Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 02:10:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcd_31524/04_2023/7fcd_31524.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcd_31524/04_2023/7fcd_31524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcd_31524/04_2023/7fcd_31524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcd_31524/04_2023/7fcd_31524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcd_31524/04_2023/7fcd_31524.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcd_31524/04_2023/7fcd_31524.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 0.002 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 110 5.16 5 C 15585 2.51 5 N 4036 2.21 5 O 4713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 24444 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7901 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 50, 'TRANS': 956} Chain breaks: 13 Chain: "B" Number of atoms: 8009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 8009 Classifications: {'peptide': 1021} Link IDs: {'PTRANS': 51, 'TRANS': 969} Chain breaks: 13 Chain: "C" Number of atoms: 8044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8044 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 52, 'TRANS': 974} Chain breaks: 12 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 chiralities: 10 Chain: "B" 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 chiralities: 11 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 12.94, per 1000 atoms: 0.53 Number of scatterers: 24444 At special positions: 0 Unit cell: (150.412, 146.021, 182.251, 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 110 16.00 O 4713 8.00 N 4036 7.00 C 15585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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 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=2.02 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=2.03 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=2.02 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 538 " - pdb=" SG CYS B 590 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.03 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=2.03 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 282 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 657 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 370 " " NAG C1304 " - " ASN C 61 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 717 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C1134 " " NAG C1313 " - " ASN C 331 " " NAG C1314 " - " ASN C1098 " Time building additional restraints: 9.07 Conformation dependent library (CDL) restraints added in 3.3 seconds 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5742 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 45 sheets defined 23.4% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.145A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 757 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.586A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.110A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.245A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.299A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.775A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 4.256A 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 404 through 408 removed outlier: 4.277A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 757 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 939 removed outlier: 7.138A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.534A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 6.648A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.904A 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 383 through 389 removed outlier: 3.932A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.729A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 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 738 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 757 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 852 through 856 removed outlier: 3.583A pdb=" N ASN C 856 " --> pdb=" O GLN C 853 " (cutoff:3.500A) 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 908 Processing helix chain 'C' and resid 912 through 939 removed outlier: 4.084A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.536A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 6.130A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.544A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.908A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.908A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A 268 " --> pdb=" O TYR A 91 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 removed outlier: 4.049A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.579A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 11.595A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 154 removed outlier: 6.877A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 276 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.688A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.584A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.516A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.335A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.711A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 5.193A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.520A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.864A 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 1081 through 1082 removed outlier: 5.370A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.260A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.260A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 53 removed outlier: 3.570A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.527A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.527A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.971A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR B 313 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 326 