Starting phenix.real_space_refine on Mon Feb 19 10:35:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcd_31524/02_2024/7fcd_31524.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcd_31524/02_2024/7fcd_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_31524/02_2024/7fcd_31524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcd_31524/02_2024/7fcd_31524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcd_31524/02_2024/7fcd_31524.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fcd_31524/02_2024/7fcd_31524.pdb" } resolution = 3.9 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= 0.000 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 dihedrals: 30 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 dihedrals: 33 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 dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 12.66, per 1000 atoms: 0.52 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: 9.22 Conformation dependent library (CDL) restraints added in 4.1 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: 2.88 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: 10.41 Time building geometry restraints manager: 9.93 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: 14191 17.98 - 35.96: 952 35.96 - 53.94: 160 53.94 - 71.93: 36 71.93 - 89.91: 9 Dihedral angle restraints: 15348 sinusoidal: 6459 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 15345 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: 1.350 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: 5.880 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 64.990 Find NCS groups from input model: 1.860 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.600 ------------------------------------------------------------------------------- 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 : 12.310 89.908 9489 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 % Allowed : 3.36 % Favored : 94.55 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 258 HIS 0.005 0.001 HIS C1048 PHE 0.030 0.002 PHE C 565 TYR 0.024 0.002 TYR A 453 ARG 0.011 0.001 ARG A 273 *********************** 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 : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7222 (t) REVERT: A 166 CYS cc_start: 0.0972 (OUTLIER) cc_final: 0.0739 (t) REVERT: A 456 PHE cc_start: 0.7114 (m-10) cc_final: 0.6733 (t80) REVERT: A 509 ARG cc_start: 0.5482 (mtt180) cc_final: 0.4405 (mmt180) REVERT: B 62 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.9009 (p) REVERT: B 353 TRP cc_start: 0.3838 (p-90) cc_final: 0.3339 (p-90) REVERT: B 423 TYR cc_start: 0.1134 (t80) cc_final: 0.0749 (t80) REVERT: B 822 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9025 (tp) REVERT: B 878 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8549 (mm) REVERT: C 172 SER cc_start: 0.0429 (OUTLIER) cc_final: -0.0004 (t) REVERT: C 374 PHE cc_start: 0.4599 (m-80) cc_final: 0.4036 (p90) REVERT: C 469 SER cc_start: 0.6463 (OUTLIER) cc_final: 0.6134 (p) REVERT: C 473 TYR cc_start: 0.5377 (m-80) cc_final: 0.5102 (m-80) REVERT: C 710 ASN cc_start: 0.7567 (p0) cc_final: 0.7266 (p0) outliers start: 56 outliers final: 8 residues processed: 203 average time/residue: 0.3369 time to fit residues: 110.8367 Evaluate side-chains 109 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 469 SER 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: 7.9990 chunk 123 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 276 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 A 125 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 370 ASN B 448 ASN B 580 GLN C 955 ASN C1135 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24978 Z= 0.204 Angle : 0.603 9.879 33955 Z= 0.312 Chirality : 0.046 0.467 3963 Planarity : 0.005 0.090 4336 Dihedral : 6.774 67.395 4009 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.28 % Rotamer: Outliers : 1.72 % Allowed : 7.20 % Favored : 91.08 % 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: -1.87 (0.15), residues: 2973 helix: 1.41 (0.21), residues: 634 sheet: -1.36 (0.19), residues: 653 loop : -2.36 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 258 HIS 0.005 0.001 HIS C1048 PHE 0.019 0.002 PHE C 140 TYR 0.025 0.001 TYR C1110 ARG 0.005 0.001 ARG A 273 *********************** 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 171 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 125 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.7176 (m-10) cc_final: 0.6825 (t80) REVERT: B 423 TYR cc_start: 0.1271 (t80) cc_final: 0.0855 (t80) REVERT: B 822 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9010 (tp) REVERT: C 153 MET