Starting phenix.real_space_refine (version: dev) on Mon May 16 06:14:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b18_11981/05_2022/7b18_11981.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b18_11981/05_2022/7b18_11981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b18_11981/05_2022/7b18_11981.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b18_11981/05_2022/7b18_11981.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b18_11981/05_2022/7b18_11981.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b18_11981/05_2022/7b18_11981.pdb" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 30105 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7896 Classifications: {'peptide': 1011} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 960} Chain breaks: 7 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 7897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7897 Classifications: {'peptide': 1012} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 49, 'TRANS': 962} Chain breaks: 9 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8125 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 972 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 885 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 972 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 885 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "H" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 972 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 885 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 17.20, per 1000 atoms: 0.57 Number of scatterers: 30105 At special positions: 0 Unit cell: (153, 148.92, 219.3, 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 140 16.00 O 5895 8.00 N 4935 7.00 C 19135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.02 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.02 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=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " 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 BETA1-4 " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A1098 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A1134 " " NAG A1313 " - " ASN A 801 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 331 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 717 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 709 " " NAG B1313 " - " ASN B 603 " " NAG B1314 " - " ASN B 801 " " NAG C1301 " - " ASN C 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 717 " " NAG C1312 " - " ASN C1074 " " NAG C1313 " - " ASN C1098 " " NAG C1314 " - " ASN C1134 " " NAG C1315 " - " ASN C 801 " " NAG J 1 " - " ASN C 343 " NAG-THR " NAG B1302 " - " THR B 124 " Time building additional restraints: 12.18 Conformation dependent library (CDL) restraints added in 4.4 seconds 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7040 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 63 sheets defined 20.2% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.622A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.924A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.669A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.824A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.503A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.642A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.540A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.012A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.647A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.583A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.852A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.209A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.608A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.506A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.705A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.641A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.873A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.603A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.150A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.633A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.710A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 61 through 64 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.067A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.347A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.832A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 326 through 328 removed outlier: 5.031A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.618A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.115A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 664 through 667 removed outlier: 5.950A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.664A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.547A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.489A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.636A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.310A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.534A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.018A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 153 through 158 removed outlier: 5.537A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.710A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 326 through 328 removed outlier: 5.417A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.751A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG G 100C" --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.022A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.447A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 728 removed outlier: 5.977A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.372A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.628A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.280A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.598A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.649A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.734A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.643A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 