Starting phenix.real_space_refine on Sat Nov 18 16:50:29 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyn_23596/11_2023/7lyn_23596.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyn_23596/11_2023/7lyn_23596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyn_23596/11_2023/7lyn_23596.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyn_23596/11_2023/7lyn_23596.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyn_23596/11_2023/7lyn_23596.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lyn_23596/11_2023/7lyn_23596.pdb" } resolution = 3.32 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= 0.001 sd= 0.072 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 103 5.16 5 C 15097 2.51 5 N 3887 2.21 5 O 4554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 23641 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7713 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 7712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 996, 7712 Classifications: {'peptide': 996} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 47, 'TRANS': 948} Chain breaks: 7 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 7684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7684 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 47, 'TRANS': 945} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 11.37, per 1000 atoms: 0.48 Number of scatterers: 23641 At special positions: 0 Unit cell: (130.418, 133.625, 193.489, 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 103 16.00 O 4554 8.00 N 3887 7.00 C 15097 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.01 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=1.98 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.02 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 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=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 122 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B 717 " " NAG B1310 " - " ASN B 801 " " NAG B1311 " - " ASN B1074 " " NAG B1312 " - " ASN B1098 " " NAG B1313 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C1134 " " NAG C1313 " - " ASN C 801 " Time building additional restraints: 8.58 Conformation dependent library (CDL) restraints added in 4.8 seconds 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 46 sheets defined 27.3% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.818A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.980A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.696A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.947A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.685A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.034A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.061A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.989A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.661A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.852A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.536A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (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 removed outlier: 3.682A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.979A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.108A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.814A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.015A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.892A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.576A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.121A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.669A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.569A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.321A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 5.085A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.930A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.614A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.773A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.595A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.615A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.659A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.755A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (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 1033 removed outlier: 3.899A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.348A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.594A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.787A 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: 3.818A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.329A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.488A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.961A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.959A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.622A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.398A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.352A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.279A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.769A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.872A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.784A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.516A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.295A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.149A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.617A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.770A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.124A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.995A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.987A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.778A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.307A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.649A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.631A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.800A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (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 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.600A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.915A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.522A 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: 4.364A 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 1125 removed outlier: 4.286A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1098 removed outlier: 3.886A pdb=" N HIS C1101 " --> pdb=" O ASN C1098 " (cutoff:3.500A) 1029 hydrogen bonds defined for protein. 