through 488 Processing sheet with id=AB3, first strand: chain 'B' and resid 505 through 509 Processing sheet with id=AB4, first strand: chain 'B' and resid 556 through 557 Processing sheet with id=AB5, first strand: chain 'B' and resid 948 through 951 removed outlier: 5.177A pdb=" N TYR B1052 " --> pdb=" O PRO B 949 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET B1050 " --> pdb=" O SER B 951 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 968 through 969 removed outlier: 4.367A pdb=" N LYS B 991 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1036 through 1038 removed outlier: 3.933A pdb=" N THR B1046 " --> pdb=" O ASN B1037 " (cutoff:3.500A) 802 hydrogen bonds defined for protein. 2316 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: 5.28 Time building geometry restraints manager: 4.76 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: 2382 1.31 - 1.44: 4275 1.44 - 1.57: 8975 1.57 - 1.69: 4 1.69 - 1.82: 138 Bond restraints: 15774 Sorted by residual: bond pdb=" N ILE B 470 " pdb=" CA ILE B 470 " ideal model delta sigma weight residual 1.456 1.500 -0.044 9.50e-03 1.11e+04 2.13e+01 bond pdb=" N ILE A 470 " pdb=" CA ILE A 470 " ideal model delta sigma weight residual 1.456 1.499 -0.043 9.50e-03 1.11e+04 2.05e+01 bond pdb=" N VAL A 701 " pdb=" CA VAL A 701 " ideal model delta sigma weight residual 1.456 1.499 -0.042 9.50e-03 1.11e+04 1.97e+01 bond pdb=" N VAL B 701 " pdb=" CA VAL B 701 " ideal model delta sigma weight residual 1.456 1.498 -0.042 9.50e-03 1.11e+04 1.91e+01 bond pdb=" N LEU A1012 " pdb=" CA LEU A1012 " ideal model delta sigma weight residual 1.463 1.492 -0.029 6.90e-03 2.10e+04 1.80e+01 ... (remaining 15769 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 17325 2.37 - 4.73: 4001 4.73 - 7.10: 156 7.10 - 9.47: 20 9.47 - 11.83: 4 Bond angle restraints: 21506 Sorted by residual: angle pdb=" C ALA B 914 " pdb=" N GLY B 915 " pdb=" CA GLY B 915 " ideal model delta sigma weight residual 119.94 125.22 -5.28 1.11e+00 8.12e-01 2.26e+01 angle pdb=" C SER B 433 " pdb=" N GLY B 434 " pdb=" CA GLY B 434 " ideal model delta sigma weight residual 119.98 125.24 -5.26 1.11e+00 8.12e-01 2.25e+01 angle pdb=" C ALA A 914 " pdb=" N GLY A 915 " pdb=" CA GLY A 915 " ideal model delta sigma weight residual 119.94 125.19 -5.25 1.11e+00 8.12e-01 2.24e+01 angle pdb=" C SER A1137 " pdb=" N GLY A1138 " pdb=" CA GLY A1138 " ideal model delta sigma weight residual 119.98 125.22 -5.24 1.11e+00 8.12e-01 2.23e+01 angle pdb=" C SER B1137 " pdb=" N GLY B1138 " pdb=" CA GLY B1138 " ideal model delta sigma weight residual 119.98 125.22 -5.24 1.11e+00 8.12e-01 2.23e+01 ... (remaining 21501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 9490 30.32 - 60.63: 363 60.63 - 90.95: 55 90.95 - 121.27: 16 121.27 - 151.59: 2 Dihedral angle restraints: 9926 sinusoidal: 4374 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 93.00 162.69 -69.69 1 1.00e+01 1.00e-02 6.27e+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 93.00 162.66 -69.66 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS A 966 " pdb=" SG CYS A 966 " pdb=" SG CYS A1024 " pdb=" CB CYS A1024 " ideal model delta sinusoidal sigma weight residual 93.00 158.05 -65.05 1 1.00e+01 1.00e-02 5.55e+01 ... (remaining 9923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.932: 2546 0.932 - 1.864: 0 1.864 - 2.796: 0 2.796 - 3.727: 0 3.727 - 4.659: 4 Chirality restraints: 2550 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 2.26 -4.66 2.00e-02 2.50e+03 5.43e+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 2.26 -4.66 2.00e-02 2.50e+03 5.42e+04 chirality pdb=" C1 NAG A1403 " pdb=" ND2 ASN A1075 " pdb=" C2 NAG A1403 " pdb=" O5 