Starting phenix.real_space_refine on Sat Jan 20 04:50:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eoj_3908/01_2024/6eoj_3908.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eoj_3908/01_2024/6eoj_3908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eoj_3908/01_2024/6eoj_3908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eoj_3908/01_2024/6eoj_3908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eoj_3908/01_2024/6eoj_3908.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6eoj_3908/01_2024/6eoj_3908.pdb" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 66 5.16 5 C 8747 2.51 5 N 2319 2.21 5 O 2554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 334": "OE1" <-> "OE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 818": "NH1" <-> "NH2" Residue "A GLU 1046": "OE1" <-> "OE2" Residue "A GLU 1175": "OE1" <-> "OE2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13688 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1233, 9801 Classifications: {'peptide': 1233} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 52, 'TRANS': 1180} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 788 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 82} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3097 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'UNK:plan-1': 5, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10352 SG CYS B 67 58.725 56.406 18.932 1.00100.70 S ATOM 10424 SG CYS B 75 55.446 56.386 18.299 1.00 99.83 S ATOM 10473 SG CYS B 81 57.496 53.730 16.587 1.00104.94 S ATOM 10088 SG CYS B 34 57.372 31.929 22.523 1.00162.41 S ATOM 10186 SG CYS B 46 54.315 29.542 20.976 1.00180.34 S ATOM 10229 SG CYS B 52 54.559 30.589 24.714 1.00164.23 S Time building chain proxies: 7.62, per 1000 atoms: 0.56 Number of scatterers: 13688 At special positions: 0 Unit cell: (96.6, 109.2, 127.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 66 16.00 O 2554 8.00 N 2319 7.00 C 8747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 5.12 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 85 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 75 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 67 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 81 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 56 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 46 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 34 " pdb="ZN ZN B 302 " - pdb=" SG CYS B 52 " Number of angles added : 6 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3264 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 29 sheets defined 8.2% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 697 through 702 removed outlier: 4.133A pdb=" N GLU A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET A 702 " --> pdb=" O ILE A 698 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 697 through 702' Processing helix chain 'A' and resid 841 through 846 removed outlier: 4.301A pdb=" N SER A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1207 Processing helix chain 'A' and resid 1262 through 1280 removed outlier: 3.579A pdb=" N ARG A1267 " --> pdb=" O GLU A1263 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A1269 " --> pdb=" O LYS A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1292 Processing helix chain 'A' and resid 1310 through 1319 removed outlier: 4.008A pdb=" N ARG A1315 " --> pdb=" O ASN A1311 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A1316 " --> pdb=" O VAL A1312 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A1317 " --> pdb=" O ILE A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1327 Processing helix chain 'A' and resid 1335 through 1348 removed outlier: 3.830A pdb=" N ASP A1342 " --> pdb=" O GLU A1338 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN A1345 " --> pdb=" O ARG A1341 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1355 removed outlier: 3.708A pdb=" N SER A1352 " --> pdb=" O SER A1349 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.569A pdb=" N GLN B 21 " --> pdb=" O PRO B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 removed outlier: 4.268A pdb=" N LEU B 51 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS B 52 " --> pdb=" O GLY B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 52' Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.534A pdb=" N ILE D 63 " --> pdb=" O SER D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 75 through 79 Processing sheet with id= A, first strand: chain 'A' and resid 14 through 18 removed outlier: 6.315A pdb=" N ARG A 41 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N LEU A 50 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR A 43 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 48 " --> pdb=" O THR A 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 60 through 66 removed outlier: 6.578A pdb=" N CYS A 79 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A 63 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 77 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU A 65 " --> pdb=" O CYS A 75 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N CYS A 75 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS A 84 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 101 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LYS A 89 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR A 99 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASN A 91 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE A 97 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 122 through 126 removed outlier: 3.792A pdb=" N ASP A 126 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N CYS A 131 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER A 130 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE A 139 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 213 through 219 removed outlier: 5.451A pdb=" N ILE A 213 " --> pdb=" O GLN A 232 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN A 232 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 217 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N THR A 226 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR A 248 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS A 275 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR A 250 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N PHE A 273 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A 252 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 267 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 258 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 283 through 287 removed outlier: 4.482A pdb=" N GLU A 298 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 310 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 12.811A pdb=" N THR A 311 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER A 331 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASN A 329 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 12.703A pdb=" N ASN A 315 " --> pdb=" O ILE A 327 " (cutoff:3.500A) removed outlier: 15.173A pdb=" N ILE A 327 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 343 through 347 removed outlier: 4.403A pdb=" N THR A 343 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLU A 361 " --> pdb=" O MET A 377 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N MET A 377 " --> pdb=" O GLU A 361 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 363 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE A 372 " --> pdb=" O LYS A 391 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LYS A 391 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR A 374 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE A 389 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN A 376 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE A 387 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU A 378 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 385 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 407 through 410 removed outlier: 6.741A pdb=" N ARG A 435 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU A 501 " --> pdb=" O ARG A 435 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 511 through 517 removed outlier: 6.456A pdb=" N THR A 542 " --> pdb=" O THR A 512 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 514 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 540 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL A 516 " --> pdb=" O SER A 538 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER A 538 " --> pdb=" O VAL A 516 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 561 through 567 removed outlier: 3.786A pdb=" N LEU A 564 " --> pdb=" O VAL A 913 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASN A 910 " --> pdb=" O ASP A 906 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 906 " --> pdb=" O ASN A 910 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 901 " --> pdb=" O TRP A 897 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER A 893 " --> pdb=" O VAL A 905 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 584 through 590 removed outlier: 3.662A pdb=" N ARG A 595 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE A 598 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASN A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 619 through 626 Processing sheet with id= L, first strand: chain 'A' and resid 658 through 664 removed outlier: 4.475A pdb=" N ASP A 676 " --> pdb=" O VAL A 672 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 704 through 712 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 704 through 712 current: chain 'A' and resid 740 through 744 removed outlier: 4.314A pdb=" N ILE A 741 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR A 766 " --> pdb=" O ASN A 756 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 782 through 791 removed outlier: 5.129A pdb=" N GLU A 797 " --> pdb=" O LYS A 813 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU A 807 " --> pdb=" O THR A 803 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 850 through 855 removed