cc_start: 0.4744 (tmm) cc_final: 0.2084 (pmm) REVERT: C 374 PHE cc_start: 0.4497 (m-80) cc_final: 0.4237 (p90) REVERT: C 400 PHE cc_start: 0.8311 (p90) cc_final: 0.8019 (p90) REVERT: C 473 TYR cc_start: 0.5762 (m-80) cc_final: 0.4798 (m-80) REVERT: C 887 THR cc_start: 0.8587 (p) cc_final: 0.8303 (t) outliers start: 46 outliers final: 20 residues processed: 169 average time/residue: 0.3414 time to fit residues: 94.2919 Evaluate side-chains 115 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 229 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 125 ASN A 370 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 949 GLN A 953 ASN A1106 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN C 164 ASN C 394 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24978 Z= 0.267 Angle : 0.587 9.764 33955 Z= 0.305 Chirality : 0.045 0.427 3963 Planarity : 0.004 0.061 4336 Dihedral : 6.120 58.794 4002 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.87 % Allowed : 9.81 % Favored : 88.32 % 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: -1.71 (0.15), residues: 2973 helix: 1.67 (0.21), residues: 629 sheet: -1.31 (0.19), residues: 662 loop : -2.28 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 258 HIS 0.005 0.001 HIS C1048 PHE 0.019 0.002 PHE C 497 TYR 0.020 0.002 TYR B 904 ARG 0.006 0.001 ARG B 905 *********************** 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 153 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 103 time to evaluate : 2.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.5937 (mp0) cc_final: 0.5435 (mt-10) REVERT: A 208 THR cc_start: 0.7872 (m) cc_final: 0.7654 (p) REVERT: A 456 PHE cc_start: 0.7048 (m-10) cc_final: 0.6792 (t80) REVERT: A 900 MET cc_start: 0.8634 (mtp) cc_final: 0.8375 (mtp) REVERT: B 822 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9149 (mt) REVERT: C 153 MET cc_start: 0.4725 (tmm) cc_final: 0.2042 (pmm) REVERT: C 258 TRP cc_start: 0.3562 (p-90) cc_final: 0.3339 (p-90) REVERT: C 400 PHE cc_start: 0.8151 (p90) cc_final: 0.7599 (p90) REVERT: C 473 TYR cc_start: 0.6037 (m-80) cc_final: 0.5142 (m-80) REVERT: C 524 VAL cc_start: 0.6976 (OUTLIER) cc_final: 0.6736 (t) REVERT: C 887 THR cc_start: 0.8667 (p) cc_final: 0.8344 (t) outliers start: 50 outliers final: 31 residues processed: 149 average time/residue: 0.3410 time to fit residues: 83.1261 Evaluate side-chains 125 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 92 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 2.9990 chunk 207 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 277 optimal weight: 0.9990 chunk 293 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 263 optimal weight: 0.8980 chunk 79 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 317 ASN A 370 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN A 949 GLN A 953 ASN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24978 Z= 0.182 Angle : 0.538 9.122 33955 Z= 0.277 Chirality : 0.043 0.235 3963 Planarity : 0.004 0.058 4336 Dihedral : 5.822 55.524 4002 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.09 % Allowed : 10.56 % Favored : 87.35 % 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: -1.54 (0.15), residues: 2973 helix: 1.93 (0.21), residues: 630 sheet: -1.26 (0.19), residues: 663 loop : -2.20 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 104 HIS 0.006 0.001 HIS A 655 PHE 0.026 0.001 PHE B 168 TYR 0.018 0.001 TYR B 904 ARG 0.005 0.000 ARG B 319 *********************** 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 163 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 107 time to evaluate : 2.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8668 (mtp) cc_final: 0.8436 (mtp) REVERT: B 62 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.9084 (p) REVERT: B 613 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8250 (mm-40) REVERT: C 153 MET cc_start: 0.4830 (tmm) cc_final: 0.2047 (pmm) REVERT: C 400 PHE cc_start: 0.8199 (p90) cc_final: 0.7689 (p90) REVERT: C 473 TYR cc_start: 0.6092 (m-80) cc_final: 0.5149 (m-80) REVERT: C 524 VAL cc_start: 0.7098 (OUTLIER) cc_final: 0.6864 (t) outliers start: 56 outliers final: 29 residues processed: 160 average time/residue: 0.3312 time to fit residues: 88.2810 Evaluate side-chains 127 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 95 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 0.4980 chunk 166 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 218 optimal weight: 0.7980 chunk 121 optimal weight: 40.0000 chunk 250 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 8.9990 chunk 263 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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** ** B 