327 removed outlier: 4.947A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.578A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.955A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.695A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.695A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.507A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.686A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.528A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR D 79 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.501A pdb=" N GLY D 35 " --> pdb=" O ALA D 93 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N TYR D 32 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLY D 52 " --> pdb=" O TYR D 32 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE D 34 " --> pdb=" O CYS D 50 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N CYS D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 98 through 100 Processing sheet with id=AF3, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.513A pdb=" N VAL E 78 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.818A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E 102 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.818A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.601A pdb=" N TYR F 79 " --> pdb=" O SER F 70 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.593A pdb=" N GLY F 35 " --> pdb=" O ALA F 93 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR F 32 " --> pdb=" O GLY F 52 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY F 52 " --> pdb=" O TYR F 32 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE F 34 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N CYS F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 98 through 100 Processing sheet with id=AF9, first strand: chain 'G' and resid 6 through 7 Processing sheet with id=AG1, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.861A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TYR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N MET G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER G 102 " --> pdb=" O THR G 94 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.861A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N TYR G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N MET G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.644A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.514A pdb=" N GLY H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TYR H 32 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N GLY H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE H 34 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N CYS H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AG6, first strand: chain 'H' and resid 98 through 100 Processing sheet with id=AG7, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.650A pdb=" N VAL I 5 " --> pdb=" O ALA I 23 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.212A pdb=" N MET I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N TYR I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.511A pdb=" N SER I 102 " --> pdb=" O THR I 94 " (cutoff:3.500A) 1258 hydrogen bonds defined for protein. 3348 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: 15.41 Time building geometry restraints manager: 13.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9568 1.34 - 1.46: 7811 1.46 - 1.59: 13216 1.59 - 1.71: 0 1.71 - 1.84: 179 Bond restraints: 30774 Sorted by residual: bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.453 1.484 -0.031 8.30e-03 1.45e+04 1.39e+01 bond pdb=" N GLU B 619 " pdb=" CA GLU B 619 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.29e-02 6.01e+03 1.13e+01 bond pdb=" N ILE B 233 " pdb=" CA ILE B 233 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" C5 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.435 1.399 0.036 1.10e-02 8.26e+03 1.07e+01 bond pdb=" N GLY A 219 " pdb=" CA GLY A 219 " ideal model delta sigma weight residual 1.448 1.477 -0.028 8.80e-03 1.29e+04 1.03e+01 ... (remaining 30769 not shown) Histogram of bond angle deviations from ideal: 97.50 - 104.81: 467 104.81 - 112.11: 15155 112.11 - 119.42: 10051 119.42 - 126.72: 15888 126.72 - 134.03: 306 Bond angle restraints: 41867 Sorted by residual: angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.16 98.83 14.33 1.24e+00 6.50e-01 1.34e+02 angle pdb=" C ASN C 616 " pdb=" N CYS C 617 " pdb=" CA CYS C 617 " ideal model delta sigma weight residual 122.66 111.75 10.91 1.63e+00 3.76e-01 4.48e+01 angle pdb=" C2 NAG J 1 " pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 109.64 112.97 -3.33 5.38e-01 3.45e+00 3.84e+01 angle pdb=" CA GLY A 219 " pdb=" C GLY A 219 " pdb=" O GLY A 219 " ideal model delta sigma weight residual 122.37 118.26 4.11 7.30e-01 1.88e+00 3.17e+01 angle pdb=" C LYS B1073 " pdb=" N ASN B1074 " pdb=" CA ASN B1074 " ideal model delta sigma weight residual 121.97 130.90 -8.93 1.73e+00 3.34e-01 2.67e+01 ... (remaining 41862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.05: 17077 22.05 - 44.11: 862 44.11 - 66.16: 90 66.16 - 88.22: 35 88.22 - 110.27: 3 Dihedral angle restraints: 18067 sinusoidal: 7053 harmonic: 11014 Sorted by residual: dihedral pdb=" CA VAL B1133 " pdb=" C VAL B1133 " pdb=" N ASN B1134 " pdb=" CA ASN B1134 " ideal model delta harmonic sigma weight residual -180.00 -130.23 -49.77 0 5.00e+00 4.00e-02 9.91e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -10.34 -75.66 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 158.60 -65.60 1 1.00e+01 1.00e-02 5.63e+01 ... (remaining 18064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.310: 4830 0.310 - 0.620: 4 0.620 - 0.930: 0 0.930 - 1.240: 1 1.240 - 1.550: 1 Chirality restraints: 4836 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.67e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.85 -1.55 2.00e-01 2.50e+01 6.00e+01 chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.36 -1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 