outlier: 3.934A pdb=" N ILE A 850 " --> pdb=" O THR A 866 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER A 861 " --> pdb=" O LYS A 875 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS A 875 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 943 through 950 removed outlier: 6.086A pdb=" N LEU A 944 " --> pdb=" O CYS A 961 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N CYS A 961 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS A 946 " --> pdb=" O SER A 959 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 959 " --> pdb=" O LYS A 946 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 964 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N SER A 991 " --> pdb=" O PHE A1009 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE A1009 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ASN A 997 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL A1003 " --> pdb=" O ASN A 997 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 1013 through 1021 removed outlier: 7.250A pdb=" N GLY A1039 " --> pdb=" O ASN A1016 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N MET A1018 " --> pdb=" O ILE A1037 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE A1037 " --> pdb=" O MET A1018 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER A1020 " --> pdb=" O TYR A1035 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR A1035 " --> pdb=" O SER A1020 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N GLU A1034 " --> pdb=" O VAL A1059 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VAL A1059 " --> pdb=" O GLU A1034 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR A1051 " --> pdb=" O ASN A1042 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 1087 through 1093 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1087 through 1093 current: chain 'A' and resid 1104 through 1111 removed outlier: 5.953A pdb=" N ASP A1109 " --> pdb=" O PRO A1118 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N GLN A1111 " --> pdb=" O VAL A1116 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL A1116 " --> pdb=" O GLN A1111 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 1128 through 1134 No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'A' and resid 1172 through 1179 removed outlier: 3.979A pdb=" N SER A1173 " --> pdb=" O THR A1188 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N MET A1183 " --> pdb=" O TYR A1199 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN A1193 " --> pdb=" O ASP A1189 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ARG A1192 " --> pdb=" O LEU A1220 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS A1198 " --> pdb=" O HIS A1214 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N HIS A1214 " --> pdb=" O LYS A1198 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 1224 through 1232 No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 83 through 88 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 83 through 88 current: chain 'D' and resid 364 through 369 Processing sheet with id= W, first strand: chain 'D' and resid 96 through 101 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 96 through 101 current: chain 'D' and resid 107 through 112 removed outlier: 5.706A pdb=" N PHE D 117 " --> pdb=" O MET D 131 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU D 119 " --> pdb=" O THR D 129 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N THR D 129 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASN D 121 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE D 127 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 138 through 144 removed outlier: 5.289A pdb=" N THR D 140 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N TRP D 149 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS D 160 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N MET D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS D 170 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 179 through 186 removed outlier: 3.865A pdb=" N ASP D 182 " --> pdb=" O CYS D 195 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS D 191 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER D 196 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 201 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL D 214 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE D 203 " --> pdb=" O GLU D 212 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 222 through 227 removed outlier: 3.537A pdb=" N LYS D 244 " --> pdb=" O SER D 236 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU D 242 " --> pdb=" O ILE D 257 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE D 257 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS D 244 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER D 255 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TRP D 246 " --> pdb=" O CYS D 253 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS D 253 " --> pdb=" O TRP D 246 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'D' and resid 264 through 269 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 264 through 269 current: chain 'D' and resid 276 through 281 removed outlier: 5.423A pdb=" N SER D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 288 " --> pdb=" O MET D 299 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET D 299 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP D 290 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU D 297 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'D' and resid 309 through 312 Processing sheet with id= AC, first strand: chain 'D' and resid 328 through 332 No H-bonds generated for sheet with id= AC 328 hydrogen bonds defined for protein. 