Starting phenix.real_space_refine on Mon Sep 30 15:00:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r19_14235/09_2024/7r19_14235.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r19_14235/09_2024/7r19_14235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r19_14235/09_2024/7r19_14235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r19_14235/09_2024/7r19_14235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r19_14235/09_2024/7r19_14235.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r19_14235/09_2024/7r19_14235.cif" } resolution = 3.3 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= 0.004 sd= 0.057 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 16167 2.51 5 N 4190 2.21 5 O 4917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25388 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8308 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 53, 'TRANS': 1008} Chain breaks: 5 Chain: "B" Number of atoms: 8274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8274 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 5 Chain: "C" Number of atoms: 8274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8274 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 5 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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 16.85, per 1000 atoms: 0.66 Number of scatterers: 25388 At special positions: 0 Unit cell: (159.544, 156.31, 197.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4917 8.00 N 4190 7.00 C 16167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 331 " " NAG B1309 " - " ASN B1098 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 801 " " NAG C1309 " - " ASN C1134 " " NAG C1310 " - " ASN C 717 " " NAG C1311 " - " ASN C1098 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1134 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B 717 " Time building additional restraints: 6.63 Conformation dependent library (CDL) restraints added in 3.4 seconds 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5942 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 45 sheets defined 23.5% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.884A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.629A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.511A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.548A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.523A pdb=" N ILE A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.420A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 5.121A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.897A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.618A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 753 removed outlier: 3.904A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.664A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.600A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.765A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.704A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.548A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.119A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.706A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.993A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.066A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.721A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 371' Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.297A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.513A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.530A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.549A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.537A pdb=" N ASP C 950 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.643A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.271A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.040A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.159A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.018A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 7.186A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 4.060A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.503A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.044A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.797A pdb=" N LYS A 424 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLU A 465 " --> pdb=" O LYS A 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 448 through 454 removed outlier: 8.278A pdb=" N ASN A 450 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 10.258A pdb=" N GLN A 493 " --> pdb=" O ASN A 450 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.148A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.445A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.617A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.178A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.178A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.765A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.546A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 