removed outlier: 6.533A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.010A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.890A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 702 removed outlier: 7.344A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.616A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.888A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 28 removed outlier: 3.998A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 50 removed outlier: 4.046A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.868A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.906A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 14.898A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 13.461A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.893A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.906A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 14.898A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 13.461A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.893A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 246 " --> pdb=" O VAL C 143 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.671A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.938A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.938A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 392 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.578A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 719 through 728 removed outlier: 3.525A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 939 hydrogen bonds defined for protein. 2574 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: 10.73 Time building geometry restraints manager: 9.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4446 1.33 - 1.45: 6681 1.45 - 1.58: 13711 1.58 - 1.70: 2 1.70 - 1.83: 138 Bond restraints: 24978 Sorted by residual: bond pdb=" N VAL B1068 " pdb=" CA VAL B1068 " ideal model delta sigma weight residual 1.454 1.494 -0.039 7.70e-03 1.69e+04 2.59e+01 bond pdb=" N ILE B 664 " pdb=" CA ILE B 664 " ideal model delta sigma weight residual 1.458 1.493 -0.036 7.70e-03 1.69e+04 2.14e+01 bond pdb=" CA ASP B 88 " pdb=" CB ASP B 88 " ideal model delta sigma weight residual 1.526 1.584 -0.058 1.25e-02 6.40e+03 2.14e+01 bond pdb=" N VAL B 729 " pdb=" CA VAL B 729 " ideal model delta sigma weight residual 1.458 1.494 -0.036 9.00e-03 1.23e+04 1.58e+01 bond pdb=" CA PRO B 792 " pdb=" C PRO B 792 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.50e+01 ... (remaining 24973 not shown) Histogram of bond angle deviations from ideal: 95.58 - 103.45: 265 103.45 - 111.33: 10303 111.33 - 119.20: 10828 119.20 - 127.07: 12367 127.07 - 134.95: 192 Bond angle restraints: 33955 Sorted by residual: angle pdb=" N THR A 716 " pdb=" CA THR A 716 " pdb=" C THR A 716 " ideal model delta sigma weight residual 114.56 107.21 7.35 1.27e+00 6.20e-01 3.35e+01 angle pdb=" C ARG B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 121.31 129.91 -8.60 1.49e+00 4.50e-01 3.33e+01 angle pdb=" N THR C 716 " pdb=" CA THR C 716 " pdb=" C THR C 716 " ideal model delta sigma weight residual 114.75 107.70 7.05 1.26e+00 6.30e-01 3.13e+01 angle pdb=" C LEU A 293 " pdb=" N ASP A 294 " pdb=" CA ASP A 294 " ideal model delta sigma weight residual 123.65 133.79 -10.14 1.88e+00 2.83e-01 2.91e+01 angle pdb=" O PHE C 329 " pdb=" C PHE C 329 " pdb=" N PRO C 330 " ideal model delta sigma weight residual 121.84 117.72 4.12 7.80e-01 1.64e+00 2.79e+01 ... (remaining 33950 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13494 17.98 - 35.96: 926 35.96 - 53.94: 149 53.94 - 71.93: 35 71.93 - 89.91: 9 Dihedral angle restraints: 14613 sinusoidal: 5724 harmonic: 8889 Sorted by residual: dihedral pdb=" CA PHE B 329 " pdb=" C PHE B 329 " pdb=" N PRO B 330 " pdb=" CA PRO B 330 " ideal model delta harmonic sigma weight residual 180.00 112.30 67.70 0 5.00e+00 4.00e-02 1.83e+02 dihedral pdb=" CA VAL B1096 " pdb=" C VAL B1096 " pdb=" N SER B1097 " pdb=" CA SER B1097 " ideal model delta harmonic sigma weight residual 180.00 116.41 63.59 0 5.00e+00 4.00e-02 1.62e+02 dihedral pdb=" CA ASN C1074 " pdb=" C ASN C1074 " pdb=" N PHE C1075 " pdb=" CA PHE C1075 " ideal model delta harmonic sigma weight residual 180.00 120.85 59.15 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 14610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 3917 0.224 - 0.449: 40 0.449 - 0.673: 1 0.673 - 0.898: 0 0.898 - 1.122: 5 Chirality restraints: 3963 Sorted by residual: chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 717 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.28 -1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.41 -0.99 2.00e-01 2.50e+01 2.43e+01 ... (remaining 3960 not shown) Planarity restraints: 4371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.362 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG B1309 " -0.097 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.539 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " 0.359 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG A1308 " -0.093 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " -0.542 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " 0.330 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG C1306 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " 0.023 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " -0.492 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " 0.215 2.00e-02 2.50e+03 ... (remaining 4368 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 528 2.66 - 3.22: 22465 3.22 - 3.78: 37137 3.78 - 4.34: 50351 4.34 - 4.90: 80899 Nonbonded interactions: 191380 Sorted by model distance: nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.103 2.440 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.141 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.142 2.440 nonbonded pdb=" O PRO A 85 " pdb=" OH TYR A 269 " model vdw 2.166 2.440 nonbonded pdb=" O PHE A 329 " pdb=" OG SER A 530 " model vdw 2.172 2.440 ... (remaining 191375 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 