Starting phenix.real_space_refine on Wed Mar 20 12:09:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy4_33510/03_2024/7xy4_33510.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy4_33510/03_2024/7xy4_33510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy4_33510/03_2024/7xy4_33510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy4_33510/03_2024/7xy4_33510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy4_33510/03_2024/7xy4_33510.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy4_33510/03_2024/7xy4_33510.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 17349 2.51 5 N 4524 2.21 5 O 5300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27297 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8299 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 50, 'TRANS': 1009} Chain breaks: 5 Chain: "B" Number of atoms: 8299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8299 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 50, 'TRANS': 1009} Chain breaks: 5 Chain: "C" Number of atoms: 8299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8299 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 50, 'TRANS': 1009} Chain breaks: 5 Chain: "D" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "E" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 920 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} 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 dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 13.66, per 1000 atoms: 0.50 Number of scatterers: 27297 At special positions: 0 Unit cell: (153.92, 158.08, 197.6, 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 124 16.00 O 5300 8.00 N 4524 7.00 C 17349 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, 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=2.89 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=1.33 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=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=1.97 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " 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 A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 234 " " NAG A1203 " - " ASN A 282 " " NAG A1204 " - " ASN A 331 " " NAG A1205 " - " ASN A 343 " " NAG A1206 " - " ASN A 616 " " NAG A1207 " - " ASN A 657 " " NAG A1208 " - " ASN A 709 " " NAG A1209 " - " ASN A1074 " " NAG A1210 " - " ASN A 717 " " NAG A1211 " - " ASN A 801 " " NAG A1212 " - " ASN A1098 " " NAG A1213 " - " ASN A1134 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 282 " " NAG B1203 " - " ASN B 331 " " NAG B1204 " - " ASN B 343 " " NAG B1205 " - " ASN B 603 " " NAG B1206 " - " ASN B 616 " " NAG B1207 " - " ASN B 657 " " NAG B1208 " - " ASN B 709 " " NAG B1209 " - " ASN B1074 " " NAG B1210 " - " ASN B 717 " " NAG B1211 " - " ASN B 801 " " NAG B1212 " - " ASN B1098 " " NAG B1213 " - " ASN B1134 " " NAG C1201 " - " ASN C 122 " " NAG C1202 " - " ASN C 234 " " NAG C1203 " - " ASN C 282 " " NAG C1204 " - " ASN C 343 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 616 " " NAG C1207 " - " ASN C 657 " " NAG C1208 " - " ASN C 709 " " NAG C1209 " - " ASN C 717 " " NAG C1210 " - " ASN C1074 " " NAG C1211 " - " ASN C 165 " " NAG C1212 " - " ASN C 801 " " NAG C1213 " - " ASN C1098 " " NAG C1214 " - " ASN C1134 " Time building additional restraints: 9.58 Conformation dependent library (CDL) restraints added in 4.9 seconds 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6394 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 53 sheets defined 20.1% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.32 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 385 through 389 removed outlier: 4.020A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.804A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.557A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.609A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 964 removed outlier: 4.116A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN A 954 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.942A 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 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.769A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.664A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.711A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.535A