197 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.630A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.504A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.565A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.441A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 152 through 157 removed outlier: 6.445A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 318 removed outlier: 7.181A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.896A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 653 through 655 removed outlier: 6.381A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.470A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 713 removed outlier: 4.044A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.509A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.566A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.687A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 152 through 157 removed outlier: 3.573A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.505A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.645A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.631A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.525A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.543A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.648A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1124 removed outlier: 5.768A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 974 hydrogen bonds defined for protein. 2676 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.09 Time building geometry restraints manager: 7.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8032 1.34 - 1.46: 5642 1.46 - 1.58: 12147 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 25965 Sorted by residual: bond pdb=" N VAL C 608 " pdb=" CA VAL C 608 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.16e+01 bond pdb=" N VAL B 395 " pdb=" CA VAL B 395 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.17e-02 7.31e+03 1.03e+01 bond pdb=" N GLY B 431 " pdb=" CA GLY B 431 " ideal model delta sigma weight residual 1.445 1.474 -0.029 9.20e-03 1.18e+04 9.99e+00 bond pdb=" N ILE C 598 " pdb=" CA ILE C 598 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.20e-02 6.94e+03 9.10e+00 bond pdb=" N VAL C 362 " pdb=" CA VAL C 362 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.24e-02 6.50e+03 8.92e+00 ... (remaining 25960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 34120 1.47 - 2.93: 1026 2.93 - 4.40: 155 4.40 - 5.87: 19 5.87 - 7.33: 8 Bond angle restraints: 35328 Sorted by residual: angle pdb=" CA SER A 591 " pdb=" C SER A 591 " pdb=" O SER A 591 " ideal model delta sigma weight residual 121.84 117.25 4.59 1.16e+00 7.43e-01 1.57e+01 angle pdb=" C PHE A 592 " pdb=" CA PHE A 592 " pdb=" CB PHE A 592 " ideal model delta sigma weight residual 110.22 116.60 -6.38 1.67e+00 3.59e-01 1.46e+01 angle pdb=" CA VAL A1040 " pdb=" C VAL A1040 " pdb=" O VAL A1040 " ideal model delta sigma weight residual 121.17 117.23 3.94 1.06e+00 8.90e-01 1.38e+01 angle pdb=" C GLY C 757 " pdb=" N SER C 758 " pdb=" CA SER C 758 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+01 angle pdb=" C ALA C1070 " pdb=" N GLN C1071 " pdb=" CA GLN C1071 " ideal model delta sigma weight residual 122.35 127.64 -5.29 1.46e+00 4.69e-01 1.31e+01 ... (remaining 35323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14997 17.99 - 35.99: 788 35.99 - 53.98: 146 53.98 - 71.97: 25 71.97 - 89.97: 13 Dihedral angle restraints: 15969 sinusoidal: 6729 harmonic: 9240 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -1.36 -84.64 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -140.82 54.82 1 1.00e+01 1.00e-02 4.07e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -48.41 -37.59 1 1.00e+01 1.00e-02 1.99e+01 ... (remaining 15966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3521 0.064 - 0.129: 532 0.129 - 0.193: 39 0.193 - 0.258: 6 0.258 - 0.322: 2 Chirality restraints: 4100 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA TYR A 508 " pdb=" N TYR A 508 " pdb=" C TYR A 508 " pdb=" CB TYR A 508 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 4097 not shown) Planarity restraints: 4572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " -0.316 2.00e-02 2.50e+03 2.77e-01 9.56e+02 pdb=" C7 NAG B1307 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " -0.081 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " 0.494 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " -0.164 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 353 " -0.010 2.00e-02 2.50e+03 1.12e-02 3.12e+00 pdb=" CG TRP B 353 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 353 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 353 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 353 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 353 