Starting phenix.real_space_refine (version: dev) on Mon Feb 27 04:04:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc1_26879/02_2023/7sc1_26879.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc1_26879/02_2023/7sc1_26879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc1_26879/02_2023/7sc1_26879.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc1_26879/02_2023/7sc1_26879.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc1_26879/02_2023/7sc1_26879.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sc1_26879/02_2023/7sc1_26879.pdb" } resolution = 3.2 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= 0.023 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 Process input model Symmetric amino acids flipped Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 985": "OD1" <-> "OD2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 29415 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7896 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 54, 'TRANS': 956} Chain breaks: 7 Chain: "H" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "L" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "B" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7896 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 54, 'TRANS': 956} Chain breaks: 7 Chain: "M" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "C" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7896 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 54, 'TRANS': 956} Chain breaks: 7 Chain: "P" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 890 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "A" 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 Chain: "B" 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 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: 15.72, per 1000 atoms: 0.53 Number of scatterers: 29415 At special positions: 0 Unit cell: (142.272, 143.936, 212.992, 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 126 16.00 O 5727 8.00 N 4851 7.00 C 18711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 603 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A 717 " " NAG A1313 " - " ASN A1074 " " NAG A1314 " - " ASN A1098 " " NAG A1315 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 603 " " NAG B1309 " - " ASN B 616 " " NAG B1310 " - " ASN B 657 " " NAG B1311 " - " ASN B 709 " " NAG B1312 " - " ASN B 717 " " NAG B1313 " - " ASN B1074 " " NAG B1314 " - " ASN B1098 " " NAG B1315 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 603 " " NAG C1309 " - " ASN C 616 " " NAG C1310 " - " ASN C 657 " " NAG C1311 " - " ASN C 709 " " NAG C1312 " - " ASN C 717 " " NAG C1313 " - " ASN C1074 " " NAG C1314 " - " ASN C1098 " " NAG C1315 " - " ASN C1134 " Time building additional restraints: 10.60 Conformation dependent library (CDL) restraints added in 3.9 seconds 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 64 sheets defined 21.7% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.395A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.948A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.642A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.359A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 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 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.215A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.102A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.800A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.755A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.387A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.960A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.596A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.643A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.341A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 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 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.329A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.097A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.747A pdb=" N ASN M 32 " --> pdb=" O VAL M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 75 No H-bonds generated for 'chain 'M' and resid 73 through 75' Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.736A pdb=" N THR M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 Processing helix chain 'C' and resid 383 through 388 removed outlier: 4.381A pdb=" N ASN C 388 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.921A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.637A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) 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 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.327A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.137A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 3.871A pdb=" N ASN P 32 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 83 through 87 removed outlier: 3.737A pdb=" N THR P 87 " --> pdb=" O ALA P 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.738A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.206A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.611A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.860A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.849A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.565A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.592A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.852A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.833A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.038A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 