30 ASN ** 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 394 ASN C 655 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24978 Z= 0.250 Angle : 0.555 9.020 33955 Z= 0.285 Chirality : 0.043 0.194 3963 Planarity : 0.004 0.061 4336 Dihedral : 5.693 54.819 4000 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.01 % Allowed : 11.53 % Favored : 86.46 % 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: -1.53 (0.15), residues: 2973 helix: 1.94 (0.21), residues: 624 sheet: -1.26 (0.20), residues: 660 loop : -2.18 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 258 HIS 0.004 0.001 HIS B 66 PHE 0.021 0.001 PHE B 400 TYR 0.023 0.001 TYR B 904 ARG 0.005 0.000 ARG B 319 *********************** 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 151 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 97 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 MET cc_start: 0.8650 (mtp) cc_final: 0.8445 (mtp) REVERT: B 62 VAL cc_start: 0.9355 (OUTLIER) cc_final: 0.9104 (p) REVERT: B 613 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8340 (mm-40) REVERT: C 153 MET cc_start: 0.4639 (tmm) cc_final: 0.1691 (pmm) REVERT: C 400 PHE cc_start: 0.8235 (p90) cc_final: 0.7734 (p90) REVERT: C 473 TYR cc_start: 0.6151 (m-80) cc_final: 0.5184 (m-80) REVERT: C 516 GLU cc_start: 0.7048 (mp0) cc_final: 0.6779 (mp0) REVERT: C 524 VAL cc_start: 0.7319 (OUTLIER) cc_final: 0.7114 (t) outliers start: 54 outliers final: 35 residues processed: 146 average time/residue: 0.3446 time to fit residues: 84.0852 Evaluate side-chains 131 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 93 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 0.1980 chunk 264 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 136 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24978 Z= 0.265 Angle : 0.564 9.024 33955 Z= 0.290 Chirality : 0.044 0.203 3963 Planarity : 0.004 0.065 4336 Dihedral : 5.795 57.517 3999 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.98 % Allowed : 12.84 % Favored : 85.19 % 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: -1.56 (0.15), residues: 2973 helix: 1.79 (0.21), residues: 640 sheet: -1.27 (0.19), residues: 668 loop : -2.17 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 258 HIS 0.004 0.001 HIS B 66 PHE 0.021 0.002 PHE B 400 TYR 0.036 0.001 TYR A 351 ARG 0.010 0.000 ARG B 319 *********************** 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 154 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 101 time to evaluate : 2.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7249 (OUTLIER) cc_final: 0.6743 (t0) REVERT: B 62 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9115 (p) REVERT: B 353 TRP cc_start: 0.4740 (p-90) cc_final: 0.3719 (p-90) REVERT: B 794 ILE cc_start: 0.8362 (tp) cc_final: 0.8138 (tp) REVERT: C 392 PHE cc_start: 0.7195 (m-80) cc_final: 0.6874 (m-80) REVERT: C 473 TYR cc_start: 0.5987 (m-80) cc_final: 0.5101 (m-80) REVERT: C 516 GLU cc_start: 0.7357 (mp0) cc_final: 0.6963 (mp0) outliers start: 53 outliers final: 40 residues processed: 150 average time/residue: 0.3364 time to fit residues: 84.5407 Evaluate side-chains 136 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 94 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE 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: 3.9990 chunk 167 optimal weight: 4.9990 chunk 214 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 247 optimal weight: 9.9990 chunk 164 optimal weight: 0.0370 chunk 293 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 135 optimal weight: 20.0000 overall best weight: 1.1862 ------------------------------------------------------------------------------- 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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN A1088 HIS ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN C 955 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 24978 Z= 0.166 Angle : 0.516 8.620 33955 Z= 0.263 Chirality : 0.043 0.208 3963 Planarity : 0.004 0.061 4336 Dihedral : 5.471 58.685 3999 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.90 % Allowed : 13.21 % Favored : 84.89 % 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: -1.31 (0.15), residues: 2973 helix: 2.12 (0.21), residues: 630 sheet: -1.16 (0.20), residues: 663 loop : -2.03 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 258 HIS 0.003 0.001 HIS C1048 PHE 0.021 0.001 PHE B 400 TYR 0.040 0.001 TYR A 453 ARG 0.007 0.000 ARG B 319 *********************** 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 161 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 110 