NAG A1403 " both_signs ideal model delta sigma weight residual False -2.40 2.24 -4.64 2.00e-01 2.50e+01 5.37e+02 ... (remaining 2547 not shown) Planarity restraints: 2662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1602 " -0.335 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG B1602 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG B1602 " -0.043 2.00e-02 2.50e+03 pdb=" N2 NAG B1602 " 0.507 2.00e-02 2.50e+03 pdb=" O7 NAG B1602 " -0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1401 " 0.335 2.00e-02 2.50e+03 2.89e-01 1.05e+03 pdb=" C7 NAG A1401 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1401 " 0.043 2.00e-02 2.50e+03 pdb=" N2 NAG A1401 " -0.507 2.00e-02 2.50e+03 pdb=" O7 NAG A1401 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " -0.252 2.00e-02 2.50e+03 2.12e-01 5.61e+02 pdb=" C7 NAG F 1 " 0.135 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " -0.202 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " 0.319 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.001 2.00e-02 2.50e+03 ... (remaining 2659 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2166 2.81 - 3.33: 16307 3.33 - 3.86: 23807 3.86 - 4.38: 30269 4.38 - 4.90: 50150 Nonbonded interactions: 122699 Sorted by model distance: nonbonded pdb=" ND2 ASN A1170 " pdb=" O PHE A1238 " model vdw 2.288 3.120 nonbonded pdb=" ND2 ASN B1170 " pdb=" O PHE B1238 " model vdw 2.289 3.120 nonbonded pdb=" OG SER B 433 " pdb=" O ALA B 567 " model vdw 2.308 3.040 nonbonded pdb=" OG SER A 433 " pdb=" O ALA A 567 " model vdw 2.309 3.040 nonbonded pdb=" O SER B1207 " pdb=" OG SER B1210 " model vdw 2.313 3.040 ... (remaining 122694 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 \ through 1407)) selection = (chain 'B' and (resid 333 through 1285 or resid 1602 through 1604 or resid 1606 \ through 1607)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 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: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.760 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 0.073 15774 Z= 0.901 Angle : 1.776 11.833 21506 Z= 1.307 Chirality : 0.203 4.659 2550 Planarity : 0.012 0.290 2648 Dihedral : 16.543 151.585 6310 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.64 % 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: -3.22 (0.16), residues: 1902 helix: -1.55 (0.13), residues: 1052 sheet: -3.15 (0.33), residues: 130 loop : -2.66 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 457 HIS 0.010 0.003 HIS B1184 PHE 0.027 0.003 PHE A 791 TYR 0.029 0.003 TYR A 646 ARG 0.004 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 198 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 TYR cc_start: 0.8582 (t80) cc_final: 0.8342 (t80) REVERT: A 487 ILE cc_start: 0.8406 (mt) cc_final: 0.8101 (mp) REVERT: A 623 ASP cc_start: 0.7479 (t0) cc_final: 0.7071 (t0) REVERT: A 743 VAL cc_start: 0.7736 (m) cc_final: 0.7504 (p) REVERT: A 894 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7717 (m-10) REVERT: A 1011 TYR cc_start: 0.7871 (m-10) cc_final: 0.7294 (m-10) REVERT: A 1218 MET cc_start: 0.8177 (mmt) cc_final: 0.7951 (mmm) REVERT: B 457 TRP cc_start: 0.6069 (t-100) cc_final: 0.5225 (t-100) REVERT: B 588 GLN cc_start: 0.8065 (mt0) cc_final: 0.7631 (mm-40) REVERT: B 591 LEU cc_start: 0.8114 (mt) cc_final: 0.7863 (mt) REVERT: B 894 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8171 (m-10) REVERT: B 1064 GLU cc_start: 0.6870 (mm-30) cc_final: 0.6493 (mp0) REVERT: B 1091 GLU cc_start: 0.7366 (pt0) cc_final: 0.6999 (tt0) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.2925 time to fit residues: 85.8034 Evaluate side-chains 135 