4833 not shown) Planarity restraints: 5390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1306 " 0.345 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG A1306 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A1306 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG A1306 " -0.525 2.00e-02 2.50e+03 pdb=" O7 NAG A1306 " 0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.279 2.00e-02 2.50e+03 2.39e-01 7.13e+02 pdb=" C7 NAG J 1 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.171 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.415 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1134 " 0.066 2.00e-02 2.50e+03 6.37e-02 5.08e+01 pdb=" CG ASN B1134 " -0.074 2.00e-02 2.50e+03 pdb=" OD1 ASN B1134 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN B1134 " -0.075 2.00e-02 2.50e+03 pdb=" C1 NAG B1311 " 0.068 2.00e-02 2.50e+03 ... (remaining 5387 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 310 2.60 - 3.18: 25834 3.18 - 3.75: 44169 3.75 - 4.33: 63674 4.33 - 4.90: 105602 Nonbonded interactions: 239589 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.028 2.440 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.058 2.440 nonbonded pdb=" OG1 THR C 323 " pdb=" NZ LYS C 537 " model vdw 2.099 2.520 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.111 2.440 nonbonded pdb=" O ASN A 856 " pdb=" ND2 ASN A 856 " model vdw 2.139 2.520 ... (remaining 239584 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 29 through 65 or resid 80 through 172 or resid 175 through \ 212 or resid 215 through 577 or resid 584 through 1146 or resid 1301 through 13 \ 13)) selection = (chain 'B' and (resid 29 through 144 or resid 153 through 243 or resid 265 throu \ gh 577 or resid 584 through 1146 or resid 1301 through 1313)) selection = (chain 'C' and (resid 29 through 65 or resid 80 through 144 or resid 153 through \ 172 or resid 175 or resid 187 through 212 or resid 215 through 243 or resid 265 \ through 1146 or resid 1301 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 19135 2.51 5 N 4935 2.21 5 O 5895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.460 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: 0.030 Extract box with map and model: 48.720 Check model and map are aligned: 0.430 Convert atoms to be neutral: 0.240 Process input model: 80.950 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 : 0.007 0.073 30774 Z= 0.484 Angle : 0.839 14.333 41867 Z= 0.499 Chirality : 0.062 1.550 4836 Planarity : 0.008 0.298 5354 Dihedral : 12.739 110.273 10895 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.81 % Rotamer Outliers : 0.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.36 (0.13), residues: 3748 helix: 1.17 (0.20), residues: 664 sheet: 0.35 (0.16), residues: 990 loop : -1.02 (0.13), residues: 2094 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 623 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 633 average time/residue: 1.1700 time to fit residues: 897.5442 Evaluate side-chains 560 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 554 time to evaluate : 3.135 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 3 average time/residue: 0.7380 time to fit residues: 7.5648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 0.6980 chunk 286 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 193 optimal weight: 0.2980 chunk 153 optimal weight: 0.5980 chunk 296 optimal weight: 0.0980 chunk 114 optimal weight: 2.9990 chunk 180 optimal weight: 0.6980 chunk 220 optimal weight: 0.6980 chunk 343 optimal weight: 0.0000 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 ASN A 493 GLN A 613 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN A 955 ASN A1005 GLN A1010 GLN A1011 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 755 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1101 HIS ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 657 ASN C 658 ASN C 856 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN C1010 GLN ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN G 81 GLN G 108 GLN I 108 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 30774 Z= 0.218 Angle : 0.603 15.063 41867 Z= 0.321 Chirality : 0.046 0.410 4836 Planarity : 0.005 0.081 5354 Dihedral : 5.529 111.993 4373 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.15 (0.13), residues: 3748 helix: 1.65 (0.20), residues: 680 sheet: 0.38 (0.16), residues: 964 loop : -0.95 (0.13), residues: 2104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 568 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 41 residues processed: 595 average time/residue: 1.1918 time to fit residues: 859.1743 Evaluate side-chains 596 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 555 time to evaluate : 3.187 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 18 residues processed: 24 average time/residue: 0.5903 time to fit residues: 24.3674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 285 optimal weight: 0.9990 chunk 233 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 343 optimal weight: 0.2980 chunk 371 optimal weight: 0.0050 chunk 306 optimal weight: 0.4980 chunk 341 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 275 optimal weight: 0.0370 overall best weight: 0.3072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 779 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1010 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 774 GLN B 955 ASN C 196 ASN C 314 GLN C 321 GLN C 370 ASN C 493 GLN C 657 ASN C 658 ASN C 710 ASN C 751 ASN C1005 GLN C1135 ASN F 108 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 30774 Z= 0.231 Angle : 0.584 19.212 41867 Z= 0.308 Chirality : 0.046 0.436 4836 Planarity : 0.005 0.095 5354 Dihedral : 5.383 112.904 4373 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.13), residues: 3748 helix: 1.86 (0.20), residues: 674 sheet: 0.45 (0.16), residues: 998 loop : -0.96 (0.13), residues: 2076 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 566 time to evaluate : 3.