pdb=" N GLY B 908 " --> pdb=" O TYR B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.838A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.944A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.838A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.607A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.228A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.754A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.743A pdb=" N LYS C 386 " --> pdb=" O SER C 383 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 383 through 387' Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.824A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN C 409 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.914A pdb=" N ASP C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 443' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.842A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.596A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.819A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.924A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.632A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1032 removed outlier: 4.433A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.588A pdb=" N HIS D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.336A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 8.882A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.057A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.527A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.676A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.888A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.925A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 316 removed outlier: 7.057A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.523A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AB1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.649A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 573 through 575 removed outlier: 6.591A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AB6, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.387A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.912A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.912A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.430A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC2, first strand: chain 'A' and resid 1081 through 1082 Processing sheet with id=AC3, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.743A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.773A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 116 through 120 removed outlier: 4.003A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.995A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.637A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY B 431 " --> pdb=" O CYS B 379 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N CYS B 379 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 433 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE B 377 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA B 435 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 538 through 539 removed outlier: 5.748A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 656 removed outlier: 5.970A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.624A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 722 removed outlier: 6.650A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 725 through 728 removed outlier: 3.747A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.348A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.470A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA C 263 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 51 removed outlier: 6.479A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.941A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 318 removed outlier: 6.725A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 327 removed outlier: 3.607A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.653A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.532A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.592A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 719 Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 719 removed