2805 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: 9.77 Time building geometry restraints manager: 9.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6190 1.33 - 1.45: 4512 1.45 - 1.58: 13331 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 24160 Sorted by residual: bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.43e+01 bond pdb=" C5 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C5 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 NAG C1313 " pdb=" O5 NAG C1313 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 24155 not shown) Histogram of bond angle deviations from ideal: 96.67 - 104.42: 319 104.42 - 112.16: 10415 112.16 - 119.91: 10746 119.91 - 127.65: 11275 127.65 - 135.40: 133 Bond angle restraints: 32888 Sorted by residual: angle pdb=" CA PHE A 559 " pdb=" CB PHE A 559 " pdb=" CG PHE A 559 " ideal model delta sigma weight residual 113.80 119.54 -5.74 1.00e+00 1.00e+00 3.29e+01 angle pdb=" CB HIS C1064 " pdb=" CG HIS C1064 " pdb=" CD2 HIS C1064 " ideal model delta sigma weight residual 131.20 123.94 7.26 1.30e+00 5.92e-01 3.12e+01 angle pdb=" CA PHE B 106 " pdb=" CB PHE B 106 " pdb=" CG PHE B 106 " ideal model delta sigma weight residual 113.80 119.23 -5.43 1.00e+00 1.00e+00 2.95e+01 angle pdb=" CA PHE B 559 " pdb=" CB PHE B 559 " pdb=" CG PHE B 559 " ideal model delta sigma weight residual 113.80 119.22 -5.42 1.00e+00 1.00e+00 2.94e+01 angle pdb=" CA PHE B 515 " pdb=" CB PHE B 515 " pdb=" CG PHE B 515 " ideal model delta sigma weight residual 113.80 119.19 -5.39 1.00e+00 1.00e+00 2.91e+01 ... (remaining 32883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 13102 17.82 - 35.64: 756 35.64 - 53.46: 119 53.46 - 71.28: 44 71.28 - 89.11: 22 Dihedral angle restraints: 14043 sinusoidal: 5370 harmonic: 8673 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 -178.30 -88.70 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -164.98 78.98 1 1.00e+01 1.00e-02 7.77e+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 -154.58 68.58 1 1.00e+01 1.00e-02 6.09e+01 ... (remaining 14040 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.271: 3864 0.271 - 0.543: 23 0.543 - 0.814: 0 0.814 - 1.085: 0 1.085 - 1.356: 1 Chirality restraints: 3888 Sorted by residual: chirality pdb=" C1 NAG C1311 " pdb=" ND2 ASN C1098 " pdb=" C2 NAG C1311 " pdb=" O5 NAG C1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.04 -1.36 2.00e-01 2.50e+01 4.60e+01 chirality pdb=" CA ASP C 198 " pdb=" N ASP C 198 " pdb=" C ASP C 198 " pdb=" CB ASP C 198 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CA ARG B1107 " pdb=" N ARG B1107 " pdb=" C ARG B1107 " pdb=" CB ARG B1107 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 3885 not shown) Planarity restraints: 4229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 904 " 0.230 2.00e-02 2.50e+03 1.30e-01 3.39e+02 pdb=" CG TYR C 904 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR C 904 " -0.121 2.00e-02 2.50e+03 pdb=" CD2 TYR C 904 " -0.105 2.00e-02 2.50e+03 pdb=" CE1 TYR C 904 " -0.076 2.00e-02 2.50e+03 pdb=" CE2 TYR C 904 " -0.088 2.00e-02 2.50e+03 pdb=" CZ TYR C 904 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 904 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.205 2.00e-02 2.50e+03 1.08e-01 2.94e+02 pdb=" CG TRP C 886 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " 0.100 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " 0.158 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.120 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.128 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " -0.138 2.00e-02 2.50e+03 1.46e-01 2.66e+02 pdb=" CG ASN A 657 " 0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " 0.224 2.00e-02 2.50e+03 pdb=" C1 NAG A1306 " -0.173 2.00e-02 2.50e+03 ... (remaining 4226 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 11206 2.98 - 3.46: 22483 3.46 - 3.94: 39045 3.94 - 4.42: 43175 4.42 - 4.90: 74093 Nonbonded interactions: 190002 Sorted by model distance: nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.504 2.440 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.529 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.539 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.540 2.440 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.550 2.440 ... (remaining 189997 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 87 or (resi \ d 88 and (name N or name CA or name C or name O or name CB )) or resid 89 throug \ h 95 or (resid 96 through 97 and (name N or name CA or name C or name O or name \ CB )) or resid 98 through 109 or (resid 110 and (name N or name CA or name C or \ name O or name CB )) or resid 111 through 114 or (resid 115 and (name N or name \ CA or name C or name O or name CB )) or resid 116 through 131 or (resid 132 and \ (name N or name CA or name C or name O or name CB )) or resid 133 or (resid 134 \ through 138 and (name N or name CA or name C or name O or name CB )) or resid 13 \ 9 through 143 or (resid 165 and (name N or name CA or name C or name O or name C \ B )) or resid 166 through 168 or (resid 169 and (name N or name CA or name C or \ name O or name CB )) or resid 170 through 171 or (resid 172 and (name N or name \ CA or name C or name O or name CB )) or resid 186 through 190 or (resid 191 and \ (name N or name CA or name C or name O or name CB )) or resid 192 through 196 or \ (resid 197 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 8 through 213 or (resid 214 and (name N or name CA or name C or name O or name C \ B )) or resid 215 through 217 or (resid 218 and (name N or name CA or name C or \ name O or name CB )) or resid 219 through 238 or (resid 239 and (name N or name \ CA or name C or name O or name CB )) or resid 240 through 308 or (resid 309 and \ (name N or name CA or name C or name O or name CB )) or resid 310 through 527 or \ (resid 528 and (name N or name CA or name C or name O or name CB )) or resid 52 \ 9 through 810 or (resid 811 and (name N or name CA or name C or name O or name C \ B )) or resid 812 through 827 or resid 855 through 866 or (resid 867 through 868 \ and (name N or name CA or name C or name O or name CB )) or resid 869 through 1 \ 141 or (resid 1142 and (name N or name CA or name C or name O or name CB )) or r \ esid 1143 through 1144 or (resid 1145 through 1146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1147 or resid 1301 through 1312)) selection = (chain 'B' and (resid 27 through 66 or resid 82 through 87 or (resid 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 96 or (resi \ d 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (re \ sid 99 and (name N or name CA or name C or name O or name CB )) or resid 100 thr \ ough 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) \ or resid 111 through 114 or (resid 115 and (name N or name CA or name C or name \ O or name CB )) or resid 116 through 130 or (resid 131 through 132 and (name N o \ r name CA or name C or name O or name CB )) or resid 133 through 134 or (resid 1 \ 35 through 138 and (name N or name CA or name C or name O or name CB )) or resid \ 139 through 164 or resid 166 through 168 or (resid 169 and (name N or name CA o \ r name C or name O or name CB )) or resid 170 through 190 or (resid 191 and (nam \ e N or name CA or name C or name O or name CB )) or resid 192 through 195 or (re \ sid 196 through 197 and (name N or name CA or name C or name O or name CB )) or \ resid 198 through 241 or (resid 242 through 264 and (name N or name CA or name C \ or name O or name CB )) or resid 265 through 280 or (resid 281 and (name N or n \ ame CA or name C or name O or name CB )) or resid 282 through 567 or (resid 568 \ and (name N or name CA or name C or name O or name CB )) or resid 569 through 58 \ 2 or (resid 583 and (name N or name CA or name C or name O or name CB )) or resi \ d 584 through 585 or (resid 586 and (name N or name CA or name C or name O or na \ me CB )) or resid 587 through 618 or (resid 619 and (name N or name CA or name C \ or name O or name CB )) or resid 620 through 676 or resid 690 through 744 or (r \ esid 745 and (name N or name CA or name C or name O or name CB )) or resid 746 t \ hrough 747 or (resid 748 and (name N or name CA or name C or name O or name CB ) \ ) or resid 749 through 810 or (resid 811 and (name N or name CA or name C or nam \ e O or name CB )) or resid 812 through 813 or (resid 814 and (name N or name CA \ or name C or name O or name CB )) or resid 815 through 827 or resid 855 through \ 866 or (resid 867 through 868 and (name N or name CA or name C or name O or name \ CB )) or resid 869 through 1091 or (resid 1092 and (name N or name CA or name C \ or name O or name CB )) or resid 1093 through 1143 or (resid 1144 through 1146 \ and (name N or name CA or name C or name O or name CB )) or resid 1147 or resid \ 1301 through 1312)) selection = (chain 'C' and (resid 27 through 52 or (resid 53 and (name N or name CA or name \ C or name O or name CB )) or resid 54 through 66 or resid 82 through 95 or (resi \ d 96 through 97 and (name N or name CA or name C or name O or name CB )) or resi \ d 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or re \ sid 100 through 130 or (resid 131 through 132 and (name N or name CA or name C o \ r name O or name CB )) or resid 133 through 134 or (resid 135 through 138 and (n \ ame N or name CA or name C or name O or name CB )) or resid 139 through 143 or ( \ resid 165 and (name N or name CA or name C or name O or name CB )) or resid 166 \ through 195 or (resid 196 through 197 and (name N or name CA or name C or name O \ or name CB )) or resid 198 through 213 or (resid 214 and (name N or name CA or \ name C or name O or name CB )) or resid 215 through 217 or (resid 218 and (name \ N or name CA or name C or name O or name CB )) or resid 219 through 238 or (resi \ d 239 and (name N or name CA or name C or name O or name CB )) or resid 240 thro \ ugh 308 or (resid 309 and (name N or name CA or name C or name O or name CB )) o \ r resid 310 through 527 or (resid 528 and (name N or name CA or name C or name O \ or name CB )) or resid 529 through 567 or (resid 568 and (name N or name CA or \ name C or name O or name CB )) or resid 569 through 582 or (resid 583 and (name \ N or name CA or name C or name O or name CB )) or resid 584 through 585 or (resi \ d 586 and (name N or name CA or name C or name O or name CB )) or resid 587 thro \ ugh 618 or (resid 619 and (name N or name CA or name C or name O or name CB )) o \ r resid 620 through 813 or (resid 814 and (name N or name CA or name C or name O \ or name CB )) or resid 815 through 1091 or (resid 1092 and (name N or name CA o \ r name C or name O or name CB )) or resid 1093 through 1141 or (resid 1142 and ( \ name N or name CA or name C or name O or name CB )) or resid 1143 or (resid 1144 \ through 1146 and (name N or name CA or name C or name O or name CB )) or resid \ 1147 or resid 1301 through 1312)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 7.030 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 62.050 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.013 0.076 24160 Z= 0.869 Angle : 1.746 10.278 32888 Z= 1.173 Chirality : 0.096 1.356 3888 Planarity : 0.013 0.192 4191 Dihedral : 12.794 89.105 8349 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 0.