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 49 residues processed: 612 average time/residue: 1.1656 time to fit residues: 869.1183 Evaluate side-chains 596 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 547 time to evaluate : 3.271 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 29 residues processed: 23 average time/residue: 0.8433 time to fit residues: 29.9124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 0.9980 chunk 258 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 230 optimal weight: 0.7980 chunk 345 optimal weight: 1.9990 chunk 365 optimal weight: 0.9980 chunk 180 optimal weight: 0.2980 chunk 327 optimal weight: 1.9990 chunk 98 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 282 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN C 196 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 657 ASN C 751 ASN C 957 GLN C1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.117 30774 Z= 0.333 Angle : 0.627 19.829 41867 Z= 0.329 Chirality : 0.047 0.413 4836 Planarity : 0.005 0.090 5354 Dihedral : 5.522 112.454 4373 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.92 % Rotamer Outliers : 3.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.17 (0.13), residues: 3748 helix: 1.76 (0.20), residues: 682 sheet: 0.41 (0.16), residues: 1017 loop : -1.07 (0.13), residues: 2049 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 564 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 124 outliers final: 78 residues processed: 625 average time/residue: 1.1603 time to fit residues: 889.7975 Evaluate side-chains 627 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 549 time to evaluate : 3.620 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 42 residues processed: 40 average time/residue: 0.6408 time to fit residues: 40.6495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 0.0870 chunk 207 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 272 optimal weight: 0.0980 chunk 150 optimal weight: 0.3980 chunk 311 optimal weight: 0.5980 chunk 252 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 327 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1083 HIS C 196 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 370 ASN C 657 ASN C 751 ASN C 957 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 30774 Z= 0.232 Angle : 0.584 17.467 41867 Z= 0.309 Chirality : 0.046 0.706 4836 Planarity : 0.005 0.094 5354 Dihedral : 5.390 112.344 4373 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 3.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.08 (0.14), residues: 3748 helix: 1.91 (0.20), residues: 684 sheet: 0.41 (0.16), residues: 1037 loop : -1.02 (0.13), residues: 2027 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 554 time to evaluate : 2.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 78 residues processed: 624 average time/residue: 1.1438 time to fit residues: 871.4361 Evaluate side-chains 622 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 544 time to evaluate : 3.258 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 47 residues processed: 33 average time/residue: 0.7176 time to fit residues: 36.3487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 1.9990 chunk 329 optimal weight: 0.2980 chunk 72 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 365 optimal weight: 0.0060 chunk 303 optimal weight: 0.9990 chunk 169 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 703 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 907 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 955 ASN C 30 ASN C 196 ASN C 314 GLN C 317 ASN C 321 GLN C 657 ASN C 751 ASN C 957 GLN C1005 GLN C1010 GLN E 81 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 30774 Z= 0.263 Angle : 0.603 17.629 41867 Z= 0.317 Chirality : 0.046 0.521 4836 Planarity : 0.004 0.094 5354 Dihedral : 5.406 112.048 4373 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 3.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3748 helix: 1.91 (0.20), residues: 683 sheet: 0.40 (0.16), residues: 1024 loop : -1.05 (0.13), residues: 2041 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 555 time to evaluate : 3.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 81 residues processed: 626 average time/residue: 1.1830 time to fit residues: 910.8970 Evaluate side-chains 626 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 545 time to evaluate : 3.355 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 52 residues processed: 32 average time/residue: 0.7195 time to fit residues: 36.0061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 208 optimal weight: 0.1980 chunk 267 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 chunk 307 optimal weight: 0.2980 chunk 204 optimal weight: 0.5980 chunk 364 optimal weight: 0.9990 chunk 228 optimal weight: 0.3980 chunk 222 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 955 ASN C 196 ASN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 321 GLN C 370 ASN C 657 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.174 30774 Z= 0.310 Angle : 0.626 17.648 41867 Z= 0.331 Chirality : 0.046 0.474 4836 Planarity : 0.005 0.105 5354 Dihedral : 5.483 111.801 4373 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 3748 helix: 1.84 (0.20), residues: 683 sheet: 0.33 (0.16), residues: 1014 loop : -1.11 (0.13), residues: 2051 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 554 time to evaluate : 3.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 84 residues processed: 618 average time/residue: 1.2180 time to fit residues: 926.9982 Evaluate side-chains 629 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 545 time to evaluate : 3.286 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 54 residues processed: 32 average time/residue: 0.6916 time to fit residues: 34.9187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 0.0980 chunk 145 optimal weight: 0.0570 chunk 217 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 231 optimal weight: 0.7980 chunk 248 optimal weight: 0.7980 chunk 180 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 286 optimal weight: 0.