outlier: 6.021A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.990A pdb=" N TYR D 80 " --> pdb=" O SER D 71 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 11 through 12 removed outlier: 7.552A pdb=" N MET D 34 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N THR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AF7, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.657A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 81 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 58 through 60 removed outlier: 3.932A pdb=" N TYR E 59 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG E 38 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N THR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N MET E 34 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2490 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: 11.56 Time building geometry restraints manager: 10.60 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: 8733 1.34 - 1.47: 7281 1.47 - 1.60: 11731 1.60 - 1.73: 0 1.73 - 1.86: 160 Bond restraints: 27905 Sorted by residual: bond pdb=" C1 NAG B1203 " pdb=" O5 NAG B1203 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG B1204 " pdb=" O5 NAG B1204 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" C1 NAG C1204 " pdb=" O5 NAG C1204 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.47e+00 bond pdb=" CG LEU B 916 " pdb=" CD2 LEU B 916 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.41e+00 bond pdb=" C1 NAG B1209 " pdb=" O5 NAG B1209 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.07e+00 ... (remaining 27900 not shown) Histogram of bond angle deviations from ideal: 96.07 - 103.67: 349 103.67 - 111.26: 11236 111.26 - 118.86: 10876 118.86 - 126.46: 15155 126.46 - 134.06: 331 Bond angle restraints: 37947 Sorted by residual: angle pdb=" C GLU A 619 " pdb=" N VAL A 620 " pdb=" CA VAL A 620 " ideal model delta sigma weight residual 121.70 128.73 -7.03 1.80e+00 3.09e-01 1.53e+01 angle pdb=" C GLU B 619 " pdb=" N VAL B 620 " pdb=" CA VAL B 620 " ideal model delta sigma weight residual 121.70 128.38 -6.68 1.80e+00 3.09e-01 1.38e+01 angle pdb=" N ASP B 215 " pdb=" CA ASP B 215 " pdb=" C ASP B 215 " ideal model delta sigma weight residual 110.80 118.69 -7.89 2.13e+00 2.20e-01 1.37e+01 angle pdb=" C GLU C 619 " pdb=" N VAL C 620 " pdb=" CA VAL C 620 " ideal model delta sigma weight residual 121.70 128.26 -6.56 1.80e+00 3.09e-01 1.33e+01 angle pdb=" N ASN C 334 " pdb=" CA ASN C 334 " pdb=" C ASN C 334 " ideal model delta sigma weight residual 109.07 114.59 -5.52 1.61e+00 3.86e-01 1.18e+01 ... (remaining 37942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.94: 16673 20.94 - 41.87: 376 41.87 - 62.80: 66 62.80 - 83.74: 5 83.74 - 104.67: 8 Dihedral angle restraints: 17128 sinusoidal: 7182 harmonic: 9946 Sorted by residual: dihedral pdb=" CA ARG B 214 " pdb=" C ARG B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA PHE C 275 " pdb=" C PHE C 275 " pdb=" N LEU C 276 " pdb=" CA LEU C 276 " ideal model delta harmonic sigma weight residual 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA CYS C 525 " pdb=" C CYS C 525 " pdb=" N GLY C 526 " pdb=" CA GLY C 526 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 17125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 4360 0.163 - 0.326: 33 0.326 - 0.489: 5 0.489 - 0.652: 3 0.652 - 0.814: 1 Chirality restraints: 4402 Sorted by residual: chirality pdb=" C1 NAG C1202 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1202 " pdb=" O5 NAG C1202 " both_signs ideal model delta sigma weight residual False -2.40 -1.59 -0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C1 NAG A1212 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1212 " pdb=" O5 NAG A1212 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" C1 NAG C1208 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1208 " pdb=" O5 NAG C1208 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.48e+00 ... (remaining 4399 not shown) Planarity restraints: 4902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 801 " -0.091 2.00e-02 2.50e+03 9.33e-02 1.09e+02 pdb=" CG ASN C 801 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 801 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN C 801 " 0.152 2.00e-02 2.50e+03 pdb=" C1 NAG C1212 