900 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: 5.41 Time building geometry restraints manager: 5.55 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: 4343 1.34 - 1.46: 2053 1.46 - 1.58: 7479 1.58 - 1.70: 0 1.70 - 1.81: 107 Bond restraints: 13982 Sorted by residual: bond pdb=" N PRO A 510 " pdb=" CA PRO A 510 " ideal model delta sigma weight residual 1.474 1.446 0.028 7.40e-03 1.83e+04 1.44e+01 bond pdb=" CA ASP A 665 " pdb=" C ASP A 665 " ideal model delta sigma weight residual 1.523 1.552 -0.028 1.00e-02 1.00e+04 8.07e+00 bond pdb=" CA VAL A 777 " pdb=" CB VAL A 777 " ideal model delta sigma weight residual 1.540 1.565 -0.026 9.00e-03 1.23e+04 8.03e+00 bond pdb=" CA ILE A 782 " pdb=" CB ILE A 782 " ideal model delta sigma weight residual 1.532 1.563 -0.031 1.08e-02 8.57e+03 8.00e+00 bond pdb=" N LEU A 246 " pdb=" CA LEU A 246 " ideal model delta sigma weight residual 1.458 1.478 -0.020 7.40e-03 1.83e+04 7.44e+00 ... (remaining 13977 not shown) Histogram of bond angle deviations from ideal: 97.33 - 104.68: 246 104.68 - 112.03: 5848 112.03 - 119.38: 5419 119.38 - 126.72: 7265 126.72 - 134.07: 159 Bond angle restraints: 18937 Sorted by residual: angle pdb=" C PRO D 67 " pdb=" N PRO D 68 " pdb=" CA PRO D 68 " ideal model delta sigma weight residual 119.84 127.25 -7.41 1.25e+00 6.40e-01 3.51e+01 angle pdb=" N VAL A1178 " pdb=" CA VAL A1178 " pdb=" C VAL A1178 " ideal model delta sigma weight residual 111.81 116.85 -5.04 8.60e-01 1.35e+00 3.43e+01 angle pdb=" C THR D 102 " pdb=" N PRO D 103 " pdb=" CA PRO D 103 " ideal model delta sigma weight residual 119.84 126.88 -7.04 1.25e+00 6.40e-01 3.17e+01 angle pdb=" N TYR D 44 " pdb=" CA TYR D 44 " pdb=" C TYR D 44 " ideal model delta sigma weight residual 112.13 105.06 7.07 1.37e+00 5.33e-01 2.67e+01 angle pdb=" N MET D 158 " pdb=" CA MET D 158 " pdb=" C MET D 158 " ideal model delta sigma weight residual 110.50 117.60 -7.10 1.41e+00 5.03e-01 2.54e+01 ... (remaining 18932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 7231 16.62 - 33.23: 920 33.23 - 49.85: 212 49.85 - 66.47: 84 66.47 - 83.08: 15 Dihedral angle restraints: 8462 sinusoidal: 3431 harmonic: 5031 Sorted by residual: dihedral pdb=" CA GLU A1155 " pdb=" C GLU A1155 " pdb=" N PRO A1156 " pdb=" CA PRO A1156 " ideal model delta harmonic sigma weight residual 180.00 152.57 27.43 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" C THR A 414 " pdb=" N THR A 414 " pdb=" CA THR A 414 " pdb=" CB THR A 414 " ideal model delta harmonic sigma weight residual -122.00 -134.53 12.53 0 2.50e+00 1.60e-01 2.51e+01 dihedral pdb=" C ASN A 221 " pdb=" N ASN A 221 " pdb=" CA ASN A 221 " pdb=" CB ASN A 221 " ideal model delta harmonic sigma weight residual -122.60 -133.87 11.27 0 2.50e+00 1.60e-01 2.03e+01 ... (remaining 8459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1551 0.085 - 0.170: 453 0.170 - 0.254: 113 0.254 - 0.339: 21 0.339 - 0.424: 6 Chirality restraints: 2144 Sorted by residual: chirality pdb=" CA ASN A 221 " pdb=" N ASN A 221 " pdb=" C ASN A 221 " pdb=" CB ASN A 221 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CA THR A 414 " pdb=" N THR A 414 " pdb=" C THR A 414 " pdb=" CB THR A 414 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA LYS A 926 " pdb=" N LYS A 926 " pdb=" C LYS A 926 " pdb=" CB LYS A 926 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 2141 not shown) Planarity restraints: 2412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 509 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 510 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 510 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 510 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 665 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO A 666 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 666 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 666 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1155 " -0.037 5.00e-02 4.00e+02 5.67e-02 5.14e+00 pdb=" N PRO A1156 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A1156 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1156 " -0.032 5.00e-02 4.00e+02 ... (remaining 2409 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 6239 3.00 - 3.48: 14845 3.48 - 3.95: 25357 3.95 - 4.43: 27926 4.43 - 4.90: 46268 Nonbonded interactions: 120635 Sorted by model distance: nonbonded pdb=" O THR A 34 " pdb=" N ILE A 60 " model vdw 2.526 2.520 nonbonded pdb=" OG SER A1088 " pdb=" OG SER A1100 " model vdw 2.529 2.440 nonbonded pdb=" OH TYR A1266 " pdb=" O PRO A1306 " model vdw 2.530 2.440 nonbonded pdb=" O PRO A1231 " pdb=" OG SER A1352 " model vdw 2.532 2.440 nonbonded pdb=" O MET D 66 " pdb=" NH1 ARG D 379 " model vdw 2.541 2.520 ... (remaining 120630 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.240 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: 0.010 Extract box with map and model: 1.800 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 42.000 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 13982 Z= 0.463 Angle : 1.326 10.821 18937 Z= 0.818 Chirality : 0.089 0.424 2144 Planarity : 0.005 0.064 2412 Dihedral : 16.646 83.085 5198 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 1.66 % Allowed : 10.14 % Favored : 88.20 % Rotamer: Outliers : 4.80 % Allowed : 13.67 % Favored : 81.53 % Cbeta Deviations : 0.43 % 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: -3.75 (0.17), residues: 1686 helix: -3.58 (0.29), residues: 101 sheet: -2.16 (0.19), residues: 530 loop : -2.66 (0.16), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 101 HIS 0.007 0.001 HIS A1221 PHE 0.016 0.002 PHE D 269 TYR 0.017 0.002 TYR A1184 ARG 0.003 0.001 ARG D 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 505 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8501 (mp) cc_final: 0.8221 (mt) REVERT: A 44 ARG cc_start: 0.6933 (mtt180) cc_final: 0.6732 (tpt170) REVERT: A 55 LYS cc_start: 0.8422 (tttt) cc_final: 0.7648 (ttpt) REVERT: A 75 CYS cc_start: 0.8654 (m) cc_final: 0.8037 (m) REVERT: A 79 CYS cc_start: 0.8513 (m) cc_final: 0.8215 (m) REVERT: A 92 THR cc_start: 0.8985 (m) cc_final: 0.8686 (p) REVERT: A 110 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7688 (mttm) REVERT: A 115 VAL cc_start: 0.8603 (p) cc_final: 0.8321 (p) REVERT: A 129 SER cc_start: 0.8185 (m) cc_final: 0.7524 (p) REVERT: A 201 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8461 (pp) REVERT: A 205 GLU cc_start: 0.7666 (tt0) cc_final: 0.7328 (tp30) REVERT: A 215 ASP cc_start: 0.8580 (t0) cc_final: 0.8350 (t0) REVERT: A 265 LYS cc_start: 0.7858 (mttt) cc_final: 0.7649 (ttpt) REVERT: A 341 ASN cc_start: 0.8437 (p0) cc_final: 0.8127 (t0) REVERT: A 366 MET cc_start: 0.8916 (mtp) cc_final: 0.8676 (mtp) REVERT: A 372 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8312 (mm) REVERT: A 411 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7961 (pp) REVERT: A 507 ASN cc_start: 0.8822 (t0) cc_final: 0.8567 (t0) REVERT: A 512 THR cc_start: 0.8543 (m) cc_final: 0.8117 (m) REVERT: A 527 LYS cc_start: 0.7553 (mmtp) cc_final: 0.6937 (mmtm) REVERT: A 536 GLU cc_start: 0.8619 (tm-30) cc_final: 0.7950 (tt0) REVERT: A 539 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8890 (pt) REVERT: A 542 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 545 ASN cc_start: 0.8478 (t0) cc_final: 0.8255 (t0) REVERT: A 550 HIS cc_start: 0.9058 (p-80) cc_final: 0.8797 (p90) REVERT: A 564 LEU cc_start: 0.7750 (tp) cc_final: 0.7091 (mp) REVERT: A 614 ARG cc_start: 0.6794 (tpt90) cc_final: 0.6522 (tpt90) REVERT: A 629 LYS cc_start: 0.7446 (mtpp) cc_final: 0.6738 (mttp) REVERT: A 643 ASP cc_start: 0.6660 (t70) cc_final: 0.6375 (t0) REVERT: A 647 ARG cc_start: 0.6376 (ptt-90) cc_final: 0.5911 (ptm160) REVERT: A 653 LYS cc_start: 0.8414 (pttp) cc_final: 0.7673 (tptp) REVERT: A 655 ASP cc_start: 0.6599 (t70) cc_final: 0.6249 (t70) REVERT: A 657 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7427 (tt0) REVERT: A 659 ILE cc_start: 0.8665 (tp) cc_final: 0.8355 (pt) REVERT: A 681 GLU cc_start: 0.7215 (tt0) cc_final: 0.6984 (tp30) REVERT: A 688 ARG cc_start: 0.6722 (tpt170) cc_final: 0.6384 (mmm-85) REVERT: A 713 ASN cc_start: 0.8227 (p0) cc_final: 0.7399 (p0) REVERT: A 714 MET cc_start: 0.7775 (ptm) cc_final: 0.7474 (ptt) REVERT: A 724 LYS cc_start: 0.7161 (tptm) cc_final: 0.6882 (tttt) REVERT: A 728 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6862 (pm20) REVERT: A 736 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8456 (m) REVERT: A 753 PHE cc_start: 0.8501 (m-80) cc_final: 0.8089 (m-10) REVERT: A 760 GLN cc_start: 0.6490 (pt0) cc_final: 0.6036 (pm20) REVERT: A 782 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8852 (mt) REVERT: A 786 MET cc_start: 0.7447 (ptp) cc_final: 0.6883 (ptp) REVERT: A 807 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: A 817 ARG cc_start: 0.7126 (ttm-80) cc_final: 0.6870 (mtp85) REVERT: A 818 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7669 (mtt90) REVERT: A 824 ASN cc_start: 0.6735 (OUTLIER) cc_final: 0.6491 (p0) REVERT: A 828 ASN cc_start: 0.7437 (m-40) cc_final: 0.7172 (m110) REVERT: A 933 LYS cc_start: 0.8074 (ptpt) cc_final: 0.7783 (mtmm) REVERT: A 939 ASP cc_start: 0.7351 (p0) cc_final: 0.7075 (p0) REVERT: A 942 LYS cc_start: 0.7683 (pttm) cc_final: 0.7433 (ptpp) REVERT: A 965 PRO cc_start: 0.9069 (Cg_endo) cc_final: 0.8829 (Cg_endo) REVERT: A 996 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8334 (pt) REVERT: A 1002 