14 through 121 or resid 127 through 145 or resid 150 throu \ gh 161 or resid 164 through 170 or resid 187 through 246 or resid 259 through 34 \ 1 or resid 343 through 827 or resid 851 through 1146 or resid 1301 through 1310) \ ) selection = (chain 'B' and (resid 14 through 17 or resid 22 through 121 or resid 127 through \ 145 or resid 150 through 170 or resid 187 through 195 or resid 200 through 246 \ or resid 259 through 341 or resid 343 through 444 or resid 447 through 617 or re \ sid 641 through 827 or resid 851 through 1146 or resid 1301 through 1310)) selection = (chain 'C' and (resid 14 through 17 or resid 22 through 121 or resid 127 through \ 145 or resid 150 through 161 or resid 164 through 170 or resid 187 through 195 \ or resid 200 through 246 or resid 259 through 444 or resid 447 through 467 or re \ sid 489 through 1146 or resid 1301 through 1310)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.910 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 62.110 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.110 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.009 0.087 24978 Z= 0.557 Angle : 1.126 14.483 33955 Z= 0.772 Chirality : 0.082 1.122 3963 Planarity : 0.016 0.307 4336 Dihedral : 12.543 89.908 8754 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.90 % Favored : 91.86 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.14), residues: 2973 helix: 0.25 (0.20), residues: 626 sheet: -1.78 (0.20), residues: 614 loop : -2.64 (0.13), residues: 1733 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 148 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 8 residues processed: 203 average time/residue: 0.3492 time to fit residues: 115.1107 Evaluate side-chains 99 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 2.869 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.2108 time to fit residues: 7.2318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 276 optimal weight: 0.0050 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN A 370 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A1106 GLN A1125 ASN B 30 ASN B 196 ASN B 370 ASN B 448 ASN B 580 GLN C1135 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 24978 Z= 0.188 Angle : 0.619 9.405 33955 Z= 0.317 Chirality : 0.046 0.548 3963 Planarity : 0.005 0.094 4336 Dihedral : 5.236 45.287 3253 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.35 % Favored : 94.62 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.15), residues: 2973 helix: 1.46 (0.21), residues: 633 sheet: -1.36 (0.19), residues: 652 loop : -2.35 (0.14), residues: 1688 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 123 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 17 residues processed: 161 average time/residue: 0.3601 time to fit residues: 94.2276 Evaluate side-chains 104 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 2.926 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.2287 time to fit residues: 11.2027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 229 optimal weight: 0.2980 chunk 187 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 chunk 246 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 221 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 949 GLN A 953 ASN A1106 GLN B 234 ASN C 164 ASN C 955 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 24978 Z= 0.294 Angle : 0.606 9.846 33955 Z= 0.313 Chirality : 0.045 0.337 3963 Planarity : 0.004 0.069 4336 Dihedral : 5.045 41.131 3253 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.15), residues: 2973 helix: 1.62 (0.21), residues: 629 sheet: -1.38 (0.20), residues: 639 loop : -2.29 (0.14), residues: 1705 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 126 average time/residue: 0.3840 time to fit residues: 79.7782 Evaluate side-chains 97 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 3.058 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.2246 time to fit residues: 9.2909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 277 optimal weight: 0.9980 chunk 293 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 263 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 370 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 953 ASN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 24978 Z= 0.219 Angle : 0.569 9.282 33955 Z= 0.290 Chirality : 0.044 0.396 3963 Planarity : 0.004 0.063 4336 Dihedral : 4.770 38.300 3253 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.15), residues: 2973 helix: 1.77 (0.21), residues: 635 sheet: -1.33 (0.19), residues: 674 loop : -2.20 (0.14), residues: 1664 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 3.139 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 7 residues processed: 121 average time/residue: 0.3504 time to fit residues: 71.6153 Evaluate side-chains 95 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 3.056 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 7 average time/residue: 0.2414 time to fit residues: 6.9580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 121 optimal weight: 40.0000 chunk 250 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 207 HIS ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1083 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.081 24978 Z= 0.445 Angle : 0.712 12.260 33955 Z= 0.363 Chirality : 0.048 0.473 3963 Planarity : 0.005 0.065 4336 Dihedral : 5.249 38.339 3253 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 2973 helix: 1.24 (0.21), residues: 633 sheet: -1.42 (0.20), residues: 659 loop : -2.36 (0.14), residues: 1681 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 94 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 26 residues processed: 138 average time/residue: 0.3449 time to fit residues: 80.4233 Evaluate side-chains 111 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 85 time to evaluate : 2.871 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 26 outliers final: 1 residues processed: 26 average time/residue: 0.2186 time to fit residues: 14.6826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.0970 chunk 264 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 294 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 154 optimal weight: 0.0970 overall best weight: 1.