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1212 " 0.081 2.00e-02 2.50e+03 6.66e-02 5.54e+01 pdb=" C7 NAG C1212 " -0.022 2.00e-02 2.50e+03 pdb=" C8 NAG C1212 " 0.061 2.00e-02 2.50e+03 pdb=" N2 NAG C1212 " -0.105 2.00e-02 2.50e+03 pdb=" O7 NAG C1212 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 958 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C ALA A 958 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA A 958 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU A 959 " 0.017 2.00e-02 2.50e+03 ... (remaining 4899 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4080 2.76 - 3.30: 23940 3.30 - 3.83: 44108 3.83 - 4.37: 50218 4.37 - 4.90: 88591 Nonbonded interactions: 210937 Sorted by model distance: nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.227 2.440 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.279 2.440 nonbonded pdb=" OG1 THR C 393 " pdb=" O GLU C 516 " model vdw 2.289 2.440 nonbonded pdb=" OG1 THR B 393 " pdb=" O GLU B 516 " model vdw 2.300 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.302 2.440 ... (remaining 210932 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' and (resid 14 through 1145 or resid 1201 through 1213)) } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.490 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 69.670 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 0.102 27905 Z= 0.486 Angle : 0.865 11.404 37947 Z= 0.462 Chirality : 0.061 0.814 4402 Planarity : 0.006 0.067 4862 Dihedral : 9.934 104.675 10611 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.07 % Allowed : 1.28 % Favored : 98.66 % 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: -3.83 (0.12), residues: 3382 helix: -1.90 (0.16), residues: 620 sheet: -2.36 (0.18), residues: 684 loop : -2.95 (0.11), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 64 HIS 0.009 0.002 HIS C1064 PHE 0.047 0.004 PHE A 906 TYR 0.042 0.003 TYR B 204 ARG 0.012 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 528 time to evaluate : 2.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.7086 (Cg_endo) cc_final: 0.6687 (Cg_exo) REVERT: A 153 MET cc_start: 0.4109 (ptp) cc_final: 0.3547 (tpt) REVERT: A 238 PHE cc_start: 0.7346 (p90) cc_final: 0.6953 (p90) REVERT: A 409 GLN cc_start: 0.8267 (mt0) cc_final: 0.8061 (mt0) REVERT: A 503 VAL cc_start: 0.8336 (m) cc_final: 0.8088 (t) REVERT: A 734 THR cc_start: 0.8617 (m) cc_final: 0.8299 (p) REVERT: B 177 MET cc_start: -0.0442 (tpp) cc_final: -0.0977 (mtt) REVERT: B 453 TYR cc_start: 0.4873 (p90) cc_final: 0.4197 (p90) REVERT: B 547 THR cc_start: 0.7946 (m) cc_final: 0.7372 (p) REVERT: B 574 ASP cc_start: 0.6844 (t70) cc_final: 0.6587 (t0) REVERT: B 1138 TYR cc_start: 0.6986 (t80) cc_final: 0.6634 (t80) REVERT: C 133 PHE cc_start: 0.7038 (m-10) cc_final: 0.6630 (m-10) REVERT: C 269 TYR cc_start: 0.6932 (m-10) cc_final: 0.6658 (m-10) REVERT: C 340 GLU cc_start: 0.6355 (mt-10) cc_final: 0.6101 (mp0) REVERT: C 614 ASP cc_start: 0.6362 (t70) cc_final: 0.6072 (t0) REVERT: C 809 PRO cc_start: 0.6620 (Cg_endo) cc_final: 0.6246 (Cg_exo) REVERT: C 859 THR cc_start: 0.8827 (m) cc_final: 0.8513 (p) REVERT: D 4 LEU cc_start: 0.7182 (mt) cc_final: 0.6567 (mt) REVERT: D 18 LEU cc_start: 0.6265 (mt) cc_final: 0.5870 (tp) REVERT: D 20 LEU cc_start: 0.7446 (mt) cc_final: 0.7222 (mp) REVERT: D 38 ARG cc_start: 0.7634 (ptt180) cc_final: 0.7342 (ptt90) REVERT: D 39 GLN cc_start: 0.7383 (tt0) cc_final: 0.6831 (tm-30) REVERT: D 73 ASP cc_start: 0.6916 (t0) cc_final: 0.6422 (t0) REVERT: D 99 ASP cc_start: 0.7690 (t0) cc_final: 0.7482 (t0) REVERT: D 116 GLN cc_start: 0.7763 (tp40) cc_final: 0.7205 (tp40) outliers start: 2 outliers final: 0 residues processed: 530 average time/residue: 0.4431 time to fit residues: 356.7037 Evaluate side-chains 253 residues out of total 2977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 4.9990 chunk 259 optimal weight: 40.0000 chunk 143 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 268 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 310 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 448 ASN A 450 ASN A 474 GLN A 501 ASN A 613 GLN A 658 ASN A 965 GLN A1005 GLN A1101 HIS A1119 ASN B 66 HIS B 234 ASN B 354 ASN B 450 ASN B 613 GLN B 655 HIS B 751 ASN B 965 GLN B1048 HIS C 81 ASN C 207 HIS C 239 GLN C 450 ASN C 501 