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: A 61 ASN cc_start: 0.7222 (OUTLIER) cc_final: 0.6729 (t0) REVERT: A 166 CYS cc_start: 0.0851 (OUTLIER) cc_final: 0.0629 (t) REVERT: A 191 GLU cc_start: 0.6289 (mp0) cc_final: 0.5074 (mt-10) REVERT: A 208 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7503 (p) REVERT: A 386 LYS cc_start: 0.7506 (ptpt) cc_final: 0.6878 (pttt) REVERT: A 440 ASN cc_start: 0.7210 (m110) cc_final: 0.6866 (t0) REVERT: A 509 ARG cc_start: 0.4728 (mtt180) cc_final: 0.4492 (mtt90) REVERT: A 900 MET cc_start: 0.8699 (mtp) cc_final: 0.8458 (mtp) REVERT: B 62 VAL cc_start: 0.9352 (OUTLIER) cc_final: 0.9122 (p) REVERT: B 353 TRP cc_start: 0.4691 (p-90) cc_final: 0.3667 (p-90) REVERT: C 473 TYR cc_start: 0.5920 (m-80) cc_final: 0.5180 (m-80) REVERT: C 516 GLU cc_start: 0.7260 (mp0) cc_final: 0.6811 (mp0) REVERT: C 751 ASN cc_start: 0.8381 (m-40) cc_final: 0.8172 (m110) outliers start: 51 outliers final: 34 residues processed: 158 average time/residue: 0.3379 time to fit residues: 88.8969 Evaluate side-chains 136 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 98 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 437 ASN Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE 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: 3.9990 chunk 174 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 0.0980 chunk 186 optimal weight: 5.9990 chunk 199 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 230 optimal weight: 0.1980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 30 ASN ** 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: 0.7801 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24978 Z= 0.191 Angle : 0.530 10.090 33955 Z= 0.271 Chirality : 0.043 0.280 3963 Planarity : 0.004 0.078 4336 Dihedral : 5.475 59.675 3999 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.79 % Allowed : 13.66 % Favored : 84.55 % 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: -1.23 (0.15), residues: 2973 helix: 2.19 (0.21), residues: 629 sheet: -1.09 (0.19), residues: 672 loop : -1.98 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 258 HIS 0.003 0.001 HIS C1048 PHE 0.022 0.001 PHE B 168 TYR 0.052 0.001 TYR A 453 ARG 0.008 0.000 ARG A 158 *********************** 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 155 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 107 time to evaluate : 2.923 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: A 166 CYS cc_start: 0.0777 (OUTLIER) cc_final: 0.0567 (t) REVERT: A 386 LYS cc_start: 0.7486 (ptpt) cc_final: 0.6851 (pttt) REVERT: A 440 ASN cc_start: 0.7245 (m110) cc_final: 0.6867 (t0) REVERT: A 855 PHE cc_start: 0.6481 (OUTLIER) cc_final: 0.5609 (t80) REVERT: A 900 MET cc_start: 0.8723 (mtp) cc_final: 0.8453 (mtp) REVERT: B 62 VAL cc_start: 0.9336 (OUTLIER) cc_final: 0.9113 (p) REVERT: B 796 ASP cc_start: 0.7559 (p0) cc_final: 0.7312 (p0) REVERT: C 392 PHE cc_start: 0.6963 (m-80) cc_final: 0.6694 (m-80) REVERT: C 473 TYR cc_start: 0.5817 (m-80) cc_final: 0.5071 (m-80) REVERT: C 516 GLU cc_start: 0.7535 (mp0) cc_final: 0.6938 (mp0) REVERT: C 751 ASN cc_start: 0.8364 (m-40) cc_final: 0.8164 (m110) outliers start: 48 outliers final: 37 residues processed: 150 average time/residue: 0.3427 time to fit residues: 85.6142 Evaluate side-chains 141 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 101 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 1.9990 chunk 280 optimal weight: 0.7980 chunk 256 optimal weight: 0.8980 chunk 273 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 214 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 246 optimal weight: 8.9990 chunk 258 optimal weight: 7.9990 chunk 272 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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** B 30 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 955 ASN C1106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24978 Z= 0.155 Angle : 0.511 10.725 33955 Z= 0.260 Chirality : 0.042 0.202 3963 Planarity : 0.004 0.075 4336 Dihedral : 5.302 58.287 3999 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.68 % Allowed : 13.69 % Favored : 84.63 % 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: -1.10 (0.16), residues: 2973 helix: 2.26 (0.21), residues: 639 sheet: -0.97 (0.19), residues: 664 loop : -1.92 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 258 HIS 0.003 0.001 HIS C1048 PHE 0.020 0.001 PHE B 168 TYR 0.047 0.001 TYR A 453 ARG 0.007 0.000 ARG C1107 *********************** 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 160 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 115 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.5318 (t-100) cc_final: 