Starting phenix.real_space_refine on Fri Aug 9 10:51:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy3_33509/08_2024/7xy3_33509.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy3_33509/08_2024/7xy3_33509.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy3_33509/08_2024/7xy3_33509.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy3_33509/08_2024/7xy3_33509.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy3_33509/08_2024/7xy3_33509.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xy3_33509/08_2024/7xy3_33509.cif" } resolution = 4.6 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= 0.003 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 120 5.16 5 C 16773 2.51 5 N 4355 2.21 5 O 5115 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "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 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 26363 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8266 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 7 Chain: "B" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8297 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 52, 'TRANS': 1007} Chain breaks: 5 Chain: "C" Number of atoms: 8268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1056, 8268 Classifications: {'peptide': 1056} Link IDs: {'PTRANS': 51, 'TRANS': 1004} Chain breaks: 6 Chain: "D" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "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: 14.67, per 1000 atoms: 0.56 Number of scatterers: 26363 At special positions: 0 Unit cell: (156, 157.04, 195.52, 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 120 16.00 O 5115 8.00 N 4355 7.00 C 16773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.04 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=2.03 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=2.03 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 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=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 99 " 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 616 " " NAG A1205 " - " ASN A 657 " " NAG A1206 " - " ASN A 709 " " NAG A1207 " - " ASN A1074 " " NAG A1208 " - " ASN A 717 " " NAG A1209 " - " ASN A 801 " " NAG A1210 " - " ASN A1098 " " NAG A1211 " - " 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 331 " " 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: 10.28 Conformation dependent library (CDL) restraints added in 4.8 seconds 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6174 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 51 sheets defined 21.1% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.75 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.529A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 408' Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 756 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 886 through 891 removed outlier: 3.600A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.580A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.561A 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 965 removed outlier: 3.865A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN A 954 " --> pdb=" O ASP A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 removed outlier: 3.989A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 3.708A pdb=" N LEU A1145 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.905A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 442 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 747 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.866A 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 removed outlier: 3.514A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 891 removed outlier: 4.154A pdb=" N PHE B 888 " --> pdb=" O GLY B 885 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.676A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.519A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.734A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.237A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.757A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 4.250A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.635A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 417 through 422' Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.597A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) 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 783 removed outlier: 3.674A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.962A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 4.001A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.798A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.639A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1032 Processing helix chain 'C' and resid 1141 through 1145 removed outlier: 3.919A pdb=" N LEU C1145 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 removed outlier: 4.256A pdb=" N GLY D 116 " --> pdb=" O ARG D 113 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR D 117 " --> pdb=" O SER D 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 