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.75 % Favored : 93.97 % Rotamer: Outliers : 0.86 % Allowed : 2.39 % Favored : 96.75 % Cbeta Deviations : 0.04 % 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: -0.95 (0.14), residues: 2937 helix: -1.01 (0.17), residues: 694 sheet: 0.33 (0.22), residues: 499 loop : -0.72 (0.14), residues: 1744 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 364 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 6 residues processed: 383 average time/residue: 0.3756 time to fit residues: 219.5678 Evaluate side-chains 181 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 2.601 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1983 time to fit residues: 5.6275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 232 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 269 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN A 207 HIS A 354 ASN A 394 ASN A 935 GLN A1088 HIS B 414 GLN B1002 GLN C 165 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN C 388 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 24160 Z= 0.194 Angle : 0.601 7.562 32888 Z= 0.319 Chirality : 0.046 0.217 3888 Planarity : 0.004 0.048 4191 Dihedral : 5.412 27.199 3188 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.62 % Favored : 97.24 % Rotamer: Outliers : 1.02 % Allowed : 7.25 % Favored : 91.73 % 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: 2937 helix: 1.49 (0.20), residues: 657 sheet: 0.31 (0.19), residues: 652 loop : -0.45 (0.15), residues: 1628 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 220 time to evaluate : 2.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 238 average time/residue: 0.3466 time to fit residues: 134.7449 Evaluate side-chains 166 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 154 time to evaluate : 2.375 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1985 time to fit residues: 7.8389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.5980 chunk 83 optimal weight: 0.3980 chunk 224 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 74 optimal weight: 0.2980 chunk 270 optimal weight: 0.6980 chunk 291 optimal weight: 3.9990 chunk 240 optimal weight: 8.9990 chunk 267 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 165 ASN A 207 HIS A 388 ASN A 394 ASN A1048 HIS A1083 HIS B 207 HIS B 414 GLN B 498 GLN B 751 ASN B1048 HIS C 165 ASN C 196 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1005 GLN C1048 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24160 Z= 0.144 Angle : 0.512 7.174 32888 Z= 0.270 Chirality : 0.043 0.184 3888 Planarity : 0.003 0.041 4191 Dihedral : 4.656 22.102 3188 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.73 % Rotamer: Outliers : 0.74 % Allowed : 9.40 % Favored : 89.85 % 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: 0.56 (0.15), residues: 2937 helix: 2.11 (0.21), residues: 646 sheet: 0.42 (0.20), residues: 638 loop : -0.32 (0.15), residues: 1653 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 207 average time/residue: 0.3412 time to fit residues: 115.1075 Evaluate side-chains 163 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 2.726 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2940 time to fit residues: 8.7371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 140 optimal weight: 30.0000 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 181 optimal weight: 0.4980 chunk 271 optimal weight: 3.9990 chunk 287 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 256 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 207 HIS A 388 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 207 HIS B 804 GLN B 914 ASN B 965 GLN C 87 ASN C 165 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24160 Z= 0.353 Angle : 0.584 6.800 32888 Z= 0.303 Chirality : 0.046 0.191 3888 Planarity : 0.004 0.040 4191 Dihedral : 4.753 20.885 3188 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 1.18 % Allowed : 10.38 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 2937 helix: 1.60 (0.21), residues: 662 sheet: 0.32 (0.19), residues: 664 loop : -0.48 (0.15), residues: 1611 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 200 average time/residue: 0.3544 time to fit residues: 113.4315 Evaluate side-chains 164 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 2.520 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2111 time to fit residues: 9.8837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 10.0000 chunk 162 optimal weight: 0.6980 chunk 4 optimal weight: 0.0030 chunk 213 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 257 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 965 GLN C 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24160 Z= 0.144 Angle : 0.488 6.633 32888 Z= 0.255 Chirality : 0.043 0.174 3888 Planarity : 0.003 0.046 4191 Dihedral : 4.341 21.734 3188 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 0.63 % Allowed : 11.36 % Favored : 88.01 % 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: 0.51 (0.15), residues: 2937 helix: 2.06 (0.21), residues: 654 sheet: 0.35 (0.19), residues: 682 loop : -0.36 (0.15), residues: 1601 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 163 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 176 average time/residue: 0.3380 time to fit residues: 99.6272 Evaluate side-chains 152 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 2.579 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2373 time to fit residues: 7.2538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 168 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 287 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 95 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 218 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24160 Z= 0.189 Angle : 0.489 6.605 32888 Z= 0.253 Chirality : 0.043 0.177 3888 Planarity : 0.003 0.037 4191 Dihedral : 4.233 21.314 3188 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.73 % Rotamer: Outliers : 0.82 % Allowed : 11.32 % Favored : 87.85 % 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: 0.49 (0.15), residues: 2937 helix: 2.05 (0.21), residues: 661 sheet: 0.32 (0.18), residues: 710 loop : -0.40 (0.15), residues: 1566 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 8 residues processed: 162 average time/residue: 0.3385 time to fit residues: 90.7617 Evaluate side-chains 151 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 2.582 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2232 time to fit residues: 6.9201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 241 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 chunk 286 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 218 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 935 GLN B 965 GLN C 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24160 Z= 0.262 Angle : 0.516 8.831 32888 Z= 0.266 Chirality : 0.044 0.177 3888 Planarity : 0.003 0.038 4191 Dihedral : 4.296 22.459 3188 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.63 % Rotamer: Outliers : 0.67 % Allowed : 11.48 % Favored : 87.85 % 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: 0.43 (0.15), residues: 2937 helix: 1.86 (0.21), residues: 669 sheet: 0.33 (0.19), residues: 702 loop : -0.39 (0.15), residues: 1566 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 2.533 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 162 average time/residue: 0.3479 time to fit residues: 94.0191 Evaluate side-chains 151 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 2.536 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2283 time to fit residues: 7.1344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 225 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 907 ASN B 914 ASN B 965 GLN C 207 HIS C 409 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24160 Z= 0.191 Angle : 0.491 8.713 32888 Z= 0.254 Chirality : 0.043 0.172 3888 Planarity : 0.003 0.038 4191 Dihedral : 4.166 21.446 3188 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.17 % Favored : 96.77 % Rotamer: Outliers : 0.35 % Allowed : 12.30 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 2937 helix: 1.97 (0.21), residues: 664 sheet: 0.35 (0.19), residues: 692 loop : -0.37 (0.15), residues: 1581 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 161 average time/residue: 0.3374 time to fit residues: 89.6378 Evaluate side-chains 155 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 148 time to evaluate : 2.425 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2313 time to fit residues: 6.3486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 252 optimal weight: 0.0470 chunk 265 optimal weight: 0.0980 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 422 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24160 Z= 0.134 Angle : 0.470 8.036 32888 Z= 0.243 Chirality : 0.042 0.171 3888 Planarity : 0.003 0.039 4191 Dihedral : 3.970 22.042 3188 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 0.24 % Allowed : 12.50 % Favored : 87.26 % 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: 0.67 (0.15), residues: 2937 helix: 2.23 (0.21), residues: 671 sheet: 0.39 (0.19), residues: 683 loop : -0.27 (0.15), residues: 1583 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 2.560 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 168 average time/residue: 0.3340 time to fit residues: 93.4002 Evaluate side-chains 156 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 2.643 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2131 time to fit residues: 4.8787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 0.6980 chunk 282 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 30.0000 chunk 196 optimal weight: 4.9990 chunk 295 optimal weight: 0.7980 chunk 272 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 207 HIS A 519 HIS A 690 GLN A 935 GLN A1135 ASN B 901 GLN B 914 ASN B 965 GLN C 901 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 24160 Z= 0.374 Angle : 0.563 8.103 32888 Z= 0.291 Chirality : 0.045 0.178 3888 Planarity : 0.003 0.040 4191 Dihedral : 4.337 27.093 3188 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.51 % Favored : 96.42 % Rotamer: Outliers : 0.12 % Allowed : 13.09 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.15), residues: 2937 helix: 1.71 (0.21), residues: 682 sheet: 0.31 (0.19), residues: 682 loop : -0.44 (0.15), residues: 1573 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5874 Ramachandran restraints generated. 2937 Oldfield, 0 Emsley, 2937 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 151 time to evaluate : 2.367 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 151 average time/residue: 0.3357 time to fit residues: 84.3397 Evaluate side-chains 145 residues out of total 2609 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 2.713 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2803 time to fit residues: 4.7669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 217 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 235 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 690 GLN B 901 GLN C 394 ASN C 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115894 restraints weight = 33435.213| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.89 r_work: 0.3048 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24160 Z= 0.201 Angle : 0.497 8.603 32888 Z= 0.257 Chirality : 0.043 0.169 3888 Planarity : 0.003 0.039 4191 Dihedral : 4.150 27.700 3188 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.20 % Favored : 96.73 % Rotamer: Outliers : 0.20 % Allowed : 13.17 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.15), residues: 2937 helix: 1.89 (0.21), residues: 676 sheet: 0.28 (0.19), residues: 686 loop : -0.38 (0.15), residues: 1575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4376.43 seconds wall clock time: 81 minutes 1.57 seconds (4861.57 seconds total)