734 removed outlier: 4.346A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.588A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.463A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 6 through 7 removed outlier: 4.054A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.866A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.668A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC8, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.164A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.172A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 141 through 142 removed outlier: 5.682A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.864A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.578A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.590A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 512 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.862A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.086A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AE1, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AE2, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.309A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE5, first strand: chain 'M' and resid 3 through 7 removed outlier: 3.590A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 58 through 59 removed outlier: 5.466A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA M 88 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR M 90 " --> pdb=" O THR M 107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR M 107 " --> pdb=" O TYR M 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 6 through 7 removed outlier: 4.061A pdb=" N THR N 22 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.860A pdb=" N GLU N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR N 102 " --> pdb=" O TYR N 86 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.716A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.149A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.625A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.869A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.832A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.522A pdb=" N VAL C 539 " --> pdb=" O GLY C 550 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.585A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.870A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF9, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.066A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AG2, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.799A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AG4, first strand: chain 'C' and resid 733 through 734 removed outlier: 4.331A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG6, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AG7, first strand: chain 'P' and resid 3 through 7 removed outlier: 3.586A pdb=" N GLN P 3 " --> pdb=" O SER P 25 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 58 through 59 removed outlier: 5.467A pdb=" N TRP P 47 " --> pdb=" O ARG P 38 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG P 38 " --> pdb=" O TRP P 47 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA P 88 " --> pdb=" O VAL P 109 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR P 107 " --> pdb=" O TYR P 90 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 6 through 7 removed outlier: 4.045A pdb=" N THR Q 22 " --> pdb=" O SER Q 7 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Q' and resid 10 through 13 removed outlier: 3.874A pdb=" N GLU Q 105 " --> pdb=" O LEU Q 11 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR Q 102 " --> pdb=" O TYR Q 86 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP Q 35 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 3012 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: 13.35 Time building geometry restraints manager: 11.67 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: 9361 1.34 - 1.46: 6074 1.46 - 1.58: 14469 1.58 - 1.70: 0 1.70 - 1.81: 159 Bond restraints: 30063 Sorted by residual: bond pdb=" C LEU C 223 " pdb=" N GLU C 224 " ideal model delta sigma weight residual 1.331 1.381 -0.050 2.07e-02 2.33e+03 5.91e+00 bond pdb=" CB ASN B 777 " pdb=" CG ASN B 777 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.58e+00 bond pdb=" CB ASN A 777 " pdb=" CG ASN A 777 " ideal model delta sigma weight residual 1.516 1.457 0.059 2.50e-02 1.60e+03 5.55e+00 bond pdb=" CB CYS B 760 " pdb=" SG CYS B 760 " ideal model delta sigma weight residual 1.808 1.731 0.077 3.30e-02 9.18e+02 5.51e+00 bond pdb=" CB CYS C 760 " pdb=" SG CYS C 760 " ideal model delta sigma weight residual 1.808 1.731 0.077 3.30e-02 9.18e+02 5.49e+00 ... (remaining 30058 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.64: 611 105.64 - 112.75: 16248 112.75 - 119.87: 9328 119.87 - 126.98: 14421 126.98 - 134.09: 282 Bond angle restraints: 40890 Sorted by residual: angle pdb=" N GLY C 857 " pdb=" CA GLY C 857 " pdb=" C GLY C 857 " ideal model delta sigma weight residual 114.48 109.15 5.33 1.19e+00 7.06e-01 2.00e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.75 -4.05 1.22e+00 6.72e-01 1.10e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 114.64 -3.94 1.22e+00 6.72e-01 1.04e+01 angle pdb=" C1 NAG C1309 " pdb=" O5 NAG C1309 " pdb=" C5 NAG C1309 " ideal model delta sigma weight residual 113.34 118.84 -5.50 1.74e+00 3.30e-01 9.97e+00 angle pdb=" C4 NAG C1309 " pdb=" C5 NAG C1309 " pdb=" O5 NAG C1309 " ideal model delta