113 through 117' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.731A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.863A 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 55 removed outlier: 7.076A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.748A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.779A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 95 through 96 removed outlier: 4.233A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 143 through 144 removed outlier: 3.588A pdb=" N TYR A 144 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 317 removed outlier: 7.077A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.524A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 327 removed outlier: 6.524A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.003A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB4, first strand: chain 'A' and resid 573 through 575 removed outlier: 5.739A 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 removed outlier: 5.661A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 3.557A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 4.008A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 4.008A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.913A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.258A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.588A 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 118 through 121 removed outlier: 3.636A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.663A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.581A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.687A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL B 433 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N PHE B 377 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 435 " --> pdb=" O SER B 375 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 584 through 586 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.892A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 703 removed outlier: 5.988A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 719 removed outlier: 3.646A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 722 through 728 removed outlier: 4.390A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.209A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.687A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU C 226 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 6.554A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.740A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.892A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 143 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 313 through 319 removed outlier: 5.803A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.710A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA C 435 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 538 through 542 removed outlier: 3.676A pdb=" N ASP C 586 " --> pdb=" O THR C 553 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.335A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER C 673 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 719 removed outlier: 3.641A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 722 through 728 removed outlier: 4.019A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.576A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) 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 2 through 7 removed outlier: 3.625A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.655A pdb=" N VAL D 52 " --> pdb=" O TRP D 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP D 40 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA D 54 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N MET D 38 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY D 39 " --> pdb=" O ALA D 100 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR D 119 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 61 through 63 removed outlier: 3.655A pdb=" N VAL D 52 " --> pdb=" O TRP D 40 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N TRP D 40 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA D 54 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N MET D 38 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY D 39 " --> pdb=" O ALA D 100 " (cutoff:3.500A) 866 hydrogen bonds defined for protein. 