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8096 (mmtt) REVERT: A 1011 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8517 (mtpp) REVERT: A 1017 GLU cc_start: 0.7691 (mt-10) cc_final: 0.6424 (tt0) REVERT: A 1019 ARG cc_start: 0.8241 (mtt-85) cc_final: 0.7233 (mtt-85) REVERT: A 1081 GLU cc_start: 0.8096 (tt0) cc_final: 0.7637 (tp30) REVERT: A 1083 VAL cc_start: 0.7311 (m) cc_final: 0.6998 (p) REVERT: A 1144 MET cc_start: 0.8711 (ptm) cc_final: 0.8255 (ppp) REVERT: A 1160 ILE cc_start: 0.8687 (tp) cc_final: 0.8475 (tp) REVERT: A 1164 ARG cc_start: 0.8020 (mtt90) cc_final: 0.7474 (mtp-110) REVERT: A 1168 LYS cc_start: 0.8566 (pttp) cc_final: 0.8045 (mtmm) REVERT: A 1172 MET cc_start: 0.8803 (tpt) cc_final: 0.8532 (tpp) REVERT: A 1177 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8217 (pp) REVERT: A 1189 ASP cc_start: 0.8201 (m-30) cc_final: 0.7792 (m-30) REVERT: A 1226 CYS cc_start: 0.8559 (t) cc_final: 0.8296 (t) REVERT: A 1233 ASN cc_start: 0.7551 (t0) cc_final: 0.7316 (t0) REVERT: A 1321 ILE cc_start: 0.8174 (tt) cc_final: 0.7948 (tp) REVERT: A 1338 GLU cc_start: 0.8073 (tt0) cc_final: 0.7847 (tt0) REVERT: A 1347 GLU cc_start: 0.7847 (tp30) cc_final: 0.7421 (tp30) REVERT: A 1350 MET cc_start: 0.8950 (tpp) cc_final: 0.8721 (mmm) REVERT: B 31 ARG cc_start: 0.7687 (ptt-90) cc_final: 0.7342 (ptt90) REVERT: B 48 ARG cc_start: 0.6594 (mtt90) cc_final: 0.6280 (mtm-85) REVERT: B 63 ASN cc_start: 0.7858 (t0) cc_final: 0.7353 (m110) REVERT: B 68 ARG cc_start: 0.7658 (mtt-85) cc_final: 0.6923 (mmm160) REVERT: B 79 ASP cc_start: 0.7782 (t70) cc_final: 0.7088 (t70) REVERT: B 86 GLU cc_start: 0.8437 (tt0) cc_final: 0.7830 (tt0) REVERT: D 34 ASP cc_start: 0.9038 (t70) cc_final: 0.7991 (t0) REVERT: D 56 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8419 (mm-30) REVERT: D 61 TYR cc_start: 0.9132 (m-80) cc_final: 0.8660 (m-80) REVERT: D 75 ASP cc_start: 0.8599 (p0) cc_final: 0.8074 (p0) REVERT: D 93 LYS cc_start: 0.6620 (mtpp) cc_final: 0.6414 (tptt) REVERT: D 99 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8281 (mm) REVERT: D 107 ARG cc_start: 0.8236 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: D 109 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8747 (t) REVERT: D 132 GLN cc_start: 0.6775 (tt0) cc_final: 0.6425 (tm-30) REVERT: D 141 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7653 (ptp) REVERT: D 150 MET cc_start: 0.8274 (ptm) cc_final: 0.7730 (ppp) REVERT: D 163 GLN cc_start: 0.8358 (mt0) cc_final: 0.7899 (mt0) REVERT: D 165 ASN cc_start: 0.8216 (p0) cc_final: 0.7978 (p0) REVERT: D 168 MET cc_start: 0.7340 (ptp) cc_final: 0.6736 (pmm) REVERT: D 183 MET cc_start: 0.8413 (mmp) cc_final: 0.8109 (mmp) REVERT: D 200 ILE cc_start: 0.9001 (tt) cc_final: 0.8551 (tt) REVERT: D 234 ILE cc_start: 0.8364 (mp) cc_final: 0.8160 (mt) REVERT: D 239 LYS cc_start: 0.7188 (ttmm) cc_final: 0.6849 (mtpt) REVERT: D 245 LEU cc_start: 0.8272 (mt) cc_final: 0.8018 (mt) REVERT: D 273 LYS cc_start: 0.8575 (mmpt) cc_final: 0.7922 (mtpt) REVERT: D 275 ASN cc_start: 0.8007 (m-40) cc_final: 0.7659 (t0) REVERT: D 297 GLU cc_start: 0.8800 (pt0) cc_final: 0.7510 (tt0) REVERT: D 303 ASP cc_start: 0.7410 (t70) cc_final: 0.7204 (t0) REVERT: D 311 GLU cc_start: 0.8006 (tp30) cc_final: 0.7468 (tp30) REVERT: D 316 ASN cc_start: 0.8286 (m110) cc_final: 0.7640 (m110) REVERT: D 326 ASP cc_start: 0.7655 (t70) cc_final: 0.7393 (p0) REVERT: D 337 ASN cc_start: 0.7641 (m-40) cc_final: 0.7203 (t0) REVERT: D 339 ASN cc_start: 0.8077 (t0) cc_final: 0.7830 (t0) REVERT: D 340 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6674 (mm-30) REVERT: D 356 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8738 (pp) REVERT: D 357 SER cc_start: 0.9253 (t) cc_final: 0.8655 (m) REVERT: D 359 ASN cc_start: 0.8536 (p0) cc_final: 0.8330 (p0) REVERT: D 373 THR cc_start: 0.8596 (p) cc_final: 0.8193 (p) REVERT: D 383 ILE cc_start: 0.8566 (tp) cc_final: 0.8182 (tt) REVERT: D 388 TYR cc_start: 0.6233 (m-80) cc_final: 0.5737 (m-80) outliers start: 74 outliers final: 21 residues processed: 549 average time/residue: 0.2669 time to fit residues: 210.4197 Evaluate side-chains 400 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 362 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 736 THR Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 800 THR Chi-restraints excluded: chain A residue 807 GLU Chi-restraints excluded: chain A residue 824 ASN Chi-restraints excluded: chain A residue 832 ILE Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 996 ILE Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 356 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 154 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** A 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN A 931 GLN A 985 HIS A1026 ASN A1145 GLN A1205 ASN ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1273 GLN A1336 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13982 Z= 0.245 Angle : 0.707 14.080 18937 Z= 0.364 Chirality : 0.049 0.244 2144 Planarity : 0.004 0.050 2412 Dihedral : 7.879 54.811 1910 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.94 % Favored : 92.70 % Rotamer: Outliers : 5.83 % Allowed : 17.89 % Favored : 76.28 % 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: -3.25 (0.18), residues: 1686 helix: -2.23 (0.39), residues: 106 sheet: -2.16 (0.19), residues: 559 loop : -2.18 (0.18), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1001 HIS 0.006 0.001 HIS A 550 PHE 0.016 0.002 PHE A 135 TYR 0.017 0.002 TYR D 358 ARG 0.006 0.000 ARG A1279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 409 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 THR cc_start: 0.8680 (m) cc_final: 0.8401 (t) REVERT: A 30 LEU cc_start: 0.8244 (mp) cc_final: 0.8041 (mt) REVERT: A 44 ARG cc_start: 0.6809 (mtt180) cc_final: 0.6554 (tpp-160) REVERT: A 55 LYS cc_start: 0.8256 (tttt) cc_final: 0.7545 (ttpt) REVERT: A 73 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7698 (pt) REVERT: A 75 CYS cc_start: 0.8842 (m) cc_final: 0.8429 (t) REVERT: A 92 THR cc_start: 0.8962 (m) cc_final: 0.8721 (p) REVERT: A 110 LYS cc_start: 0.8255 (mtmt) cc_final: 0.8001 (mttm) REVERT: A 129 SER cc_start: 0.7852 (m) cc_final: 0.7354 (p) REVERT: A 201 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8618 (pp) REVERT: A 205 GLU cc_start: 0.8010 (tt0) cc_final: 0.7603 (tp30) REVERT: A 215 ASP cc_start: 0.8571 (t0) cc_final: 0.8247 (t0) REVERT: A 265 LYS cc_start: 0.7706 (mttt) cc_final: 0.7368 (tttt) REVERT: A 297 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7363 (p0) REVERT: A 334 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7092 (mp0) REVERT: A 336 MET cc_start: 0.7930 (ptt) cc_final: 0.7407 (ptp) REVERT: A 341 ASN cc_start: 0.8468 (p0) cc_final: 0.8141 (t0) REVERT: A 366 MET cc_start: 0.8861 (mtp) cc_final: 0.8500 (mtp) REVERT: A 373 TYR cc_start: 0.8587 (m-80) cc_final: 0.8353 (m-80) REVERT: A 378 GLU cc_start: 0.6929 (tp30) cc_final: 0.6709 (tp30) REVERT: A 411 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7487 (pp) REVERT: A 518 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8133 (mtmt) REVERT: A 527 LYS cc_start: 0.7271 (mmtp) cc_final: 0.6888 (mmtm) REVERT: A 536 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8104 (tt0) REVERT: A 539 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8474 (pt) REVERT: A 542 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8626 (p) REVERT: A 550 HIS cc_start: 0.8911 (p-80) cc_final: 0.8631 (p90) REVERT: A 564 LEU cc_start: 0.8124 (tp) cc_final: 0.7429 (mp) REVERT: A 606 LYS cc_start: 0.7291 (pttp) cc_final: 0.6929 (ptpt) REVERT: A 624 MET cc_start: 0.8528 (mmt) cc_final: 0.8270 (mmt) REVERT: A 629 LYS cc_start: 0.7220 (mtpp) cc_final: 0.6535 (mttp) REVERT: A 640 TYR cc_start: 0.7667 (m-80) cc_final: 0.7426 (m-80) REVERT: A 643 ASP cc_start: 0.6639 (t70) cc_final: 0.6418 (t0) REVERT: A 647 ARG cc_start: 0.6451 (ptt-90) cc_final: 0.5948 (ptm160) REVERT: A 653 LYS cc_start: 0.8365 (pttp) cc_final: 0.7591 (tptp) REVERT: A 655 ASP cc_start: 0.6536 (t70) cc_final: 0.6165 (t70) REVERT: A 688 ARG cc_start: 0.6779 (tpt170) cc_final: 0.6455 (mmm-85) REVERT: A 710 LEU cc_start: 0.8060 (tt) cc_final: 0.7774 (tt) REVERT: A 713 ASN cc_start: 0.8383 (p0) cc_final: 0.7493 (p0) REVERT: A 728 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7075 (pm20) REVERT: A 753 PHE cc_start: 0.8604 (m-80) cc_final: 0.8116 (m-10) REVERT: A 756 ASN cc_start: 0.8365 (m-40) cc_final: 0.8123 (m-40) REVERT: A 760 GLN cc_start: 0.6511 (pt0) cc_final: 0.6229 (pm20) REVERT: A 786 MET cc_start: 0.7646 (ptp) cc_final: 0.7031 (ptp) REVERT: A 854 PHE cc_start: 0.8438 (m-80) cc_final: 0.6668 (m-80) REVERT: A 874 ILE cc_start: 0.9409 (mt) cc_final: 0.9156 (mm) REVERT: A 880 THR cc_start: 0.8934 (p) cc_final: 0.8675 (p) REVERT: A 965 PRO cc_start: 0.8979 (Cg_endo) cc_final: 0.8750 (Cg_endo) REVERT: A 1002 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7890 (mmtt) REVERT: A 1011 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8646 (mtpp) REVERT: A 1017 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6623 (tt0) REVERT: A 1074 LYS cc_start: 0.8174 (mttt) cc_final: 0.7657 (mtpt) REVERT: A 1081 GLU cc_start: 0.7944 (tt0) cc_final: 0.7506 (tp30) REVERT: A 1083 VAL cc_start: 0.7237 (m) cc_final: 0.6998 (p) REVERT: A 1144 MET cc_start: 0.8614 (ptm) cc_final: 0.8329 (ptm) REVERT: A 1157 TYR cc_start: 0.8453 (m-80) cc_final: 0.8012 (m-10) REVERT: A 1168 LYS cc_start: 0.8558 (pttp) cc_final: 0.8055 (mtmm) REVERT: A 1178 VAL cc_start: 0.7756 (m) cc_final: 0.7556 (m) REVERT: A 1189 ASP cc_start: 0.8051 (m-30) cc_final: 0.7717 (m-30) REVERT: A 1228 MET cc_start: 0.8501 (tmm) cc_final: 0.8164 (ptm) REVERT: A 1279 ARG cc_start: 0.7570 (mtt-85) cc_final: 0.7140 (mtp85) REVERT: A 1281 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8268 (pp) REVERT: A 1347 GLU cc_start: 0.8249 (tp30) cc_final: 0.7921 (tp30) REVERT: A 1353 LEU cc_start: 0.8678 (mp) cc_final: 0.8413 (mt) REVERT: B 31 ARG cc_start: 0.7503 (ptt-90) cc_final: 0.7165 (ptt-90) REVERT: B 48 ARG cc_start: 0.6675 (mtt90) cc_final: 