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 532 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 24978 Z= 0.218 Angle : 0.565 9.429 33955 Z= 0.289 Chirality : 0.044 0.262 3963 Planarity : 0.004 0.064 4336 Dihedral : 4.760 34.971 3253 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.15), residues: 2973 helix: 1.73 (0.21), residues: 635 sheet: -1.36 (0.20), residues: 649 loop : -2.22 (0.14), residues: 1689 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 113 average time/residue: 0.3627 time to fit residues: 68.6005 Evaluate side-chains 98 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 3.010 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.2337 time to fit residues: 9.0645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 214 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 chunk 247 optimal weight: 10.0000 chunk 164 optimal weight: 0.0370 chunk 293 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS C 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 24978 Z= 0.165 Angle : 0.536 10.089 33955 Z= 0.274 Chirality : 0.043 0.231 3963 Planarity : 0.004 0.063 4336 Dihedral : 4.497 35.538 3253 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.15), residues: 2973 helix: 2.03 (0.21), residues: 632 sheet: -1.19 (0.20), residues: 663 loop : -2.12 (0.14), residues: 1678 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 122 average time/residue: 0.3884 time to fit residues: 76.8836 Evaluate side-chains 97 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 2.969 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.2285 time to fit residues: 6.4956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 199 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 230 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 24978 Z= 0.186 Angle : 0.548 10.613 33955 Z= 0.279 Chirality : 0.044 0.251 3963 Planarity : 0.004 0.076 4336 Dihedral : 4.433 34.542 3253 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.15), residues: 2973 helix: 2.03 (0.21), residues: 632 sheet: -1.14 (0.19), residues: 673 loop : -2.07 (0.14), residues: 1668 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 3.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 120 average time/residue: 0.3788 time to fit residues: 75.4232 Evaluate side-chains 106 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 3.110 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 11 average time/residue: 0.2368 time to fit residues: 8.8673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 0.9990 chunk 280 optimal weight: 0.5980 chunk 256 optimal weight: 0.9980 chunk 273 optimal weight: 0.0470 chunk 164 optimal weight: 0.5980 chunk 118 optimal weight: 8.9990 chunk 214 optimal weight: 0.0070 chunk 83 optimal weight: 8.9990 chunk 246 optimal weight: 7.9990 chunk 258 optimal weight: 7.9990 chunk 272 optimal weight: 0.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 690 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 24978 Z= 0.143 Angle : 0.524 10.663 33955 Z= 0.266 Chirality : 0.043 0.265 3963 Planarity : 0.004 0.072 4336 Dihedral : 4.143 32.140 3253 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 2973 helix: 2.16 (0.21), residues: 640 sheet: -1.06 (0.19), residues: 677 loop : -1.97 (0.15), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 111 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 117 average time/residue: 0.3671 time to fit residues: 71.8921 Evaluate side-chains 99 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 97 time to evaluate : 2.947 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.2169 time to fit residues: 4.9054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 0.3980 chunk 288 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 200 optimal weight: 0.0870 chunk 302 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 186 optimal weight: 2.9990 chunk 147 optimal weight: 0.0980 overall best weight: 0.3960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 24978 Z= 0.140 Angle : 0.520 10.206 33955 Z= 0.264 Chirality : 0.044 0.592 3963 Planarity : 0.004 0.070 4336 Dihedral : 4.020 32.121 3253 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.16), residues: 2973 helix: 2.36 (0.21), residues: 628 sheet: -0.91 (0.19), residues: 672 loop : -1.89 (0.14), residues: 1673 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5946 Ramachandran restraints generated. 2973 Oldfield, 0 Emsley, 2973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 120 average time/residue: 0.3669 time to fit residues: 73.5906 Evaluate side-chains 104 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 2.889 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.2242 time to fit residues: 5.9068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.4980 chunk 256 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 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 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 955 ASN C1023 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.104830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.072888 restraints weight = 81850.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.073237 restraints weight = 57771.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.072957 restraints weight = 39131.929| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 24978 Z= 0.255 Angle : 0.571 10.373 33955 Z= 0.291 Chirality : 0.044 0.339 3963 Planarity : 0.004 0.053 4336 Dihedral : 4.289 31.714 3253 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 2973 helix: 2.05 (0.21), residues: 631 sheet: -0.92 (0.20), residues: 675 loop : -1.90 (0.15), residues: 1667 =============================================================================== Job complete usr+sys time: 3425.93 seconds wall clock time: 64 minutes 49.48 seconds (3889.48 seconds total)