2379 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: 11.16 Time building geometry restraints manager: 11.36 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: 8428 1.34 - 1.47: 6788 1.47 - 1.59: 11587 1.59 - 1.72: 0 1.72 - 1.84: 154 Bond restraints: 26957 Sorted by residual: bond pdb=" C1 NAG A1202 " pdb=" O5 NAG A1202 " ideal model delta sigma weight residual 1.406 1.480 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C1 NAG C1211 " pdb=" O5 NAG C1211 " ideal model delta sigma weight residual 1.406 1.465 -0.059 2.00e-02 2.50e+03 8.83e+00 bond pdb=" C1 NAG C1210 " pdb=" O5 NAG C1210 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.92e+00 bond pdb=" C1 NAG B1209 " pdb=" O5 NAG B1209 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.81e+00 bond pdb=" C1 NAG C1201 " pdb=" O5 NAG C1201 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.73e+00 ... (remaining 26952 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.30: 532 105.30 - 112.50: 13832 112.50 - 119.69: 8522 119.69 - 126.89: 13508 126.89 - 134.08: 269 Bond angle restraints: 36663 Sorted by residual: angle pdb=" N TYR D 32 " pdb=" CA TYR D 32 " pdb=" C TYR D 32 " ideal model delta sigma weight residual 113.02 103.80 9.22 1.20e+00 6.94e-01 5.90e+01 angle pdb=" N TYR D 29 " pdb=" CA TYR D 29 " pdb=" C TYR D 29 " ideal model delta sigma weight residual 108.49 98.11 10.38 1.65e+00 3.67e-01 3.96e+01 angle pdb=" N VAL C 382 " pdb=" CA VAL C 382 " pdb=" C VAL C 382 " ideal model delta sigma weight residual 108.81 116.99 -8.18 1.62e+00 3.81e-01 2.55e+01 angle pdb=" N GLY B 757 " pdb=" CA GLY B 757 " pdb=" C GLY B 757 " ideal model delta sigma weight residual 111.21 116.25 -5.04 1.04e+00 9.25e-01 2.35e+01 angle pdb=" C GLU C 619 " pdb=" N VAL C 620 " pdb=" CA VAL C 620 " ideal model delta sigma weight residual 121.70 128.64 -6.94 1.80e+00 3.09e-01 1.48e+01 ... (remaining 36658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.67: 16168 20.67 - 41.34: 291 41.34 - 62.02: 68 62.02 - 82.69: 5 82.69 - 103.36: 8 Dihedral angle restraints: 16540 sinusoidal: 6937 harmonic: 9603 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual 93.00 146.34 -53.34 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 141.02 -48.02 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA VAL A 951 " pdb=" C VAL A 951 " pdb=" N VAL A 952 " pdb=" CA VAL A 952 " ideal model delta harmonic sigma weight residual 180.00 -152.78 -27.22 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 16537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 4230 0.183 - 0.366: 6 0.366 - 0.549: 5 0.549 - 0.732: 1 0.732 - 0.915: 1 Chirality restraints: 4243 Sorted by residual: chirality pdb=" C1 NAG C1204 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1204 " pdb=" O5 NAG C1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.48 -0.92 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" C1 NAG C1212 " pdb=" ND2 ASN C 801 " pdb=" C2 NAG C1212 " pdb=" O5 NAG C1212 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 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 -1.86 -0.54 2.00e-01 2.50e+01 7.20e+00 ... (remaining 4240 not shown) Planarity restraints: 4742 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.020 2.00e-02 2.50e+03 1.28e-01 2.04e+02 pdb=" CG ASN C 331 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.117 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.212 2.00e-02 2.50e+03 pdb=" C1 NAG C1204 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1204 " 0.127 2.00e-02 2.50e+03 1.05e-01 1.37e+02 pdb=" C7 NAG C1204 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG C1204 " 0.095 2.00e-02 2.50e+03 pdb=" N2 NAG C1204 " -0.167 2.00e-02 2.50e+03 pdb=" O7 NAG C1204 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1212 " -0.106 2.00e-02 2.50e+03 8.70e-02 9.46e+01 pdb=" C7 NAG C1212 " 0.029 2.00e-02 2.50e+03 pdb=" C8 NAG C1212 " -0.080 2.00e-02 2.50e+03 pdb=" N2 NAG C1212 " 0.138 2.00e-02 2.50e+03 pdb=" O7 NAG C1212 " 0.018 2.00e-02 2.50e+03 ... (remaining 4739 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1954 2.74 - 3.28: 24971 3.28 - 3.82: 43735 3.82 - 4.36: 49701 4.36 - 4.90: 84689 Nonbonded interactions: 205050 Sorted by model distance: nonbonded pdb=" OE1 GLN C 804 " pdb=" CG2 ILE C 931 " model vdw 2.198 3.460 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.250 3.040 nonbonded pdb=" OG1 THR B 33 " pdb=" O GLY B 219 " model vdw 2.258 3.040 nonbonded pdb=" O TYR B 396 " pdb=" OG SER B 514 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.271 3.040 ... (remaining 205045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 525 or resid 530 through 1145 or resid 1201 thr \ ough 1211)) selection = (chain 'B' and (resid 14 through 331 or resid 334 through 525 or resid 530 throu \ gh 1145 or resid 1201 through 1211)) selection = (chain 'C' and (resid 14 through 331 or resid 334 through 1145 or resid 1201 thr \ ough 1211)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 72.490 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.120 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 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 : 0.005 0.074 26957 Z= 0.306 Angle : 0.753 12.233 36663 Z= 0.412 Chirality : 0.056 0.915 4243 Planarity : 0.006 0.105 4704 Dihedral : 9.584 103.361 10246 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.07 % Allowed : 0.69 % Favored : 99.24 % 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: -3.84 (0.12), residues: 3258 helix: -1.23 (0.17), residues: 633 sheet: -2.34 (0.20), residues: 517 loop : -3.24 (0.11), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 886 HIS 0.008 0.002 HIS C 49 PHE 0.028 0.003 PHE B 823 TYR 0.022 0.002 TYR B 204 ARG 0.011 0.001 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 381 time to evaluate : 2.834 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9456 (ttp) cc_final: 0.9199 (ttm) REVERT: A 772 VAL cc_start: 0.9607 (t) cc_final: 0.9388 (p) REVERT: A 774 GLN cc_start: 0.9461 (mm-40) cc_final: 0.9248 (mm-40) REVERT: A 777 ASN cc_start: 0.9228 (m-40) cc_final: 0.8979 (m110) REVERT: A 781 VAL cc_start: 0.9641 (t) cc_final: 0.9078 (m) REVERT: A 802 PHE cc_start: 0.8697 (m-10) cc_final: 0.8441 (m-10) REVERT: A 953 ASN cc_start: 0.8362 (m-40) cc_final: 0.7970 (m110) REVERT: A 1029 MET cc_start: 0.8800 (mtt) cc_final: 0.8561 (tpp) REVERT: A 1065 VAL cc_start: 0.9397 (t) cc_final: 0.8920 (t) REVERT: B 92 PHE cc_start: 0.9276 (t80) cc_final: 0.9065 (t80) REVERT: B 177 MET cc_start: 0.0220 (tpp) cc_final: -0.0152 (ttp) REVERT: B 192 PHE cc_start: 0.8985 (m-10) cc_final: 0.8680 (m-10) REVERT: B 389 ASP cc_start: 0.8463 (m-30) cc_final: 0.8254 (t0) REVERT: B 424 LYS cc_start: 0.8050 (tttt) cc_final: 0.7669 (tptp) REVERT: B 471 GLU cc_start: 0.9089 (tt0) cc_final: 0.8868 (mm-30) REVERT: B 731 MET cc_start: 0.9251 (ttp) cc_final: 0.9002 (ttm) REVERT: B 740 MET cc_start: 0.7691 (ttt) cc_final: 0.7113 (ttt) REVERT: B 774 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8696 (mm110) REVERT: B 1006 THR cc_start: 0.9206 (m) cc_final: 0.8898 (p) REVERT: B 1033 VAL cc_start: 0.9334 (t) cc_final: 0.9113 (t) REVERT: B 1062 PHE cc_start: 0.8921 (m-80) cc_final: 0.8245 (m-10) REVERT: C 153 MET cc_start: 0.4711 (ptp) cc_final: 0.4147 (ppp) REVERT: C 353 TRP cc_start: 0.2348 (p90) cc_final: 0.1766 (p90) REVERT: C 763 LEU cc_start: 0.9138 (mt) cc_final: 0.8816 (mt) REVERT: C 765 ARG cc_start: 0.8528 (ttp-170) cc_final: 0.8201 (ptm-80) REVERT: C 966 LEU cc_start: 0.9565 (mt) cc_final: 0.9102 (mp) REVERT: C 1050 MET cc_start: 0.9024 (ptp) cc_final: 0.8743 (ptp) REVERT: D 94 MET cc_start: 0.7521 (ttm) cc_final: 0.7217 (ptt) outliers start: 2 outliers final: 0 residues processed: 383 average time/residue: 0.4179 time to fit residues: 241.8446 Evaluate side-chains 172 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 9.9990 chunk 249 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 133 optimal weight: 0.0270 chunk 257 optimal weight: 40.0000 chunk 99 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 762 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 953 ASN ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS B 14 GLN B 99 ASN B 115 GLN B 474 GLN B 655 HIS B 658 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 901 GLN B 965 GLN B1023 ASN B1083 HIS C 49 HIS C 487 ASN C 501 ASN C 710 ASN C 777 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 907 ASN C 919 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26957 Z= 0.202 Angle : 0.609 11.100 36663 Z= 0.319 Chirality : 0.047 0.557 4243 Planarity : 0.005 0.104 4704 Dihedral : 8.155 79.800 4340 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.07 % Allowed : 1.53 % Favored : 98.40 % 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: -3.01 (0.13), residues: 3258 helix: 0.41 (0.20), residues: 637 sheet: -2.11 (0.20), residues: 571 loop : -2.95 (0.12), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.012 0.001 HIS B 655 PHE 0.028 0.001 PHE B 464 TYR 0.013 0.001 TYR D 63 ARG 0.007 0.001 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 231 time to evaluate : 2.880 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8273 (ttt) cc_final: 0.7970 (ttm) REVERT: A 777 ASN cc_start: 0.9324 (m-40) cc_final: 0.9060 (m110) REVERT: A 1050 MET cc_start: 0.8761 (pmm) cc_final: 0.8259 (pmm) REVERT: B 92 PHE cc_start: 0.9230 (t80) cc_final: 0.8969 (t80) REVERT: B 104 TRP cc_start: 0.7542 (m-90) cc_final: 0.7314 (m-90) REVERT: B 192 PHE cc_start: 0.8895 (m-10) cc_final: 0.8646 (m-10) REVERT: B 387 LEU cc_start: 0.8794 (mt) cc_final: 0.8436 (mt) REVERT: B 389 ASP cc_start: 0.8414 (m-30) cc_final: 0.8125 (t0) REVERT: B 424 LYS cc_start: 0.7962 (tttt) cc_final: 0.7749 (tptp) REVERT: B 471 GLU cc_start: 0.9079 (tt0) cc_final: 0.8863 (mm-30) REVERT: B 731 MET cc_start: 0.8999 (ttp) cc_final: 0.8637 (ttm) REVERT: B 774 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8534 (mm-40) REVERT: B 1002 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8294 (tm-30) REVERT: C 153 MET cc_start: 0.4584 (ptp) cc_final: 0.4089 (ppp) REVERT: C 583 GLU cc_start: 0.8443 (pt0) cc_final: 0.7894 (mp0) REVERT: C 869 MET cc_start: 0.9388 (mtm) cc_final: 0.8892 (mtp) REVERT: C 966 LEU cc_start: 0.9518 (mt) cc_final: 0.9124 (mp) REVERT: C 1050 MET cc_start: 0.8850 (ptp) cc_final: 0.8211 (ptp) REVERT: D 12 VAL cc_start: 0.4977 (m) cc_final: 0.4523 (m) REVERT: D 96 MET cc_start: 0.6125 (ttt) cc_final: 0.5592 (tpt) outliers start: 2 outliers final: 0 residues processed: 233 average time/residue: 0.3739 time to fit residues: 139.2873 Evaluate side-chains 132 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 299 optimal weight: 3.9990 chunk 323 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 chunk 296 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 613 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B1071 GLN C 354 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 919 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 