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain B residue 894 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN A 488 ASN A1043 GLN B 339 GLN B1043 GLN B1236 GLN B1253 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15774 Z= 0.208 Angle : 0.709 15.043 21506 Z= 0.329 Chirality : 0.048 0.717 2550 Planarity : 0.004 0.040 2648 Dihedral : 12.244 130.889 2936 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.36 % Allowed : 10.42 % Favored : 88.22 % 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: -0.86 (0.19), residues: 1902 helix: 0.47 (0.16), residues: 1068 sheet: -2.49 (0.36), residues: 130 loop : -1.76 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 953 HIS 0.005 0.001 HIS B1053 PHE 0.024 0.001 PHE B 930 TYR 0.020 0.001 TYR A 886 ARG 0.003 0.000 ARG B 693 *********************** 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 173 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 422 TYR cc_start: 0.8672 (t80) cc_final: 0.8256 (t80) REVERT: A 450 ARG cc_start: 0.7851 (ttm170) cc_final: 0.7626 (ttm170) REVERT: A 457 TRP cc_start: 0.6620 (t-100) cc_final: 0.5763 (t-100) REVERT: A 610 MET cc_start: 0.7997 (ttm) cc_final: 0.7651 (ttp) REVERT: A 766 MET cc_start: 0.6680 (mmt) cc_final: 0.6478 (mmt) REVERT: A 783 ASP cc_start: 0.7575 (t70) cc_final: 0.7308 (t0) REVERT: A 1011 TYR cc_start: 0.7973 (m-10) cc_final: 0.7529 (m-80) REVERT: A 1218 MET cc_start: 0.8251 (mmt) cc_final: 0.8034 (mmm) REVERT: B 457 TRP cc_start: 0.6169 (t-100) cc_final: 0.5402 (t-100) REVERT: B 579 TYR cc_start: 0.7582 (m-80) cc_final: 0.7083 (m-80) REVERT: B 588 GLN cc_start: 0.8112 (mt0) cc_final: 0.7608 (mm-40) REVERT: B 591 LEU cc_start: 0.8047 (mt) cc_final: 0.7834 (mt) REVERT: B 610 MET cc_start: 0.8168 (ttm) cc_final: 0.7895 (ttp) REVERT: B 894 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: B 1091 GLU cc_start: 0.7205 (pt0) cc_final: 0.6799 (tt0) outliers start: 22 outliers final: 7 residues processed: 161 average time/residue: 0.2668 time to fit residues: 65.9798 Evaluate side-chains 142 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 1162 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 143 optimal weight: 0.0670 chunk 117 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 171 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 138 optimal weight: 0.3980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A1009 HIS ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1253 HIS B 448 GLN B 496 ASN ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15774 Z= 0.183 Angle : 0.611 13.623 21506 Z= 0.286 Chirality : 0.042 0.332 2550 Planarity : 0.004 0.045 2648 Dihedral : 9.910 119.189 2936 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.91 % Allowed : 11.71 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.20), residues: 1902 helix: 0.89 (0.16), residues: 1072 sheet: -2.23 (0.39), residues: 130 loop : -1.41 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1014 HIS 0.004 0.001 HIS B1053 PHE 0.019 0.001 PHE B 930 TYR 0.020 0.001 TYR A 646 ARG 0.004 0.000 ARG A 693 *********************** 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 180 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 TYR cc_start: 0.8745 (t80) cc_final: 0.8237 (t80) REVERT: A 457 TRP cc_start: 0.6541 (t-100) cc_final: 0.5704 (t-100) REVERT: A 610 MET cc_start: 0.8032 (ttm) cc_final: 0.7629 (ttp) REVERT: A 707 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6558 (tp) REVERT: A 783 ASP cc_start: 0.7574 (t70) cc_final: 0.7302 (t0) REVERT: A 1008 PHE cc_start: 0.8347 (t80) cc_final: 0.8115 (t80) REVERT: A 1064 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6325 (mp0) REVERT: A 1218 MET