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 353 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 353 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 353 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 353 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 81 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO C 82 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 82 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 82 " -0.023 5.00e-02 4.00e+02 ... (remaining 4569 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 950 2.72 - 3.27: 24220 3.27 - 3.81: 39302 3.81 - 4.36: 47441 4.36 - 4.90: 83264 Nonbonded interactions: 195177 Sorted by model distance: nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.179 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.277 3.040 nonbonded pdb=" OG1 THR B 645 " pdb=" O GLY B 648 " model vdw 2.287 3.040 nonbonded pdb=" OG SER A 730 " pdb=" OG1 THR A 778 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR A 22 " pdb=" O THR A 76 " model vdw 2.299 3.040 ... (remaining 195172 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 14 through 827 or resid 856 through 1146 or resid 1301 thr \ ough 1309)) selection = chain 'B' selection = (chain 'C' and (resid 14 through 1146 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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=0.00 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: 7.700 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: 0.960 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 63.210 Find NCS groups from input model: 1.420 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: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.004 0.040 25965 Z= 0.253 Angle : 0.587 7.335 35328 Z= 0.341 Chirality : 0.046 0.322 4100 Planarity : 0.005 0.277 4538 Dihedral : 11.323 89.968 9901 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.18 % Allowed : 0.40 % Favored : 99.42 % 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: 0.42 (0.14), residues: 3142 helix: 2.63 (0.20), residues: 612 sheet: 0.74 (0.19), residues: 730 loop : -0.80 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 353 HIS 0.005 0.001 HIS C1064 PHE 0.017 0.001 PHE C 392 TYR 0.020 0.001 TYR C 508 ARG 0.006 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 282 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8494 (tp40) cc_final: 0.8060 (tp40) REVERT: A 591 SER cc_start: 0.7312 (m) cc_final: 0.6838 (p) REVERT: B 170 TYR cc_start: 0.6243 (t80) cc_final: 0.5930 (t80) REVERT: B 586 ASP cc_start: 0.7653 (t0) cc_final: 0.7392 (t0) REVERT: C 242 LEU cc_start: 0.9102 (mp) cc_final: 0.8595 (mt) REVERT: C 409 GLN cc_start: 0.7908 (mt0) cc_final: 0.7382 (mt0) REVERT: C 456 PHE cc_start: 0.8793 (m-80) cc_final: 0.8438 (m-10) REVERT: C 508 TYR cc_start: 0.6488 (m-10) cc_final: 0.6272 (m-80) REVERT: C 814 LYS cc_start: 0.7583 (mmtp) cc_final: 0.6998 (ptpt) outliers start: 5 outliers final: 1 residues processed: 286 average time/residue: 0.3695 time to fit residues: 167.0631 Evaluate side-chains 130 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 132 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 150 optimal weight: 6.9990 chunk 184 optimal weight: 1.9990 chunk 286 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS A 207 HIS A 856 ASN A 901 GLN A 935 GLN B 207 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25965 Z= 0.274 Angle : 0.580 10.644 35328 Z= 0.305 Chirality : 0.045 0.305 4100 Planarity : 0.004 0.042 4538 Dihedral : 5.382 54.214 4205 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.58 % Allowed : 5.95 % Favored : 93.48 % 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: 0.38 (0.14), residues: 3142 helix: 2.49 (0.21), residues: 624 sheet: 0.86 (0.18), residues: 755 loop : -0.89 (0.13), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.010 0.001 HIS B 245 PHE 0.022 0.002 PHE C 400 TYR 0.023 0.001 TYR B 265 ARG 0.009 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8604 (tp40) cc_final: 0.8346 (tp40) REVERT: A 436 TRP cc_start: 0.8124 (p90) cc_final: 0.7679 (p90) REVERT: B 436 TRP cc_start: 0.7346 (p90) cc_final: 0.7011 (p90) REVERT: C 242 LEU cc_start: 0.8840 (mp) cc_final: 0.8465 (mt) REVERT: C 456 PHE cc_start: 0.8803 (m-80) cc_final: 0.8602 (m-80) REVERT: C 508 TYR cc_start: 0.6562 (m-10) cc_final: 0.6063 (m-80) REVERT: C 814 LYS cc_start: 0.7584 (mmtp) cc_final: 0.7014 (ptpt) outliers start: 16 outliers final: 13 residues processed: 149 average time/residue: 0.3496 time to fit residues: 87.4697 Evaluate side-chains 130 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 195 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 287 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 chunk 256 optimal weight: 10.0000 chunk 285 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 230 optimal weight: 0.0770 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 207 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 