sigma weight residual 109.74 113.87 -4.13 1.35e+00 5.51e-01 9.42e+00 ... (remaining 40885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.06: 16633 22.06 - 44.11: 966 44.11 - 66.17: 102 66.17 - 88.22: 42 88.22 - 110.28: 41 Dihedral angle restraints: 17784 sinusoidal: 7056 harmonic: 10728 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -165.85 79.85 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -165.66 79.66 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -157.70 71.70 1 1.00e+01 1.00e-02 6.58e+01 ... (remaining 17781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 4406 0.090 - 0.180: 351 0.180 - 0.270: 13 0.270 - 0.360: 0 0.360 - 0.450: 3 Chirality restraints: 4773 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.87e+00 ... (remaining 4770 not shown) Planarity restraints: 5271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 526 " 0.036 5.00e-02 4.00e+02 5.37e-02 4.62e+00 pdb=" N PRO B 527 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 527 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 527 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 84 " -0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO A 85 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 881 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C THR C 881 " 0.032 2.00e-02 2.50e+03 pdb=" O THR C 881 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE C 882 " -0.011 2.00e-02 2.50e+03 ... (remaining 5268 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1260 2.72 - 3.26: 29537 3.26 - 3.81: 47622 3.81 - 4.35: 57909 4.35 - 4.90: 100555 Nonbonded interactions: 236883 Sorted by model distance: nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.169 2.440 nonbonded pdb=" OG SER N 9 " pdb=" O GLY N 101 " model vdw 2.184 2.440 nonbonded pdb=" OG SER Q 9 " pdb=" O GLY Q 101 " model vdw 2.185 2.440 nonbonded pdb=" OG SER L 9 " pdb=" O GLY L 101 " model vdw 2.188 2.440 nonbonded pdb=" O GLU B 661 " pdb=" OH TYR B 695 " model vdw 2.193 2.440 ... (remaining 236878 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'Q' } 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 126 5.16 5 C 18711 2.51 5 N 4851 2.21 5 O 5727 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: 4.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.750 Check model and map are aligned: 0.420 Process input model: 74.070 Find NCS groups from input model: 1.710 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0127 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 : 0.006 0.077 30063 Z= 0.370 Angle : 0.604 8.764 40890 Z= 0.326 Chirality : 0.047 0.450 4773 Planarity : 0.004 0.054 5226 Dihedral : 14.852 110.278 10779 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.55 (0.13), residues: 3645 helix: 1.29 (0.19), residues: 693 sheet: -0.52 (0.17), residues: 960 loop : -0.85 (0.13), residues: 1992 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 245 time to evaluate : 3.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 247 average time/residue: 0.4236 time to fit residues: 169.5521 Evaluate side-chains 155 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 3.246 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3232 time to fit residues: 5.3717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 309 optimal weight: 0.7980 chunk 277 optimal weight: 50.0000 chunk 153 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 187 optimal weight: 0.6980 chunk 148 optimal weight: 9.9990 chunk 286 optimal weight: 50.0000 chunk 111 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 213 optimal weight: 0.8980 chunk 332 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 536 ASN A 690 GLN A 762 GLN A 804 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1010 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 613 GLN B 690 GLN B 804 GLN B 919 ASN B 935 GLN B1002 GLN B1088 HIS M 105 GLN N 37 GLN C 66 HIS C 536 ASN C 690 GLN C 804 GLN C 919 ASN C 935 GLN C1106 GLN Q 37 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0379 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 30063 Z= 0.187 Angle : 0.565 9.343 40890 Z= 0.304 Chirality : 0.047 0.459 4773 Planarity : 0.004 0.047 5226 Dihedral : 11.711 111.116 4242 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.39 (0.13), residues: 3645 helix: 1.64 (0.19), residues: 684 sheet: -0.42 (0.16), residues: 954 loop : -0.83 (0.13), residues: 2007 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 169 average time/residue: 0.3977 time to fit residues: 115.5452 Evaluate side-chains 153 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 141 time to evaluate : 2.850 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3590 time to fit residues: 11.8000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 184 optimal weight: 0.0060 chunk 103 optimal weight: 6.9990 chunk 276 optimal weight: 5.9990 chunk 226 optimal weight: 50.0000 chunk 91 optimal weight: 6.9990 chunk 332 optimal weight: 0.5980 chunk 359 optimal weight: 50.0000 chunk 296 optimal weight: 2.9990 chunk 330 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 267 optimal weight: 0.6980 overall best weight: 1.