cc_start: 0.8283 (mmt) cc_final: 0.7833 (mmm) REVERT: B 421 ARG cc_start: 0.7951 (mmm160) cc_final: 0.7719 (mmm160) REVERT: B 422 TYR cc_start: 0.8717 (t80) cc_final: 0.8398 (t80) REVERT: B 457 TRP cc_start: 0.6084 (t-100) cc_final: 0.5393 (t-100) REVERT: B 579 TYR cc_start: 0.7618 (m-80) cc_final: 0.7091 (m-80) REVERT: B 588 GLN cc_start: 0.8034 (mt0) cc_final: 0.7590 (mm-40) REVERT: B 607 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7747 (mpp) REVERT: B 610 MET cc_start: 0.8148 (ttm) cc_final: 0.7821 (ttp) REVERT: B 1008 PHE cc_start: 0.8050 (t80) cc_final: 0.7618 (m-80) REVERT: B 1064 GLU cc_start: 0.6747 (mm-30) cc_final: 0.6223 (mp0) REVERT: B 1091 GLU cc_start: 0.7103 (pt0) cc_final: 0.6724 (tt0) outliers start: 31 outliers final: 16 residues processed: 169 average time/residue: 0.2569 time to fit residues: 67.3875 Evaluate side-chains 153 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 607 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 851 LEU Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1265 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 0.0470 chunk 129 optimal weight: 0.8980 chunk 89 optimal weight: 0.0270 chunk 19 optimal weight: 0.3980 chunk 82 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN A 496 ASN A 802 GLN ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15774 Z= 0.153 Angle : 0.575 9.526 21506 Z= 0.271 Chirality : 0.040 0.245 2550 Planarity : 0.004 0.047 2648 Dihedral : 9.218 108.555 2936 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.97 % Allowed : 12.89 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1902 helix: 1.23 (0.16), residues: 1070 sheet: -2.26 (0.39), residues: 138 loop : -1.18 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1014 HIS 0.003 0.001 HIS B1053 PHE 0.020 0.001 PHE A 432 TYR 0.019 0.001 TYR A 646 ARG 0.003 0.000 ARG B 421 *********************** 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 188 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 TYR cc_start: 0.8725 (t80) cc_final: 0.8226 (t80) REVERT: A 457 TRP cc_start: 0.6504 (t-100) cc_final: 0.5679 (t-100) REVERT: A 610 MET cc_start: 0.8034 (ttm) cc_final: 0.7707 (ptm) REVERT: A 707 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6529 (tp) REVERT: A 994 MET cc_start: 0.7712 (mmm) cc_final: 0.7495 (tpt) REVERT: A 1064 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6402 (mp0) REVERT: A 1218 MET cc_start: 0.8278 (mmt) cc_final: 0.7842 (mmm) REVERT: B 421 ARG cc_start: 0.7876 (mmm160) cc_final: 0.7661 (mmm160) REVERT: B 422 TYR cc_start: 0.8706 (t80) cc_final: 0.8318 (t80) REVERT: B 457 TRP cc_start: 0.5979 (t-100) cc_final: 0.5315 (t-100) REVERT: B 579 TYR cc_start: 0.7649 (m-80) cc_final: 0.7153 (m-80) REVERT: B 588 GLN cc_start: 0.8031 (mt0) cc_final: 0.7563 (mm-40) REVERT: B 610 MET cc_start: 0.8159 (ttm) cc_final: 0.7851 (ttp) REVERT: B 1064 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6431 (mp0) REVERT: B 1091 GLU cc_start: 0.7055 (pt0) cc_final: 0.6715 (tt0) outliers start: 32 outliers final: 19 residues processed: 176 average time/residue: 0.2674 time to fit residues: 73.2511 Evaluate side-chains 153 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1162 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 156 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 164 optimal weight: 0.0470 chunk 46 optimal weight: 1.