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 755 GLN C 87 ASN C 196 ASN C 314 GLN C 317 ASN C 321 GLN C 657 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN ** F 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.443 30774 Z= 0.358 Angle : 0.713 41.985 41867 Z= 0.373 Chirality : 0.047 0.481 4836 Planarity : 0.005 0.104 5354 Dihedral : 5.529 111.473 4373 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 3.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 3748 helix: 1.82 (0.20), residues: 683 sheet: 0.21 (0.15), residues: 1030 loop : -1.13 (0.13), residues: 2035 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 560 time to evaluate : 2.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 74 residues processed: 633 average time/residue: 1.1748 time to fit residues: 909.4724 Evaluate side-chains 622 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 548 time to evaluate : 3.466 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 57 residues processed: 19 average time/residue: 0.7750 time to fit residues: 24.3678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 0.8980 chunk 349 optimal weight: 0.8980 chunk 318 optimal weight: 0.9980 chunk 339 optimal weight: 0.6980 chunk 348 optimal weight: 0.0870 chunk 204 optimal weight: 0.3980 chunk 147 optimal weight: 0.8980 chunk 266 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 306 optimal weight: 0.0570 chunk 321 optimal weight: 0.5980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A1010 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 755 GLN B 762 GLN B 955 ASN C 196 ASN C 314 GLN C 317 ASN C 321 GLN C 657 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.365 30774 Z= 0.317 Angle : 0.678 31.851 41867 Z= 0.364 Chirality : 0.046 0.485 4836 Planarity : 0.005 0.123 5354 Dihedral : 5.479 111.144 4373 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.13), residues: 3748 helix: 1.79 (0.20), residues: 686 sheet: 0.23 (0.16), residues: 1011 loop : -1.12 (0.13), residues: 2051 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 550 time to evaluate : 3.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 76 residues processed: 622 average time/residue: 1.1865 time to fit residues: 910.4895 Evaluate side-chains 615 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 539 time to evaluate : 3.197 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 65 residues processed: 12 average time/residue: 0.6007 time to fit residues: 14.6694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 chunk 359 optimal weight: 0.1980 chunk 219 optimal weight: 0.4980 chunk 170 optimal weight: 0.4980 chunk 249 optimal weight: 3.9990 chunk 376 optimal weight: 0.6980 chunk 346 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 31 optimal weight: 0.0670 chunk 231 optimal weight: 0.2980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 755 GLN B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 314 GLN C 317 ASN C 321 GLN C 370 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN C1010 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.910 30774 Z= 0.404 Angle : 0.845 73.898 41867 Z= 0.417 Chirality : 0.046 0.490 4836 Planarity : 0.005 0.112 5354 Dihedral : 5.488 111.148 4373 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 3748 helix: 1.79 (0.20), residues: 686 sheet: 0.23 (0.16), residues: 1011 loop : -1.13 (0.13), residues: 2051 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7496 Ramachandran restraints generated. 3748 Oldfield, 0 Emsley, 3748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 540 time to evaluate : 3.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 81 residues processed: 608 average time/residue: 1.1574 time to fit residues: 861.4222 Evaluate side-chains 618 residues out of total 3288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 537 time to evaluate : 3.285 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 66 residues processed: 17 average time/residue: 0.9796 time to fit residues: 25.8786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.0970 chunk 238 optimal weight: 0.5980 chunk 319 optimal weight: 0.0000 chunk 91 optimal weight: 0.4980 chunk 276 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 300 optimal weight: 0.6980 chunk 125 optimal weight: 0.2980 chunk 308 optimal weight: 0.7980 chunk 38 optimal weight: 0.3980 overall best weight: 0.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 779 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 755 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 314 GLN C 317 ASN C 321 GLN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1005 GLN C1010 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.186741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.161243 restraints weight = 44597.529| |-----------------------------------------------------------------------------| r_work (start): 0.4122 rms_B_bonded: 2.68 r_work: 0.4108 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.4095 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work: 0.4082 rms_B_bonded: 2.49 restraints_weight: 0.1250 r_work: 0.4068 rms_B_bonded: 2.61 restraints_weight: 0.0625 r_work: 0.4052 rms_B_bonded: 2.78 restraints_weight: 0.0312 r_work: 0.4033 rms_B_bonded: 3.01 restraints_weight: 0.0156 r_work: 0.4013 rms_B_bonded: 3.30 restraints_weight: 0.0078 r_work: 0.3990 rms_B_bonded: 3.66 restraints_weight: 0.0039 r_work: 0.3963 rms_B_bonded: 4.10 restraints_weight: 0.0020 r_work: 0.3931 rms_B_bonded: 4.65 restraints_weight: 0.0010 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.892 30774 Z= 0.403 Angle : 0.840 73.900 41867 Z= 0.413 Chirality : 0.046 0.486 4836 Planarity : 0.005 0.118 5354 Dihedral : 5.487 111.148 4373 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 2.17 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.13), residues: 3748 helix: 1.79 (0.20), residues: 686 sheet: 0.23 (0.16), residues: 1011 loop : -1.13 (0.13), residues: 2051 =============================================================================== Job complete usr+sys time: 12892.75 seconds wall clock time: 229 minutes 9.36 seconds (13749.36 seconds total)