26957 Z= 0.185 Angle : 0.559 9.867 36663 Z= 0.291 Chirality : 0.046 0.478 4243 Planarity : 0.004 0.058 4704 Dihedral : 6.858 56.287 4340 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.07 % Allowed : 1.74 % Favored : 98.19 % 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: -2.63 (0.14), residues: 3258 helix: 0.74 (0.20), residues: 652 sheet: -1.97 (0.20), residues: 557 loop : -2.69 (0.12), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 886 HIS 0.006 0.001 HIS C1048 PHE 0.028 0.001 PHE C 823 TYR 0.024 0.001 TYR A 756 ARG 0.006 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 205 time to evaluate : 2.964 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8586 (mp) cc_final: 0.8280 (tp) REVERT: A 275 PHE cc_start: 0.8816 (m-10) cc_final: 0.8266 (m-10) REVERT: A 1050 MET cc_start: 0.9127 (pmm) cc_final: 0.8324 (pmm) REVERT: B 177 MET cc_start: 0.0041 (mmt) cc_final: -0.0173 (mtt) REVERT: B 387 LEU cc_start: 0.8756 (mt) cc_final: 0.8390 (mt) REVERT: B 424 LYS cc_start: 0.7985 (tttt) cc_final: 0.7758 (tptp) REVERT: B 774 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8761 (mm110) REVERT: B 1002 GLN cc_start: 0.8956 (tm-30) cc_final: 0.8285 (tm-30) REVERT: C 153 MET cc_start: 0.4756 (ptp) cc_final: 0.4214 (ppp) REVERT: C 869 MET cc_start: 0.9124 (mtm) cc_final: 0.8887 (mtp) REVERT: C 898 PHE cc_start: 0.8728 (t80) cc_final: 0.8523 (t80) REVERT: C 902 MET cc_start: 0.9220 (mmp) cc_final: 0.8689 (mmp) REVERT: D 96 MET cc_start: 0.6255 (ttt) cc_final: 0.5659 (tpt) outliers start: 2 outliers final: 0 residues processed: 207 average time/residue: 0.3835 time to fit residues: 130.0355 Evaluate side-chains 127 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 295 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 chunk 300 optimal weight: 0.7980 chunk 318 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 354 ASN A 613 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B 895 GLN B 913 GLN C 777 ASN C 784 GLN C 919 ASN ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26957 Z= 0.237 Angle : 0.584 10.681 36663 Z= 0.303 Chirality : 0.046 0.466 4243 Planarity : 0.004 0.053 4704 Dihedral : 6.539 56.103 4340 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.03 % Allowed : 1.70 % Favored : 98.26 % 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: -2.48 (0.14), residues: 3258 helix: 0.85 (0.20), residues: 648 sheet: -1.89 (0.21), residues: 553 loop : -2.57 (0.12), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 886 HIS 0.005 0.001 HIS B 66 PHE 0.026 0.001 PHE C 823 TYR 0.012 0.001 TYR A 756 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 186 time to evaluate : 3.107 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.8563 (mp) cc_final: 0.8325 (tp) REVERT: A 275 PHE cc_start: 0.8925 (m-10) cc_final: 0.8278 (m-10) REVERT: A 1050 MET cc_start: 0.9194 (pmm) cc_final: 0.8385 (pmm) REVERT: B 92 PHE cc_start: 0.9190 (t80) cc_final: 0.8831 (t80) REVERT: B 192 PHE cc_start: 0.8792 (m-80) cc_final: 0.8404 (m-10) REVERT: B 387 LEU cc_start: 0.8665 (mt) cc_final: 0.8392 (mt) REVERT: B 424 LYS cc_start: 0.8007 (tttt) cc_final: 0.7796 (tptp) REVERT: B 774 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8786 (mm110) REVERT: B 867 ASP cc_start: 0.8789 (m-30) cc_final: 0.8549 (p0) REVERT: B 1002 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8280 (tm-30) REVERT: C 153 MET cc_start: 0.4841 (ptp) cc_final: 0.4368 (ppp) REVERT: C 731 MET cc_start: 0.8775 (ttp) cc_final: 0.8421 (ttp) REVERT: C 763 LEU cc_start: 0.9203 (mt) cc_final: 0.8918 (mt) REVERT: C 869 MET cc_start: 0.9255 (mtm) cc_final: 0.8913 (mtp) REVERT: C 886 TRP cc_start: 0.7967 (p90) cc_final: 0.7674 (p90) REVERT: C 933 LYS cc_start: 0.9549 (mttt) cc_final: 0.9280 (mptt) REVERT: C 1050 MET cc_start: 0.9327 (pmm) cc_final: 0.7559 (pmm) REVERT: D 96 MET cc_start: 0.6266 (ttt) cc_final: 0.5391 (tpp) outliers start: 1 outliers final: 0 residues processed: 187 average time/residue: 0.3795 time to fit residues: 114.0484 Evaluate side-chains 123 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 264 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 236 optimal weight: 0.0030 chunk 131 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 chunk 219 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 162 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 895 GLN B 913 GLN C 777 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C 957 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26957 Z= 0.224 Angle : 0.574 9.924 36663 Z= 0.299 Chirality : 0.046 0.460 4243 Planarity : 0.004 0.046 4704 Dihedral : 6.392 55.977 4340 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: -2.34 (0.14), residues: 3258 helix: 0.97 (0.20), residues: 646 sheet: -1.83 (0.20), residues: 570 loop : -2.46 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 886 HIS 0.006 0.001 HIS C1048 PHE 0.029 0.001 PHE C 823 TYR 0.011 0.001 TYR C 380 ARG 0.012 0.001 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.937 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 765 ARG cc_start: 0.8704 (tpt90) cc_final: 0.8470 (mmm160) REVERT: A 1050 MET cc_start: 0.9228 (pmm) cc_final: 0.8395 (pmm) REVERT: B 192 PHE cc_start: 0.8863 (m-80) cc_final: 0.8567 (m-10) REVERT: B 387 LEU cc_start: 0.8668 (mt) cc_final: 0.8400 (mt) REVERT: B 424 LYS cc_start: 0.8125 (tttt) cc_final: 0.7899 (tptp) REVERT: B 774 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8784 (mm110) REVERT: B 867 ASP cc_start: 0.8795 (m-30) cc_final: 0.8562 (p0) REVERT: B 1002 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8309 (tm-30) REVERT: C 153 MET cc_start: 0.4800 (ptp) cc_final: 0.4351 (ppp) REVERT: C 731 MET cc_start: 0.8975 (ttp) cc_final: 0.8592 (ttp) REVERT: C 763 LEU cc_start: 0.9216 (mt) cc_final: 0.8900 (mt) REVERT: C 869 MET cc_start: 0.9198 (mtm) cc_final: 0.8911 (mtp) REVERT: C 886 TRP cc_start: 0.8082 (p90) cc_final: 0.7802 (p90) REVERT: C 933 LYS cc_start: 0.9561 (mttt) cc_final: 0.9298 (mptt) REVERT: C 966 LEU cc_start: 0.9521 (mt) cc_final: 0.9172 (mp) REVERT: C 1050 MET cc_start: 0.9320 (pmm) cc_final: 0.7698 (pmm) REVERT: D 96 MET cc_start: 0.6277 (ttt) cc_final: 0.5653 (tpt) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.3653 time to fit residues: 107.9361 Evaluate side-chains 122 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 106 optimal weight: 0.8980 chunk 286 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 318 optimal weight: 20.0000 chunk 264 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 167 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN C 919 ASN C 965 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 26957 Z= 0.295 Angle : 0.635 8.325 36663 Z= 0.331 Chirality : 0.047 0.453 4243 Planarity : 0.004 0.086 4704 Dihedral : 6.595 55.561 4340 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: -2.34 (0.14), residues: 3258 helix: 0.96 (0.21), residues: 640 sheet: -1.77 (0.21), residues: 580 loop : -2.47 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 886 HIS 0.010 0.002 HIS C1064 PHE 0.023 0.002 PHE B 464 TYR 0.015 0.002 TYR A 904 ARG 0.007 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 2.931 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 REVERT: A 763 LEU cc_start: 0.9399 (pp) cc_final: 0.9161 (pp) REVERT: A 764 ASN cc_start: 0.9299 (m-40) cc_final: 0.8778 (p0) REVERT: A 802 PHE cc_start: 0.8795 (m-80) cc_final: 0.8551 (m-80) REVERT: A 1050 MET cc_start: 0.9210 (pmm) cc_final: 0.8280 (pmm) REVERT: B 92 PHE cc_start: 0.9148 (t80) cc_final: 0.8319 (t80) REVERT: B 192 PHE cc_start: 0.8896 (m-80) cc_final: 0.8082 (m-80) REVERT: B 424 LYS cc_start: 0.8145 (tttt) cc_final: 0.7898 (tptp) REVERT: B 774 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8786 (mm110) REVERT: B 867 ASP cc_start: 0.8837 (m-30) cc_final: 0.8611 (p0) REVERT: B 902 MET cc_start: 0.9521 (mmm) cc_final: 0.9280 (mmm) REVERT: B 1002 GLN cc_start: 0.9069 (tm-30) cc_final: 0.8274 (tm-30) REVERT: C 153 MET cc_start: 0.4756 (ptp) cc_final: 0.4366 (ppp) REVERT: C 731 MET cc_start: 0.8977 (ttp) cc_final: 0.8601 (ttp) REVERT: C 763 LEU cc_start: 0.9265 (mt) cc_final: 0.8851 (mt) REVERT: C 869 MET cc_start: 0.9192 (mtm) cc_final: 0.8913 (mtp) REVERT: C 886 TRP cc_start: 0.8203 (p90) cc_final: 0.7869 (p90) REVERT: C 966 LEU cc_start: 0.9541 (mt) cc_final: 0.9179 (mp) REVERT: C 1050 MET cc_start: 0.9299 (pmm) cc_final: 0.7641 (pmm) REVERT: D 96 MET cc_start: 0.6413 (ttt) cc_final: 0.5954 (mmm) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.3593 time to fit residues: 95.6184 Evaluate side-chains 111 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 306 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 chunk 267 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 317 optimal weight: 0.1980 chunk 198 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN B 919 ASN C 66 HIS C 919 ASN C 935 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 26957 Z= 0.133 Angle : 0.532 9.444 36663 Z= 0.274 Chirality : 0.046 0.465 4243 Planarity : 0.004 0.058 4704 Dihedral : 6.014 56.329 4340 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.14), residues: 3258 helix: 1.34 (0.21), residues: 646 sheet: -1.64 (0.21), residues: 579 loop : -2.33 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 104 HIS 0.004 0.001 HIS B 207 PHE 0.029 0.001 PHE C 823 TYR 0.011 0.001 TYR C 380 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 3.093 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 REVERT: A 275 PHE cc_start: 0.8773 (m-10) cc_final: 0.7966 (m-10) REVERT: A 355 ARG cc_start: 0.7159 (mmt90) cc_final: 0.6918 (mmt90) REVERT: A 664 ILE cc_start: 0.9232 (mp) cc_final: 0.8715 (mp) REVERT: A 736 VAL cc_start: 0.9478 (t) cc_final: 0.9140 (t) REVERT: A 763 LEU cc_start: 0.9357 (pp) cc_final: 0.9101 (pp) REVERT: A 764 ASN cc_start: 0.9208 (m-40) cc_final: 0.8619 (p0) REVERT: A 765 ARG cc_start: 0.8772 (tpt90) cc_final: 0.8454 (mmm160) REVERT: A 952 VAL cc_start: 0.8969 (t) cc_final: 0.8742 (p) REVERT: A 1050 MET cc_start: 0.9129 (pmm) cc_final: 0.8287 (pmm) REVERT: B 92 PHE cc_start: 0.9086 (t80) cc_final: 0.8511 (t80) REVERT: B 192 PHE cc_start: 0.8759 (m-80) cc_final: 0.8211 (m-80) REVERT: B 424 LYS cc_start: 0.8171 (tttt) cc_final: 