913 GLN C 146 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25965 Z= 0.173 Angle : 0.499 9.613 35328 Z= 0.260 Chirality : 0.043 0.241 4100 Planarity : 0.003 0.037 4538 Dihedral : 5.025 54.684 4205 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.90 % Allowed : 6.81 % Favored : 92.29 % 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: 0.41 (0.15), residues: 3142 helix: 2.57 (0.21), residues: 628 sheet: 0.77 (0.18), residues: 769 loop : -0.87 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.007 0.001 HIS B 245 PHE 0.023 0.001 PHE C 400 TYR 0.016 0.001 TYR B1067 ARG 0.006 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 2.926 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8571 (tp40) cc_final: 0.8314 (tp40) REVERT: B 170 TYR cc_start: 0.5991 (t80) cc_final: 0.5590 (t80) REVERT: C 160 TYR cc_start: 0.7867 (p90) cc_final: 0.7567 (p90) REVERT: C 242 LEU cc_start: 0.8811 (mp) cc_final: 0.8417 (mt) REVERT: C 408 ARG cc_start: 0.8580 (ttp80) cc_final: 0.8214 (tmm-80) REVERT: C 456 PHE cc_start: 0.8802 (m-10) cc_final: 0.8435 (m-10) REVERT: C 508 TYR cc_start: 0.6543 (m-10) cc_final: 0.6182 (m-80) outliers start: 25 outliers final: 17 residues processed: 146 average time/residue: 0.3230 time to fit residues: 82.1472 Evaluate side-chains 125 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 108 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1083 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 0.0060 chunk 216 optimal weight: 6.9990 chunk 149 optimal weight: 50.0000 chunk 31 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 193 optimal weight: 0.0010 chunk 288 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 273 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.0008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 207 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 25965 Z= 0.244 Angle : 0.524 9.636 35328 Z= 0.274 Chirality : 0.044 0.230 4100 Planarity : 0.004 0.038 4538 Dihedral : 5.051 58.690 4205 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.19 % Allowed : 7.96 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3142 helix: 2.41 (0.21), residues: 627 sheet: 0.76 (0.18), residues: 766 loop : -0.88 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.008 0.002 HIS A 146 PHE 0.022 0.001 PHE C 453 TYR 0.021 0.001 TYR A 145 ARG 0.006 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8598 (tp40) cc_final: 0.8348 (tp40) REVERT: A 436 TRP cc_start: 0.8130 (p90) cc_final: 0.7681 (p90) REVERT: B 436 TRP cc_start: 0.7396 (p90) cc_final: 0.7169 (p90) REVERT: C 160 TYR cc_start: 0.7895 (p90) cc_final: 0.7500 (p90) REVERT: C 242 LEU cc_start: 0.8805 (mp) cc_final: 0.8467 (mt) REVERT: C 408 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8235 (tmm-80) REVERT: C 456 PHE cc_start: 0.8825 (m-10) cc_final: 0.8474 (m-10) REVERT: C 786 LYS cc_start: 0.7642 (mtmm) cc_final: 0.7415 (mtmt) outliers start: 33 outliers final: 25 residues processed: 146 average time/residue: 0.3183 time to fit residues: 81.0770 Evaluate side-chains 132 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 107 time to evaluate : 2.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 260 optimal weight: 0.0370 chunk 211 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 274 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 207 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 25965 Z= 0.396 Angle : 0.601 9.597 35328 Z= 0.318 Chirality : 0.047 0.239 4100 Planarity : 0.004 0.052 4538 Dihedral : 5.307 56.253 4205 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.66 % Allowed : 8.86 % Favored : 89.48 % 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: -0.05 (0.14), residues: 3142 helix: 1.95 (0.21), residues: 634 sheet: 0.50 (0.18), residues: 760 loop : -1.07 (0.13), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 886 HIS 0.012 0.002 HIS B1058 PHE 0.025 0.002 PHE B 906 TYR 0.023 0.002 TYR C 351 ARG 0.008 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 120 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8535 (tp40) cc_final: 0.8299 (tp40) REVERT: A 878 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7765 (tt) REVERT: B 436 TRP cc_start: 0.7553 (p90) cc_final: 0.7141 (p90) REVERT: B 1043 CYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8511 (m) REVERT: C 160 TYR cc_start: 0.8034 (p90) cc_final: 0.7611 (p90) REVERT: C 242 LEU cc_start: 0.8866 (mp) cc_final: 0.8555 (mt) REVERT: C 408 ARG cc_start: 0.8636 (ttp80) cc_final: 0.8263 (tmm-80) REVERT: C 453 PHE cc_start: 0.7807 (p90) cc_final: 0.6668 (p90) REVERT: C 456 PHE cc_start: 0.8845 (m-10) cc_final: 0.8493 (m-10) REVERT: C 786 LYS cc_start: 0.7743 (mtmm) cc_final: 0.7473 (mtmt) REVERT: C 814 LYS cc_start: 0.7625 (mmtp) cc_final: 0.7019 (ptpt) outliers start: 46 outliers final: 33 residues processed: 157 average time/residue: 0.3501 time to fit residues: 93.4163 Evaluate side-chains 141 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 962 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 0.7980 chunk 275 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 75 optimal weight: 0.0060 chunk 305 optimal weight: 0.8980 chunk 253 optimal weight: 20.0000 chunk 141 optimal weight: 30.0000 chunk 25 optimal weight: 0.9980 chunk 101 optimal weight: 0.2980 chunk 160 optimal weight: 1.