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15774 Z= 0.155 Angle : 0.563 10.793 21506 Z= 0.265 Chirality : 0.040 0.285 2550 Planarity : 0.004 0.048 2648 Dihedral : 9.017 108.126 2936 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.22 % Allowed : 13.69 % Favored : 84.09 % 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: 0.22 (0.20), residues: 1902 helix: 1.29 (0.16), residues: 1076 sheet: -2.33 (0.39), residues: 142 loop : -1.09 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1014 HIS 0.003 0.001 HIS B1053 PHE 0.019 0.001 PHE A 432 TYR 0.020 0.001 TYR A 646 ARG 0.004 0.000 ARG B 693 *********************** 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 171 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 TRP cc_start: 0.6460 (t-100) cc_final: 0.5643 (t-100) REVERT: A 610 MET cc_start: 0.8062 (ttm) cc_final: 0.7699 (ptm) REVERT: A 707 LEU cc_start: 0.7131 (OUTLIER) cc_final: 0.6678 (tp) REVERT: A 990 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8420 (mm) REVERT: A 1064 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6403 (mp0) REVERT: B 421 ARG cc_start: 0.7845 (mmm160) cc_final: 0.7638 (mmm160) REVERT: B 422 TYR cc_start: 0.8696 (t80) cc_final: 0.8267 (t80) REVERT: B 457 TRP cc_start: 0.5977 (t-100) cc_final: 0.5327 (t-100) REVERT: B 579 TYR cc_start: 0.7640 (m-80) cc_final: 0.7137 (m-80) REVERT: B 588 GLN cc_start: 0.8084 (mt0) cc_final: 0.7601 (mm-40) REVERT: B 943 GLN cc_start: 0.8473 (mp10) cc_final: 0.8155 (mt0) REVERT: B 990 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.7901 (mm) REVERT: B 1064 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6453 (mp0) REVERT: B 1091 GLU cc_start: 0.6959 (pt0) cc_final: 0.6587 (tt0) outliers start: 36 outliers final: 20 residues processed: 160 average time/residue: 0.2555 time to fit residues: 64.1524 Evaluate side-chains 155 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1009 HIS Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 36 optimal weight: 0.2980 chunk 107 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 152 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 60 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 ASN ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15774 Z= 0.174 Angle : 0.563 9.993 21506 Z= 0.266 Chirality : 0.040 0.240 2550 Planarity : 0.003 0.050 2648 Dihedral : 8.994 106.748 2936 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.28 % Allowed : 13.93 % Favored : 83.79 % 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: 0.25 (0.20), residues: 1902 helix: 1.30 (0.16), residues: 1076 sheet: -2.38 (0.39), residues: 142 loop : -1.03 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1014 HIS 0.003 0.001 HIS B1053 PHE 0.015 0.001 PHE A 432 TYR 0.018 0.001 TYR A 646 ARG 0.004 0.000 ARG B 693 *********************** 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 173 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6816 (pm20) REVERT: A 457 TRP cc_start: 0.6517 (t-100) cc_final: 0.5669 (t-100) REVERT: A 610 MET cc_start: 0.8090 (ttm) cc_final: 0.7694 (ptm) REVERT: A 990 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8399 (mm) REVERT: A 1064 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6429 (mp0) REVERT: B 374 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6687 (pm20) REVERT: B 421 ARG cc_start: 0.7821 (mmm160) cc_final: 0.7589 (mmm160) REVERT: B 422 TYR cc_start: 0.8702 (t80) cc_final: 0.8255 (t80) REVERT: B 457 TRP cc_start: 0.5983 (t-100) cc_final: 0.5338 (t-100) REVERT: B 579 TYR cc_start: 0.7625 (m-80) cc_final: 0.7155 (m-80) REVERT: B 943 GLN cc_start: 0.8468 (mp10) cc_final: 0.8159 (mt0) REVERT: B 990 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7847 (mm) REVERT: B 1008 PHE cc_start: 0.8056 (t80) cc_final: 0.7541 (m-80) REVERT: B 1091 GLU cc_start: 0.6961 (pt0) cc_final: 0.6622 (tt0) outliers start: 37 outliers final: 23 residues processed: 161 average time/residue: 0.2700 time to fit residues: 