ASN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 655 HIS C 804 GLN C 949 GLN C1010 GLN C1101 HIS D 32 HIS E 3 GLN E 32 HIS E 116 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 27905 Z= 0.262 Angle : 0.616 10.894 37947 Z= 0.316 Chirality : 0.047 0.443 4402 Planarity : 0.004 0.041 4862 Dihedral : 8.832 121.651 4510 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.81 % Allowed : 6.65 % Favored : 91.54 % 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: -2.76 (0.13), residues: 3382 helix: 0.09 (0.20), residues: 618 sheet: -1.86 (0.18), residues: 681 loop : -2.56 (0.11), residues: 2083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 109 HIS 0.008 0.001 HIS C 207 PHE 0.018 0.002 PHE C 135 TYR 0.023 0.002 TYR A 904 ARG 0.006 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 274 time to evaluate : 2.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.4304 (ptp) cc_final: 0.3684 (tpt) REVERT: A 238 PHE cc_start: 0.7130 (p90) cc_final: 0.6738 (p90) REVERT: A 378 LYS cc_start: 0.8471 (tptt) cc_final: 0.8185 (tppt) REVERT: A 406 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7598 (mt-10) REVERT: A 493 GLN cc_start: 0.7626 (tt0) cc_final: 0.7220 (tt0) REVERT: A 734 THR cc_start: 0.8700 (m) cc_final: 0.8378 (p) REVERT: B 177 MET cc_start: -0.0628 (tpp) cc_final: -0.1068 (mtt) REVERT: B 200 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.6035 (t80) REVERT: B 226 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7611 (tt) REVERT: B 355 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7887 (mmm160) REVERT: B 453 TYR cc_start: 0.4941 (p90) cc_final: 0.4458 (p90) REVERT: B 547 THR cc_start: 0.7906 (m) cc_final: 0.7394 (p) REVERT: B 660 TYR cc_start: 0.8590 (m-80) cc_final: 0.8252 (m-10) REVERT: B 1138 TYR cc_start: 0.6957 (t80) cc_final: 0.6689 (t80) REVERT: C 133 PHE cc_start: 0.7006 (m-10) cc_final: 0.6653 (m-10) REVERT: C 269 TYR cc_start: 0.7050 (m-10) cc_final: 0.6650 (m-10) REVERT: C 340 GLU cc_start: 0.6412 (mt-10) cc_final: 0.6198 (mp0) REVERT: C 436 TRP cc_start: 0.1803 (p90) cc_final: 0.1587 (p90) REVERT: C 614 ASP cc_start: 0.6528 (t70) cc_final: 0.6191 (t0) REVERT: C 809 PRO cc_start: 0.6620 (Cg_endo) cc_final: 0.6295 (Cg_exo) REVERT: C 859 THR cc_start: 0.8781 (m) cc_final: 0.8560 (p) REVERT: C 934 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8483 (tp) REVERT: C 988 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: D 4 LEU cc_start: 0.6886 (mt) cc_final: 0.6677 (mt) REVERT: D 36 TRP cc_start: 0.6299 (m100) cc_final: 0.5904 (m100) REVERT: D 58 THR cc_start: 0.7979 (t) cc_final: 0.7381 (t) REVERT: D 73 ASP cc_start: 0.7099 (t0) cc_final: 0.6839 (t0) REVERT: D 93 MET cc_start: 0.6772 (tpt) cc_final: 0.5372 (tmm) REVERT: D 95 TYR cc_start: 0.7555 (m-80) cc_final: 0.6969 (m-10) REVERT: D 104 ASP cc_start: 0.6737 (t0) cc_final: 0.6369 (t0) outliers start: 54 outliers final: 26 residues processed: 312 average time/residue: 0.3719 time to fit residues: 190.1412 Evaluate side-chains 236 residues out of total 2977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 258 optimal weight: 30.0000 chunk 211 optimal weight: 0.3980 chunk 85 optimal weight: 6.9990 chunk 311 optimal weight: 1.9990 chunk 336 optimal weight: 0.2980 chunk 277 optimal weight: 0.9990 chunk 308 optimal weight: 0.4980 chunk 106 optimal weight: 40.0000 chunk 249 optimal weight: 20.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN A 450 ASN A 580 GLN B 245 HIS C 207 HIS ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 935 GLN ** D 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 27905 Z= 0.151 Angle : 0.535 8.673 37947 Z= 0.273 Chirality : 0.045 0.415 4402 Planarity : 0.004 0.053 4862 Dihedral : 7.652 116.229 4510 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.51 % Allowed : 8.13 % Favored : 90.36 % 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: -2.19 (0.13), residues: 3382 helix: 1.00 (0.21), residues: 630 sheet: -1.53 (0.19), residues: 683 loop : -2.35 (0.12), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 109 HIS 0.007 0.001 HIS C 207 PHE 0.027 0.001 PHE C 135 TYR 0.022 0.001 TYR D 60 ARG 0.005 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6764 Ramachandran restraints generated. 