0.7914 (tptp) REVERT: B 774 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8971 (mm110) REVERT: B 1002 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8229 (tm-30) REVERT: C 153 MET cc_start: 0.4592 (ptp) cc_final: 0.4045 (ppp) REVERT: C 763 LEU cc_start: 0.9290 (mt) cc_final: 0.8936 (mt) REVERT: C 886 TRP cc_start: 0.8104 (p90) cc_final: 0.7817 (p90) REVERT: C 933 LYS cc_start: 0.9564 (mttt) cc_final: 0.9270 (mttp) REVERT: C 966 LEU cc_start: 0.9436 (mt) cc_final: 0.8945 (pp) REVERT: C 1050 MET cc_start: 0.9198 (pmm) cc_final: 0.7537 (pmm) REVERT: D 96 MET cc_start: 0.6477 (ttt) cc_final: 0.6020 (mmm) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3571 time to fit residues: 112.2122 Evaluate side-chains 120 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 196 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 189 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 216 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C1005 GLN C1010 GLN C1011 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 26957 Z= 0.205 Angle : 0.566 11.906 36663 Z= 0.290 Chirality : 0.047 0.457 4243 Planarity : 0.004 0.046 4704 Dihedral : 6.019 55.995 4340 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -2.01 (0.14), residues: 3258 helix: 1.34 (0.21), residues: 649 sheet: -1.58 (0.20), residues: 595 loop : -2.30 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 886 HIS 0.005 0.001 HIS C1064 PHE 0.029 0.001 PHE C 823 TYR 0.014 0.001 TYR A 313 ARG 0.006 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 736 VAL cc_start: 0.9520 (t) cc_final: 0.9158 (t) REVERT: A 763 LEU cc_start: 0.9355 (pp) cc_final: 0.9082 (pp) REVERT: A 764 ASN cc_start: 0.9226 (m-40) cc_final: 0.8618 (p0) REVERT: A 765 ARG cc_start: 0.8880 (tpt90) cc_final: 0.8537 (mmm160) REVERT: A 952 VAL cc_start: 0.8949 (t) cc_final: 0.8718 (p) REVERT: A 1050 MET cc_start: 0.9126 (pmm) cc_final: 0.8239 (pmm) REVERT: B 92 PHE cc_start: 0.9123 (t80) cc_final: 0.8548 (t80) REVERT: B 192 PHE cc_start: 0.8827 (m-80) cc_final: 0.8268 (m-80) REVERT: B 424 LYS cc_start: 0.8198 (tttt) cc_final: 0.7931 (tptp) REVERT: B 774 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8894 (mm110) REVERT: B 902 MET cc_start: 0.9373 (mmm) cc_final: 0.9119 (mmm) REVERT: B 1002 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 1089 PHE cc_start: 0.8821 (m-80) cc_final: 0.8507 (m-10) REVERT: C 153 MET cc_start: 0.4735 (ptp) cc_final: 0.4280 (ppp) REVERT: C 731 MET cc_start: 0.8952 (ttp) cc_final: 0.8517 (ttp) REVERT: C 763 LEU cc_start: 0.9303 (mt) cc_final: 0.8939 (mt) REVERT: C 886 TRP cc_start: 0.8166 (p90) cc_final: 0.7805 (p90) REVERT: C 933 LYS cc_start: 0.9575 (mttt) cc_final: 0.9291 (mttp) REVERT: C 1050 MET cc_start: 0.9221 (pmm) cc_final: 0.8004 (pmm) REVERT: D 43 GLN cc_start: 0.9076 (tt0) cc_final: 0.8856 (pp30) REVERT: D 96 MET cc_start: 0.6484 (ttt) cc_final: 0.5471 (mmm) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.3370 time to fit residues: 89.5553 Evaluate side-chains 113 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 2.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 288 optimal weight: 0.0070 chunk 303 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 177 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 232 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 294 optimal weight: 3.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN C 919 ASN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26957 Z= 0.148 Angle : 0.529 10.455 36663 Z= 0.270 Chirality : 0.046 0.458 4243 Planarity : 0.004 0.049 4704 Dihedral : 5.750 56.203 4340 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -1.88 (0.14), residues: 3258 helix: 1.43 (0.21), residues: 644 sheet: -1.46 (0.21), residues: 593 loop : -2.21 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 104 HIS 0.003 0.001 HIS B 207 PHE 0.027 0.001 PHE C 823 TYR 0.011 0.001 TYR C 380 ARG 0.005 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.909 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 REVERT: A 736 VAL cc_start: 0.9499 (t) cc_final: 0.9122 (t) REVERT: A 763 LEU cc_start: 0.9372 (pp) cc_final: 0.9094 (pp) REVERT: A 764 ASN cc_start: 0.9204 (m-40) cc_final: 0.8568 (p0) REVERT: A 765 ARG cc_start: 0.8849 (tpt90) cc_final: 0.8519 (mmm160) REVERT: A 964 LYS cc_start: 0.7660 (mttt) cc_final: 0.6989 (mttm) REVERT: A 1050 MET cc_start: 0.9057 (pmm) cc_final: 0.8260 (pmm) REVERT: B 92 PHE cc_start: 0.9092 (t80) cc_final: 0.8867 (t80) REVERT: B 424 LYS cc_start: 0.8156 (tttt) cc_final: 0.7898 (tptp) REVERT: B 774 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8926 (mm110) REVERT: B 869 MET cc_start: 0.8887 (mpp) cc_final: 0.8634 (mpp) REVERT: B 902 MET cc_start: 0.9520 (mmm) cc_final: 0.9087 (mmm) REVERT: B 1002 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8237 (tm-30) REVERT: B 1089 PHE cc_start: 0.8759 (m-80) cc_final: 0.8406 (m-10) REVERT: C 153 MET cc_start: 0.4627 (ptp) cc_final: 0.4071 (ppp) REVERT: C 582 LEU cc_start: 0.7713 (mt) cc_final: 0.7255 (tt) REVERT: C 763 LEU cc_start: 0.9299 (mt) cc_final: 0.8930 (mt) REVERT: C 864 LEU