66.7058 Evaluate side-chains 160 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1156 MET Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 134 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15774 Z= 0.180 Angle : 0.564 11.608 21506 Z= 0.267 Chirality : 0.040 0.260 2550 Planarity : 0.004 0.052 2648 Dihedral : 8.849 106.604 2936 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.28 % Allowed : 14.73 % 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: 0.27 (0.20), residues: 1902 helix: 1.35 (0.16), residues: 1064 sheet: -2.40 (0.39), residues: 142 loop : -1.05 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1014 HIS 0.003 0.001 HIS B1053 PHE 0.012 0.001 PHE A 791 TYR 0.019 0.001 TYR A 646 ARG 0.013 0.000 ARG A 605 *********************** 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 173 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6800 (pm20) REVERT: A 457 TRP cc_start: 0.6483 (t-100) cc_final: 0.5676 (t-100) REVERT: A 610 MET cc_start: 0.8078 (ttm) cc_final: 0.7657 (ptm) REVERT: A 766 MET cc_start: 0.6336 (mmt) cc_final: 0.5990 (mmt) REVERT: A 814 LYS cc_start: 0.6497 (mmtm) cc_final: 0.5915 (mttt) REVERT: A 990 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8396 (mm) REVERT: A 1064 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6429 (mp0) REVERT: B 421 ARG cc_start: 0.7787 (mmm160) cc_final: 0.7561 (mmm160) REVERT: B 422 TYR cc_start: 0.8706 (t80) cc_final: 0.8233 (t80) REVERT: B 457 TRP cc_start: 0.5975 (t-100) cc_final: 0.5339 (t-100) REVERT: B 579 TYR cc_start: 0.7630 (m-80) cc_final: 0.7176 (m-80) REVERT: B 943 GLN cc_start: 0.8443 (mp10) cc_final: 0.8155 (mt0) REVERT: B 990 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7788 (mm) REVERT: B 1008 PHE cc_start: 0.8048 (t80) cc_final: 0.7631 (m-80) REVERT: B 1064 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6463 (mp0) REVERT: B 1091 GLU cc_start: 0.6975 (pt0) cc_final: 0.6616 (tt0) outliers start: 37 outliers final: 25 residues processed: 160 average time/residue: 0.2784 time to fit residues: 67.2194 Evaluate side-chains 163 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1009 HIS Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1162 SER 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 73 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 90 optimal weight: 0.2980 chunk 17 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15774 Z= 0.230 Angle : 0.581 12.044 21506 Z= 0.276 Chirality : 0.041 0.235 2550 Planarity : 0.004 0.055 2648 Dihedral : 8.706 105.659 2936 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.47 % Allowed : 14.80 % Favored : 82.74 % 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: 0.15 (0.20), residues: 1902 helix: 1.25 (0.16), residues: 1070 sheet: -2.43 (0.39), residues: 142 loop : -1.11 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B1014 HIS 0.003 0.001 HIS A1053 PHE 0.017 0.001 PHE A 791 TYR 0.018 0.001 TYR A 646 ARG 0.005 0.000 ARG A 605 *********************** 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 181 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 1.825 Fit side-chains revert: symmetry clash REVERT: A 374 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6775 (pm20) REVERT: A 421 ARG cc_start: 0.7757 (mmm160) cc_final: 0.7477 (mmm-85) REVERT: A 457 TRP cc_start: 0.6404 (t-100) cc_final: 0.5648 (t-100) REVERT: A 610 MET cc_start: 0.8110 (ttm) cc_final: 0.7695 (ttp) REVERT: A 814 LYS cc_start: 0.6436 (mmtm) cc_final: 0.5900 (mttt) REVERT: A 990 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8274 (mm) REVERT: A 1050 MET cc_start: 0.8830 (ttt) cc_final: 0.8138 (ttt) REVERT: A 1064 GLU cc_start: 