0.4744 (m100) REVERT: A 191 GLU cc_start: 0.5670 (mp0) cc_final: 0.5199 (mt-10) REVERT: A 386 LYS cc_start: 0.7442 (ptpt) cc_final: 0.6805 (pttt) REVERT: A 440 ASN cc_start: 0.7322 (m110) cc_final: 0.7040 (t0) REVERT: A 658 ASN cc_start: 0.7269 (OUTLIER) cc_final: 0.6869 (p0) REVERT: A 900 MET cc_start: 0.8695 (mtp) cc_final: 0.8476 (mtp) REVERT: B 62 VAL cc_start: 0.9328 (OUTLIER) cc_final: 0.9112 (p) REVERT: B 796 ASP cc_start: 0.7495 (p0) cc_final: 0.7288 (p0) REVERT: C 473 TYR cc_start: 0.5880 (m-80) cc_final: 0.5108 (m-80) REVERT: C 516 GLU cc_start: 0.7492 (mp0) cc_final: 0.6914 (mp0) outliers start: 45 outliers final: 33 residues processed: 156 average time/residue: 0.3447 time to fit residues: 89.8599 Evaluate side-chains 137 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 102 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 370 ASN Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1109 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 3.9990 chunk 288 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 200 optimal weight: 0.0570 chunk 302 optimal weight: 3.9990 chunk 278 optimal weight: 0.8980 chunk 241 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 147 optimal weight: 0.8980 overall best weight: 1.3702 ------------------------------------------------------------------------------- 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 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 955 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24978 Z= 0.188 Angle : 0.522 8.697 33955 Z= 0.267 Chirality : 0.043 0.201 3963 Planarity : 0.004 0.053 4336 Dihedral : 5.271 56.917 3998 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.64 % Allowed : 13.99 % Favored : 84.37 % 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: -1.04 (0.16), residues: 2973 helix: 2.28 (0.21), residues: 632 sheet: -0.93 (0.19), residues: 672 loop : -1.87 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 258 HIS 0.003 0.001 HIS C1048 PHE 0.023 0.001 PHE B 400 TYR 0.053 0.001 TYR A 453 ARG 0.007 0.000 ARG B 319 ********************** 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 153 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 109 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.7471 (ptpt) cc_final: 0.6821 (pttt) REVERT: A 440 ASN cc_start: 0.7349 (m110) cc_final: 0.7083 (t0) REVERT: A 658 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.6889 (p0) REVERT: A 900 MET cc_start: 0.8706 (mtp) cc_final: 0.8437 (mtp) REVERT: B 62 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.9120 (p) REVERT: B 796 ASP cc_start: 0.7523 (p0) cc_final: 0.7308 (p0) REVERT: C 392 PHE cc_start: 0.7108 (m-80) cc_final: 0.6881 (m-80) REVERT: C 473 TYR cc_start: 0.5836 (m-80) cc_final: 0.5047 (m-80) REVERT: C 516 GLU cc_start: 0.7493 (mp0) cc_final: 0.6928 (mp0) outliers start: 44 outliers final: 36 residues processed: 150 average time/residue: 0.3232 time to fit residues: 80.4652 Evaluate side-chains 141 residues out of total 2680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 103 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 201 PHE Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 969 ASN Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1109 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 0.6980 chunk 256 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 241 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 248 optimal weight: 0.0020 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- 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** B 804 GLN C 690 GLN C 955 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.105945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074322 restraints weight = 81816.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074945 restraints weight = 58433.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.074809 restraints weight = 42012.826| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24978 Z= 0.183 Angle : 0.525 11.056 33955 Z= 0.267 Chirality : 0.043 0.303 3963 Planarity : 0.004 0.053 4336 Dihedral : 5.315 55.440 3996 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.42 % Allowed : 14.25 % Favored : 84.33 % 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: -1.01 (0.16), residues: 2973 helix: 2.28 (0.21), residues: 631 sheet: -0.87 (0.20), residues: 674 loop : -1.84 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 258 HIS 0.003 0.001 HIS C1048 PHE 0.022 0.001 PHE A 318 TYR 0.044 0.001 TYR A 453 ARG 0.006 0.000 ARG A 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3715.46 seconds wall clock time: 70 minutes 12.61 seconds (4212.61 seconds total)