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 703 ASN B 49 HIS B 66 HIS B 207 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B1005 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25965 Z= 0.171 Angle : 0.497 9.452 35328 Z= 0.259 Chirality : 0.043 0.235 4100 Planarity : 0.004 0.041 4538 Dihedral : 5.064 56.787 4204 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.19 % Allowed : 10.16 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3142 helix: 2.34 (0.21), residues: 634 sheet: 0.56 (0.19), residues: 759 loop : -0.97 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.009 0.001 HIS A 66 PHE 0.018 0.001 PHE A 592 TYR 0.016 0.001 TYR B1067 ARG 0.003 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8552 (tp40) cc_final: 0.8272 (tp40) REVERT: A 436 TRP cc_start: 0.8086 (p90) cc_final: 0.7624 (p90) REVERT: B 436 TRP cc_start: 0.7484 (p90) cc_final: 0.7028 (p90) REVERT: C 160 TYR cc_start: 0.8002 (p90) cc_final: 0.7598 (p90) REVERT: C 242 LEU cc_start: 0.8837 (mp) cc_final: 0.8492 (mt) REVERT: C 408 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8201 (tmm-80) REVERT: C 456 PHE cc_start: 0.8822 (m-10) cc_final: 0.8463 (m-10) outliers start: 33 outliers final: 24 residues processed: 139 average time/residue: 0.3046 time to fit residues: 74.8489 Evaluate side-chains 128 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 0.9990 chunk 34 optimal weight: 20.0000 chunk 174 optimal weight: 2.9990 chunk 223 optimal weight: 10.0000 chunk 172 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 901 GLN B 66 HIS B 207 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25965 Z= 0.316 Angle : 0.552 9.606 35328 Z= 0.288 Chirality : 0.045 0.237 4100 Planarity : 0.004 0.048 4538 Dihedral : 5.162 56.538 4204 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.33 % Allowed : 10.41 % Favored : 88.25 % 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: 0.03 (0.15), residues: 3142 helix: 2.15 (0.21), residues: 634 sheet: 0.46 (0.19), residues: 760 loop : -1.03 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 886 HIS 0.009 0.001 HIS B1058 PHE 0.034 0.002 PHE A 140 TYR 0.020 0.001 TYR B 265 ARG 0.006 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 105 time to evaluate : 2.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8483 (tp40) cc_final: 0.8215 (tp40) REVERT: A 436 TRP cc_start: 0.8078 (p90) cc_final: 0.7605 (p90) REVERT: B 436 TRP cc_start: 0.7540 (p90) cc_final: 0.7093 (p90) REVERT: C 160 TYR cc_start: 0.8063 (p90) cc_final: 0.7639 (p90) REVERT: C 242 LEU cc_start: 0.8866 (mp) cc_final: 0.8528 (mt) REVERT: C 408 ARG cc_start: 0.8614 (ttp80) cc_final: 0.8222 (tmm-80) REVERT: C 456 PHE cc_start: 0.8831 (m-10) cc_final: 0.8428 (m-10) outliers start: 37 outliers final: 31 residues processed: 138 average time/residue: 0.3198 time to fit residues: 77.2713 Evaluate side-chains 132 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 101 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1083 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 193 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 150 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 277 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 207 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25965 Z= 0.160 Angle : 0.493 9.479 35328 Z= 0.255 Chirality : 0.043 0.237 4100 Planarity : 0.004 0.043 4538 Dihedral : 5.030 56.621 4204 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.15 % Allowed : 10.88 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.15), residues: 3142 helix: 2.39 (0.21), residues: 636 sheet: 0.47 (0.18), residues: 771 loop : -0.92 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.007 0.001 HIS A 66 PHE 0.022 0.001 PHE A 592 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 107 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8470 (tp40) cc_final: 0.8191 (tp40) REVERT: A 177 MET cc_start: 0.1987 (pmm) cc_final: 0.1766 (pmm) REVERT: A 436 TRP cc_start: 0.8067 (p90) cc_final: 0.7615 (p90) REVERT: B 436 TRP cc_start: 0.7498 (p90) cc_final: 0.7020 (p90) REVERT: C 160 TYR cc_start: 0.8170 (p90) cc_final: 0.7776 (p90) REVERT: C 242 LEU cc_start: 0.8861 (mp) cc_final: 0.8529 (mt) REVERT: C 408 ARG cc_start: 0.8600 (ttp80) cc_final: 0.8223 (tmm-80) REVERT: C 456 PHE cc_start: 0.8760 (m-10) cc_final: 0.8421 (m-10) outliers start: 32 outliers final: 27 residues processed: 135 average time/residue: 0.3116 time to fit residues: 74.4512 Evaluate side-chains 127 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 2.