0.6979 (mm-30) cc_final: 0.6477 (mp0) REVERT: B 374 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6497 (pm20) REVERT: B 421 ARG cc_start: 0.7747 (mmm160) cc_final: 0.7522 (mmm160) REVERT: B 422 TYR cc_start: 0.8682 (t80) cc_final: 0.8143 (t80) REVERT: B 457 TRP cc_start: 0.6006 (t-100) cc_final: 0.5392 (t-100) REVERT: B 579 TYR cc_start: 0.7603 (m-80) cc_final: 0.7157 (m-80) REVERT: B 943 GLN cc_start: 0.8414 (mp10) cc_final: 0.8143 (mt0) REVERT: B 990 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7797 (mm) REVERT: B 1008 PHE cc_start: 0.7997 (t80) cc_final: 0.7711 (m-80) REVERT: B 1064 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6440 (mp0) REVERT: B 1091 GLU cc_start: 0.7036 (pt0) cc_final: 0.6618 (tt0) outliers start: 40 outliers final: 28 residues processed: 169 average time/residue: 0.3213 time to fit residues: 82.6054 Evaluate side-chains 166 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 616 MET Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1123 THR Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 chunk 175 optimal weight: 0.0040 chunk 102 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 0.0070 chunk 52 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 112 optimal weight: 0.0270 chunk 180 optimal weight: 0.9990 overall best weight: 0.3470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15774 Z= 0.140 Angle : 0.549 12.892 21506 Z= 0.259 Chirality : 0.039 0.309 2550 Planarity : 0.004 0.051 2648 Dihedral : 8.489 105.340 2936 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.97 % Allowed : 15.41 % Favored : 82.61 % 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: 0.40 (0.20), residues: 1902 helix: 1.42 (0.16), residues: 1072 sheet: -2.36 (0.39), residues: 142 loop : -0.96 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1014 HIS 0.002 0.001 HIS A1053 PHE 0.014 0.001 PHE A 930 TYR 0.021 0.001 TYR A 646 ARG 0.005 0.000 ARG B 693 *********************** REFINEMENT MACRO_CYCLE 9 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 180 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6748 (pm20) REVERT: A 411 ILE cc_start: 0.7196 (OUTLIER) cc_final: 0.6991 (mm) REVERT: A 421 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7489 (mmm-85) REVERT: A 457 TRP cc_start: 0.6332 (t-100) cc_final: 0.5618 (t-100) REVERT: A 610 MET cc_start: 0.8099 (ttm) cc_final: 0.7810 (ttp) REVERT: A 814 LYS cc_start: 0.6424 (mmtm) cc_final: 0.5828 (tppt) REVERT: A 990 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8294 (mm) REVERT: A 1064 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6482 (mp0) REVERT: B 374 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6448 (pm20) REVERT: B 421 ARG cc_start: 0.7811 (mmm160) cc_final: 0.7572 (mmm160) REVERT: B 422 TYR cc_start: 0.8689 (t80) cc_final: 0.8134 (t80) REVERT: B 457 TRP cc_start: 0.5955 (t-100) cc_final: 0.5385 (t-100) REVERT: B 579 TYR cc_start: 0.7587 (m-80) cc_final: 0.7153 (m-80) REVERT: B 605 ARG cc_start: 0.8395 (ttm-80) cc_final: 0.7941 (mtt90) REVERT: B 943 GLN cc_start: 0.8392 (mp10) cc_final: 0.8117 (mt0) REVERT: B 990 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7860 (mm) REVERT: B 1064 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6442 (mp0) REVERT: B 1091 GLU cc_start: 0.6953 (pt0) cc_final: 0.6539 (tt0) outliers start: 32 outliers final: 21 residues processed: 170 average time/residue: 0.2753 time to fit residues: 71.6115 Evaluate side-chains 164 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 189 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 116 optimal weight: 0.0070 chunk 92 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15774 Z= 