cc_start: 0.8508 (tp) cc_final: 0.8016 (tp) REVERT: C 933 LYS cc_start: 0.9566 (mttt) cc_final: 0.9261 (mttp) REVERT: C 966 LEU cc_start: 0.9466 (mt) cc_final: 0.8967 (pp) REVERT: C 1050 MET cc_start: 0.9169 (pmm) cc_final: 0.8011 (pmm) REVERT: D 43 GLN cc_start: 0.9090 (tt0) cc_final: 0.8868 (pp30) REVERT: D 96 MET cc_start: 0.6518 (ttt) cc_final: 0.5316 (tpt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.3526 time to fit residues: 99.6948 Evaluate side-chains 117 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 194 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 chunk 148 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 327 optimal weight: 30.0000 chunk 301 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 913 GLN C 919 ASN C1010 GLN C1011 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26957 Z= 0.193 Angle : 0.552 9.808 36663 Z= 0.283 Chirality : 0.046 0.455 4243 Planarity : 0.004 0.046 4704 Dihedral : 5.766 55.924 4340 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.85 (0.14), residues: 3258 helix: 1.44 (0.21), residues: 642 sheet: -1.40 (0.21), residues: 592 loop : -2.20 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.005 0.001 HIS C1064 PHE 0.029 0.001 PHE C 823 TYR 0.014 0.001 TYR A 756 ARG 0.006 0.000 ARG A 765 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 736 VAL cc_start: 0.9497 (t) cc_final: 0.9136 (t) REVERT: A 763 LEU cc_start: 0.9355 (pp) cc_final: 0.9079 (pp) REVERT: A 764 ASN cc_start: 0.9194 (m-40) cc_final: 0.8521 (p0) REVERT: A 765 ARG cc_start: 0.8885 (tpt90) cc_final: 0.8572 (mmm160) REVERT: A 779 GLN cc_start: 0.8875 (tp40) cc_final: 0.8556 (tm-30) REVERT: A 964 LYS cc_start: 0.7796 (mttt) cc_final: 0.7091 (mttm) REVERT: A 1050 MET cc_start: 0.9181 (pmm) cc_final: 0.8303 (pmm) REVERT: B 192 PHE cc_start: 0.8862 (m-10) cc_final: 0.8506 (m-10) REVERT: B 424 LYS cc_start: 0.8180 (tttt) cc_final: 0.7942 (tptp) REVERT: B 774 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8927 (mm110) REVERT: B 869 MET cc_start: 0.9018 (mpp) cc_final: 0.8767 (mpp) REVERT: B 902 MET cc_start: 0.9489 (mmm) cc_final: 0.9251 (mmm) REVERT: B 1002 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8293 (tm-30) REVERT: B 1089 PHE cc_start: 0.8811 (m-80) cc_final: 0.8493 (m-10) REVERT: C 153 MET cc_start: 0.4562 (ptp) cc_final: 0.4058 (ppp) REVERT: C 582 LEU cc_start: 0.7778 (mt) cc_final: 0.7276 (tt) REVERT: C 763 LEU cc_start: 0.9295 (mt) cc_final: 0.8911 (mt) REVERT: C 933 LYS cc_start: 0.9576 (mttt) cc_final: 0.9281 (mttp) REVERT: C 966 LEU cc_start: 0.9487 (mt) cc_final: 0.9035 (pp) REVERT: C 1050 MET cc_start: 0.9175 (pmm) cc_final: 0.8040 (pmm) REVERT: D 43 GLN cc_start: 0.9112 (tt0) cc_final: 0.8885 (pp30) REVERT: D 96 MET cc_start: 0.6460 (ttt) cc_final: 0.5227 (tpt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.3377 time to fit residues: 88.8150 Evaluate side-chains 112 residues out of total 2878 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 58.1128 > 50: distance: 20 - 24: 10.540 distance: 24 - 25: 38.222 distance: 25 - 26: 4.066 distance: 25 - 28: 54.101 distance: 26 - 27: 3.156 distance: 26 - 32: 43.300 distance: 28 - 29: 22.975 distance: 29 - 30: 21.814 distance: 29 - 31: 22.828 distance: 32 - 33: 6.515 distance: 32 - 187: 27.894 distance: 33 - 34: 9.697 distance: 33 - 36: 5.916 distance: 34 - 35: 14.154 distance: 34 - 43: 11.427 distance: 35 - 184: 19.785 distance: 36 - 37: 6.962 distance: 37 - 39: 28.215 distance: 38 - 40: 9.868 distance: 39 - 41: 4.376 distance: 40 - 42: 13.666 distance: 41 - 42: 10.586 distance: 43 - 44: 10.543 distance: 44 - 45: 21.586 distance: 44 - 47: 10.144 distance: 45 - 46: 7.127 distance: 45 - 54: 15.054 distance: 47 - 48: 3.474 distance: 48 - 49: 20.808 distance: 49 - 50: 4.679 distance: 50 - 51: 4.297 distance: 51 - 52: 18.948 distance: 51 - 53: 8.829 distance: 54 - 55: 16.233 distance: 55 - 56: 23.691 distance: 55 - 58: 23.316 distance: 56 - 61: 41.909 distance: 58 - 59: 5.385 distance: 58 - 60: 17.421 distance: 61 - 62: 28.614 distance: 62 - 63: 20.298 distance: 62 - 65: 17.895 distance: 63 - 64: 12.897 distance: 63 - 70: 15.967 distance: 65 - 66: 41.100 distance: 66 - 67: 35.273 distance: 67 - 68: 28.481 distance: 70 - 71: 4.720 distance: 70 - 76: 3.131 distance: 71 - 72: 20.860 distance: 71 - 74: 11.619 distance: 72 - 73: 20.064 distance: 72 - 77: 20.643 distance: 74 - 75: 6.324 distance: 75 - 76: 13.977 distance: 77 - 78: 3.472 distance: 78 - 81: 26.943 distance: 79 - 80: 22.066 distance: 79 - 84: 3.745 distance: 81 - 82: 21.372 distance: 81 - 83: 11.383 distance: 84 - 85: 30.427 distance: 85 - 86: 25.882 distance: 85 - 88: 16.726 distance: 86 - 87: 21.504 distance: 86 - 93: 28.075 distance: 88 - 89: 18.260 distance: 90 - 91: 7.690 distance: 93 - 94: 33.203 distance: 94 - 95: 23.448 distance: 94 - 97: 26.717 distance: 95 - 96: 24.833 distance: 95 - 99: 13.215 distance: 97 - 98: 6.791 distance: 99 - 100: 42.275 distance: 100 - 101: 38.737 distance: 100 - 103: 16.139 distance: 101 - 102: 10.528 distance: 101 - 107: 28.728 distance: 103 - 104: 10.817 distance: 103 - 105: 19.523 distance: 104 - 106: 28.663