3382 Oldfield, 0 Emsley, 3382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 244 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.6218 (OUTLIER) cc_final: 0.5684 (t0) REVERT: A 153 MET cc_start: 0.4246 (ptp) cc_final: 0.3605 (tpt) REVERT: A 177 MET cc_start: 0.1223 (tpp) cc_final: -0.1971 (pmm) REVERT: A 238 PHE cc_start: 0.7232 (p90) cc_final: 0.6813 (p90) REVERT: A 378 LYS cc_start: 0.8424 (tptt) cc_final: 0.8153 (tppt) REVERT: A 734 THR cc_start: 0.8689 (m) cc_final: 0.8421 (p) REVERT: A 983 ARG cc_start: 0.6993 (mtm180) cc_final: 0.6700 (mtm-85) REVERT: B 157 PHE cc_start: 0.6266 (m-80) cc_final: 0.5950 (m-80) REVERT: B 177 MET cc_start: -0.0619 (tpp) cc_final: -0.1077 (mtt) REVERT: B 200 TYR cc_start: 0.6336 (OUTLIER) cc_final: 0.6018 (t80) REVERT: B 226 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7559 (tt) REVERT: B 453 TYR cc_start: 0.4868 (p90) cc_final: 0.4434 (p90) REVERT: B 547 THR cc_start: 0.7723 (m) cc_final: 0.7292 (p) REVERT: B 904 TYR cc_start: 0.6984 (m-10) cc_final: 0.6381 (m-10) REVERT: B 981 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8607 (mm) REVERT: B 1138 TYR cc_start: 0.6982 (t80) cc_final: 0.6691 (t80) REVERT: C 102 ARG cc_start: 0.6052 (mmm-85) cc_final: 0.5783 (mmp80) REVERT: C 133 PHE cc_start: 0.6955 (m-10) cc_final: 0.6674 (m-10) REVERT: C 269 TYR cc_start: 0.6995 (m-10) cc_final: 0.6698 (m-10) REVERT: C 340 GLU cc_start: 0.6598 (mt-10) cc_final: 0.6312 (mp0) REVERT: C 614 ASP cc_start: 0.6396 (t70) cc_final: 0.6068 (t0) REVERT: C 809 PRO cc_start: 0.6576 (Cg_endo) cc_final: 0.6253 (Cg_exo) REVERT: D 4 LEU cc_start: 0.6653 (mt) cc_final: 0.6337 (mt) REVERT: D 36 TRP cc_start: 0.6070 (m100) cc_final: 0.5645 (m100) REVERT: D 39 GLN cc_start: 0.7563 (mp10) cc_final: 0.6546 (pm20) REVERT: D 73 ASP cc_start: 0.7233 (t0) cc_final: 0.6999 (t0) REVERT: D 93 MET cc_start: 0.6201 (tpt) cc_final: 0.5880 (tpt) REVERT: D 104 ASP cc_start: 0.7004 (t0) cc_final: 0.6439 (t0) outliers start: 45 outliers final: 21 residues processed: 282 average time/residue: 0.3797 time to fit residues: 177.1736 Evaluate side-chains 231 residues out of total 2977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 206 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain E residue 64 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.2161 > 50: distance: 94 - 175: 23.397 distance: 101 - 105: 27.229 distance: 105 - 106: 27.928 distance: 106 - 107: 26.370 distance: 107 - 108: 41.775 distance: 107 - 109: 27.774 distance: 109 - 110: 37.916 distance: 110 - 111: 48.366 distance: 110 - 113: 22.070 distance: 111 - 112: 30.247 distance: 111 - 118: 9.873 distance: 113 - 114: 25.929 distance: 114 - 115: 18.766 distance: 115 - 116: 18.084 distance: 115 - 117: 22.675 distance: 118 - 119: 37.586 distance: 119 - 120: 18.396 distance: 119 - 122: 33.949 distance: 120 - 121: 22.820 distance: 120 - 124: 25.939 distance: 122 - 123: 41.248 distance: 124 - 125: 17.877 distance: 125 - 126: 22.184 distance: 125 - 128: 7.726 distance: 126 - 127: 32.197 distance: 126 - 133: 15.540 distance: 128 - 129: 5.633 distance: 129 - 130: 5.209 distance: 130 - 131: 4.447 distance: 133 - 134: 33.547 distance: 134 - 135: 42.114 distance: 134 - 137: 31.878 distance: 135 - 136: 42.551 distance: 135 - 144: 40.627 distance: 137 - 138: 42.640 distance: 138 - 139: 18.075 distance: 139 - 140: 7.358 distance: 144 - 145: 27.045 distance: 145 - 146: 39.885 distance: 145 - 148: 44.033 distance: 146 - 147: 41.003 distance: 146 - 151: 22.220 distance: 148 - 149: 39.820 distance: 148 - 150: 24.506 distance: 151 - 152: 23.529 distance: 152 - 153: 20.848 distance: 152 - 155: 38.795 distance: 153 - 154: 52.366 distance: 153 - 159: 39.294 distance: 155 - 156: 30.366 distance: 156 - 157: 22.062 distance: 156 - 158: 16.902 distance: 159 - 160: 23.425 distance: 160 - 161: 34.275 distance: 160 - 163: 24.532 distance: 161 - 162: 38.839 distance: 161 - 170: 44.570 distance: 163 - 164: 19.566 distance: 164 - 165: 7.665 distance: 164 - 166: 10.250 distance: 165 - 167: 15.066 distance: 166 - 168: 17.186 distance: 167 - 169: 9.009 distance: 168 - 169: 6.894 distance: 170 - 171: 17.574 distance: 171 - 172: 43.393 distance: 171 - 174: 41.772 distance: 172 - 173: 41.990 distance: 172 - 176: 29.767 distance: 174 - 175: 29.981 distance: 176 - 177: 13.248 distance: 177 - 178: 43.938 distance: 178 - 179: 39.575 distance: 178 - 180: 35.577