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 703 ASN A 804 GLN A 919 ASN A 935 GLN H 39 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 955 ASN B1011 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN M 39 GLN C 49 HIS C 580 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 949 GLN C 955 ASN P 39 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0857 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 30063 Z= 0.232 Angle : 0.602 8.859 40890 Z= 0.323 Chirality : 0.047 0.413 4773 Planarity : 0.005 0.060 5226 Dihedral : 11.821 110.341 4242 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 3645 helix: 1.09 (0.19), residues: 672 sheet: -0.24 (0.16), residues: 927 loop : -0.83 (0.13), residues: 2046 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 22 residues processed: 193 average time/residue: 0.4011 time to fit residues: 129.7483 Evaluate side-chains 170 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 2.964 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2928 time to fit residues: 16.1145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 328 optimal weight: 2.9990 chunk 250 optimal weight: 30.0000 chunk 172 optimal weight: 0.8980 chunk 36 optimal weight: 50.0000 chunk 158 optimal weight: 30.0000 chunk 223 optimal weight: 2.9990 chunk 334 optimal weight: 2.9990 chunk 353 optimal weight: 50.0000 chunk 174 optimal weight: 9.9990 chunk 316 optimal weight: 0.0040 chunk 95 optimal weight: 3.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 314 GLN A 804 GLN A 935 GLN A1005 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN N 89 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1164 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 30063 Z= 0.240 Angle : 0.628 11.731 40890 Z= 0.337 Chirality : 0.048 0.409 4773 Planarity : 0.005 0.065 5226 Dihedral : 11.882 110.876 4242 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.59 (0.13), residues: 3645 helix: 0.68 (0.19), residues: 678 sheet: -0.04 (0.17), residues: 900 loop : -0.90 (0.13), residues: 2067 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 168 time to evaluate : 3.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 31 residues processed: 207 average time/residue: 0.3715 time to fit residues: 131.4049 Evaluate side-chains 174 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 2.985 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2613 time to fit residues: 20.0385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 294 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 263 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 301 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 chunk 0 optimal weight: 50.0000 chunk 180 optimal weight: 3.9990 chunk 317 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN B 784 GLN ** B 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN N 90 GLN C 774 GLN ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1230 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 30063 Z= 0.215 Angle : 0.577 10.105 40890 Z= 0.310 Chirality : 0.046 0.383 4773 Planarity : 0.004 0.051 5226 Dihedral : 11.841 110.954 4242 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.53 (0.13), residues: 3645 helix: 0.62 (0.19), residues: 678 sheet: 0.11 (0.17), residues: 882 loop : -0.88 (0.13), residues: 2085 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 157 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 25 residues processed: 190 average time/residue: 0.3996 time to fit residues: 127.0135 Evaluate side-chains 171 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 2.829 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3056 time to fit residues: 18.7271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 119 optimal weight: 40.0000 chunk 318 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 354 optimal weight: 50.0000 chunk 293 optimal weight: 6.9990 chunk 163 optimal weight: 40.0000 chunk 29 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 185 optimal weight: 0.0980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN A 949 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN B 949 GLN B 953 ASN B1010 GLN N 90 GLN C 804 GLN ** C 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1413 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.063 30063 Z= 0.243 Angle : 0.624 14.913 40890 Z= 0.334 Chirality : 0.047 0.373 4773 Planarity : 0.005 0.050 5226 Dihedral : 11.874 111.069 4242 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.64 (0.13), residues: 3645 helix: 0.57 (0.20), residues: 639 sheet: 0.10 (0.17), residues: 885 loop : -0.98 (0.13), residues: 2121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 29 residues processed: 198 average time/residue: 0.4112 time to fit residues: 136.7520 Evaluate side-chains 180 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 151 time to evaluate : 2.984 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2849 time to fit residues: 19.6629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 341 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 298 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 352 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 215 optimal weight: 0.5980 chunk 162 optimal weight: 40.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN N 89 GLN ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN C 935 GLN C 949 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1438 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 30063 Z= 0.213 Angle : 0.582 11.814 40890 Z= 0.310 Chirality : 0.046 0.355 4773 Planarity : 0.004 0.053 5226 Dihedral : 11.878 111.014 4242 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.60 (0.13), residues: 3645 helix: 0.61 (0.20), residues: 666 sheet: 0.19 (0.17), residues: 885 loop : -1.01 (0.13), residues: 2094 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 3.