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1083 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 chunk 283 optimal weight: 0.9990 chunk 170 optimal weight: 0.4980 chunk 123 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 256 optimal weight: 20.0000 chunk 268 optimal weight: 0.9990 chunk 282 optimal weight: 0.5980 chunk 186 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 207 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 25965 Z= 0.203 Angle : 0.511 11.486 35328 Z= 0.263 Chirality : 0.043 0.235 4100 Planarity : 0.004 0.041 4538 Dihedral : 4.996 56.345 4204 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.30 % Allowed : 11.03 % Favored : 87.68 % 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: 0.16 (0.15), residues: 3142 helix: 2.32 (0.21), residues: 632 sheet: 0.45 (0.18), residues: 783 loop : -0.94 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 152 HIS 0.008 0.001 HIS A 66 PHE 0.019 0.001 PHE A 592 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 101 time to evaluate : 2.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8455 (tp40) cc_final: 0.8182 (tp40) REVERT: A 436 TRP cc_start: 0.8069 (p90) cc_final: 0.7635 (p90) REVERT: B 436 TRP cc_start: 0.7495 (p90) cc_final: 0.7036 (p90) REVERT: B 1043 CYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8387 (m) REVERT: C 160 TYR cc_start: 0.8203 (p90) cc_final: 0.7802 (p90) REVERT: C 242 LEU cc_start: 0.8868 (mp) cc_final: 0.8529 (mt) REVERT: C 408 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8124 (ttp80) REVERT: C 456 PHE cc_start: 0.8784 (m-10) cc_final: 0.8416 (m-10) outliers start: 36 outliers final: 30 residues processed: 133 average time/residue: 0.3097 time to fit residues: 73.0680 Evaluate side-chains 131 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 100 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1083 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 142 optimal weight: 0.4980 chunk 208 optimal weight: 0.5980 chunk 314 optimal weight: 0.9980 chunk 289 optimal weight: 0.9990 chunk 250 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 153 optimal weight: 50.0000 chunk 199 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 207 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25965 Z= 0.174 Angle : 0.497 11.167 35328 Z= 0.255 Chirality : 0.043 0.237 4100 Planarity : 0.003 0.041 4538 Dihedral : 4.935 56.106 4204 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.19 % Allowed : 11.21 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.15), residues: 3142 helix: 2.40 (0.21), residues: 632 sheet: 0.39 (0.18), residues: 814 loop : -0.88 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 152 HIS 0.007 0.001 HIS A 66 PHE 0.024 0.001 PHE A 592 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG B1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 104 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8474 (tp40) cc_final: 0.8203 (tp40) REVERT: A 436 TRP cc_start: 0.8058 (p90) cc_final: 0.7642 (p90) REVERT: B 436 TRP cc_start: 0.7500 (p90) cc_final: 0.7045 (p90) REVERT: C 160 TYR cc_start: 0.8210 (p90) cc_final: 0.7813 (p90) REVERT: C 242 LEU cc_start: 0.8876 (mp) cc_final: 0.8536 (mt) REVERT: C 408 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8224 (tmm-80) REVERT: C 456 PHE cc_start: 0.8781 (m-10) cc_final: 0.8407 (m-10) REVERT: C 814 LYS cc_start: 0.7598 (mmtp) cc_final: 0.7109 (tttp) outliers start: 33 outliers final: 32 residues processed: 132 average time/residue: 0.3453 time to fit residues: 80.0045 Evaluate side-chains 133 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1065 VAL Chi-restraints excluded: chain C residue 1083 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 0.0050 chunk 76 optimal weight: 0.7980 chunk 231 optimal weight: 0.0010 chunk 37 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 257 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 46 optimal weight: 50.0000 chunk 220 optimal weight: 5.9990 overall best weight: 1.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 207 HIS ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.156774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112376 restraints weight = 41565.680| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.54 r_work: 0.3118 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25965 Z= 0.265 Angle : 0.538 11.109 35328 Z= 0.278 Chirality : 0.044 0.233 4100 Planarity : 0.004 0.041 4538 Dihedral : 5.046 56.393 4204 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.26 % Allowed : 11.24 % Favored : 87.50 % 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: 0.08 (0.15), residues: 3142 helix: 2.24 (0.21), residues: 630 sheet: 0.35 (0.18), residues: 793 loop : -0.95 (0.14), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.007 0.001 HIS B1058 PHE 0.025 0.001 PHE A 592 TYR 0.019 0.001 TYR B 265 ARG 0.005 0.000 ARG B1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4729.16 seconds wall clock time: 86 minutes 59.97 seconds (5219.97 seconds total)