0.158 Angle : 0.561 12.634 21506 Z= 0.264 Chirality : 0.040 0.321 2550 Planarity : 0.003 0.051 2648 Dihedral : 8.384 104.560 2936 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.91 % Allowed : 15.72 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1902 helix: 1.44 (0.16), residues: 1064 sheet: -2.30 (0.39), residues: 142 loop : -0.90 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B1014 HIS 0.002 0.001 HIS A1053 PHE 0.015 0.001 PHE A 853 TYR 0.020 0.001 TYR A 646 ARG 0.005 0.000 ARG B 605 ********************** REFINEMENT MACRO_CYCLE 10 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 177 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6533 (pm20) REVERT: A 411 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6981 (mm) REVERT: A 421 ARG cc_start: 0.7754 (mmm160) cc_final: 0.7488 (mmm-85) REVERT: A 457 TRP cc_start: 0.6357 (t-100) cc_final: 0.5663 (t-100) REVERT: A 610 MET cc_start: 0.8117 (ttm) cc_final: 0.7829 (ttp) REVERT: A 814 LYS cc_start: 0.6453 (mmtm) cc_final: 0.5900 (tppt) REVERT: A 990 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8281 (mm) REVERT: A 1064 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6498 (mp0) REVERT: B 374 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6409 (pm20) REVERT: B 421 ARG cc_start: 0.7837 (mmm160) cc_final: 0.7605 (mmm160) REVERT: B 422 TYR cc_start: 0.8719 (t80) cc_final: 0.8227 (t80) REVERT: B 457 TRP cc_start: 0.5945 (t-100) cc_final: 0.5387 (t-100) REVERT: B 579 TYR cc_start: 0.7572 (m-80) cc_final: 0.7141 (m-80) REVERT: B 605 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.7895 (mtt90) REVERT: B 943 GLN cc_start: 0.8387 (mp10) cc_final: 0.8117 (mt0) REVERT: B 990 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7876 (mm) REVERT: B 1064 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6441 (mp0) REVERT: B 1091 GLU cc_start: 0.7001 (pt0) cc_final: 0.6583 (tt0) outliers start: 31 outliers final: 22 residues processed: 166 average time/residue: 0.2747 time to fit residues: 69.4908 Evaluate side-chains 163 residues out of total 1622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 843 TRP Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 990 LEU Chi-restraints excluded: chain A residue 1123 THR Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain A residue 1208 MET Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 516 VAL Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 843 TRP Chi-restraints excluded: chain B residue 894 PHE Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1162 SER Chi-restraints excluded: chain B residue 1208 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.149545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.110592 restraints weight = 21281.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111513 restraints weight = 15330.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.113019 restraints weight = 12441.597| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15774 Z= 0.179 Angle : 0.573 12.266 21506 Z= 0.268 Chirality : 0.040 0.306 2550 Planarity : 0.004 0.051 2648 Dihedral : 8.321 104.028 2936 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.10 % Allowed : 15.84 % Favored : 82.06 % 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: 0.36 (0.20), residues: 1902 helix: 1.34 (0.16), residues: 1078 sheet: -2.29 (0.39), residues: 142 loop : -0.93 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B1014 HIS 0.002 0.001 HIS A1053 PHE 0.020 0.001 PHE A 853 TYR 0.019 0.001 TYR A 646 ARG 0.004 0.000 ARG B 693 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2757.45 seconds wall clock time: 52 minutes 7.78 seconds (3127.78 seconds total)