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 24 residues processed: 182 average time/residue: 0.4149 time to fit residues: 126.5316 Evaluate side-chains 178 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 3.351 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3078 time to fit residues: 18.4395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 218 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 106 optimal weight: 40.0000 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.0770 chunk 224 optimal weight: 30.0000 chunk 240 optimal weight: 50.0000 chunk 174 optimal weight: 6.9990 chunk 32 optimal weight: 40.0000 chunk 277 optimal weight: 30.0000 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1412 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 30063 Z= 0.181 Angle : 0.554 11.729 40890 Z= 0.295 Chirality : 0.046 0.350 4773 Planarity : 0.004 0.052 5226 Dihedral : 11.814 110.855 4242 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.52 (0.13), residues: 3645 helix: 0.70 (0.20), residues: 669 sheet: 0.25 (0.17), residues: 885 loop : -0.96 (0.13), residues: 2091 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 167 average time/residue: 0.4136 time to fit residues: 116.1250 Evaluate side-chains 161 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 3.028 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3296 time to fit residues: 9.4654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 320 optimal weight: 0.4980 chunk 337 optimal weight: 1.9990 chunk 308 optimal weight: 0.0000 chunk 328 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 143 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 100 optimal weight: 0.3980 chunk 297 optimal weight: 0.5980 chunk 310 optimal weight: 0.9980 chunk 327 optimal weight: 0.5980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN B1036 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1279 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 30063 Z= 0.147 Angle : 0.516 11.472 40890 Z= 0.271 Chirality : 0.048 1.125 4773 Planarity : 0.004 0.048 5226 Dihedral : 11.728 110.549 4242 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.37 (0.13), residues: 3645 helix: 1.01 (0.20), residues: 678 sheet: 0.24 (0.17), residues: 954 loop : -0.92 (0.13), residues: 2013 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 159 average time/residue: 0.4251 time to fit residues: 113.7932 Evaluate side-chains 155 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 150 time to evaluate : 3.342 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2966 time to fit residues: 7.3750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 215 optimal weight: 0.7980 chunk 347 optimal weight: 30.0000 chunk 212 optimal weight: 0.0060 chunk 164 optimal weight: 6.9990 chunk 241 optimal weight: 50.0000 chunk 364 optimal weight: 6.9990 chunk 335 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 224 optimal weight: 30.0000 chunk 178 optimal weight: 8.9990 overall best weight: 3.5602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 935 GLN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B1011 GLN ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 73 ASN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1824 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.096 30063 Z= 0.369 Angle : 0.783 14.681 40890 Z= 0.425 Chirality : 0.053 0.791 4773 Planarity : 0.006 0.077 5226 Dihedral : 12.127 111.421 4242 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.93 (0.13), residues: 3645 helix: -0.14 (0.20), residues: 630 sheet: 0.37 (0.17), residues: 843 loop : -1.19 (0.12), residues: 2172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7290 Ramachandran restraints generated. 3645 Oldfield, 0 Emsley, 3645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 175 time to evaluate : 3.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 183 average time/residue: 0.4501 time to fit residues: 137.3435 Evaluate side-chains 164 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 3.083 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2987 time to fit residues: 10.0646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 230 optimal weight: 0.0670 chunk 309 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 267 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 290 optimal weight: 0.4980 chunk 121 optimal weight: 50.0000 chunk 298 optimal weight: 6.9990 chunk 36 optimal weight: 50.0000 chunk 53 optimal weight: 5.9990 overall best weight: 1.1124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN A 804 GLN A 935 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1011 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5691 r_free = 0.5691 target = 0.369238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5669 r_free = 0.5669 target = 0.359448 restraints weight = 46490.546| |-----------------------------------------------------------------------------| r_work (start): 0.5649 rms_B_bonded: 2.66 r_work: 0.5565 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.5565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1447 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 30063 Z= 0.184 Angle : 0.578 11.510 40890 Z= 0.307 Chirality : 0.047 0.407 4773 Planarity : 0.004 0.074 5226 Dihedral : 11.952 110.949 4242 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.67 (0.13), residues: 3645 helix: 0.47 (0.20), residues: 642 sheet: 0.33 (0.17), residues: 882 loop : -1.10 (0.13), residues: 2121 =============================================================================== Job complete usr+sys time: 5111.95 seconds wall clock time: 95 minutes 46.29 seconds (5746.29 seconds total)