0.6412 (mtm-85) REVERT: B 63 ASN cc_start: 0.7602 (t0) cc_final: 0.7303 (m110) REVERT: B 68 ARG cc_start: 0.7223 (mtt-85) cc_final: 0.6400 (mmm160) REVERT: B 72 ARG cc_start: 0.6608 (mtm-85) cc_final: 0.6315 (mtp180) REVERT: B 79 ASP cc_start: 0.7789 (t70) cc_final: 0.6995 (t70) REVERT: B 86 GLU cc_start: 0.8048 (tt0) cc_final: 0.7419 (tt0) REVERT: B 91 LYS cc_start: 0.6332 (mttt) cc_final: 0.5951 (mttp) REVERT: D 56 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8562 (mm-30) REVERT: D 58 GLU cc_start: 0.7375 (tm-30) cc_final: 0.7002 (tm-30) REVERT: D 99 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8007 (mm) REVERT: D 132 GLN cc_start: 0.6871 (tt0) cc_final: 0.6462 (tm-30) REVERT: D 158 MET cc_start: 0.8329 (ptt) cc_final: 0.8039 (ptp) REVERT: D 163 GLN cc_start: 0.8343 (mt0) cc_final: 0.7888 (mt0) REVERT: D 168 MET cc_start: 0.7139 (ptp) cc_final: 0.6852 (pmm) REVERT: D 183 MET cc_start: 0.8410 (mmp) cc_final: 0.7821 (mmp) REVERT: D 200 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8758 (tt) REVERT: D 201 LEU cc_start: 0.8204 (mp) cc_final: 0.7953 (mt) REVERT: D 273 LYS cc_start: 0.8470 (mmpt) cc_final: 0.7884 (mtpt) REVERT: D 275 ASN cc_start: 0.8173 (m-40) cc_final: 0.7856 (t0) REVERT: D 283 ASP cc_start: 0.6885 (t70) cc_final: 0.6486 (t70) REVERT: D 297 GLU cc_start: 0.8713 (pt0) cc_final: 0.7658 (tt0) REVERT: D 308 MET cc_start: 0.7995 (tpp) cc_final: 0.7607 (tpp) REVERT: D 316 ASN cc_start: 0.8296 (m110) cc_final: 0.7710 (m-40) REVERT: D 328 SER cc_start: 0.8363 (m) cc_final: 0.7847 (p) REVERT: D 337 ASN cc_start: 0.7673 (m-40) cc_final: 0.7372 (t0) REVERT: D 340 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6647 (mm-30) REVERT: D 357 SER cc_start: 0.9262 (t) cc_final: 0.8586 (m) REVERT: D 359 ASN cc_start: 0.8391 (p0) cc_final: 0.8090 (p0) REVERT: D 370 LYS cc_start: 0.7389 (ptpt) cc_final: 0.6585 (mtpp) outliers start: 90 outliers final: 37 residues processed: 465 average time/residue: 0.2686 time to fit residues: 179.4538 Evaluate side-chains 398 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 350 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 1011 LYS Chi-restraints excluded: chain A residue 1036 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1185 PHE Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1224 ASN Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1312 VAL Chi-restraints excluded: chain B residue 5 HIS Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 344 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 0.2980 chunk 128 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN ** A 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN A1148 GLN ** A1246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN D 205 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13982 Z= 0.265 Angle : 0.674 11.678 18937 Z= 0.342 Chirality : 0.048 0.194 2144 Planarity : 0.004 0.047 2412 Dihedral : 6.937 56.531 1884 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.95 % Favored : 91.81 % Rotamer: Outliers : 6.93 % Allowed : 19.57 % Favored : 73.49 % 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: -2.96 (0.19), residues: 1686 helix: -1.55 (0.45), residues: 108 sheet: -2.00 (0.19), residues: 574 loop : -2.01 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 237 HIS 0.007 0.001 HIS A 660 PHE 0.016 0.002 PHE A 135 TYR 0.015 0.002 TYR D 358 ARG 0.005 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3372 Ramachandran restraints generated. 1686 Oldfield, 0 Emsley, 1686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 382 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8338 (mp) cc_final: 0.8088 (mt) REVERT: A 47 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7582 (mmtp) REVERT: A 55 LYS cc_start: 0.8305 (tttt) cc_final: 0.7603 (ttpt) REVERT: A 65 LEU cc_start: 0.9066 (mp) cc_final: 0.8670 (pp) REVERT: A 73 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7764 (pt) REVERT: A 75 CYS cc_start: 0.8900 (m) cc_final: 0.8596 (t) REVERT: A 110 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7938 (mttm) REVERT: A 125 MET cc_start: 0.8586 (mmm) cc_final: 0.8165 (mmm) REVERT: A 129 SER cc_start: 0.7818 (m) cc_final: 0.7276 (p) REVERT: A 201 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8450 (pp) REVERT: A 205 GLU cc_start: 0.8029 (tt0) cc_final: 0.7491 (tp30) REVERT: A 235 LEU cc_start: 0.9425 (mt) cc_final: 0.9098 (mt) REVERT: A 265 LYS cc_start: 0.7673 (mttt) cc_final: 0.7429 (tttt) REVERT: A 334 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7157 (mp0) REVERT: A 336 MET cc_start: 0.8007 (ptt) cc_final: 0.7594 (ptp) REVERT: A 360 ASP cc_start: 0.6820 (m-30) cc_final: 0.6555 (p0) REVERT: A 366 MET cc_start: 0.8825 (mtp) cc_final: 0.8605 (mtp) REVERT: A 378 GLU cc_start: 0.6845 (tp30) cc_final: 0.6620 (tp30) REVERT: A 518 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8148 (mtmt) REVERT: A 520 SER cc_start: 0.7692 (OUTLIER) cc_final: 0.7390 (m) REVERT: A 527 LYS cc_start: 0.6929 (mmtp) cc_final: 0.6550 (mmtm) REVERT: A 536 GLU cc_start: 0.8532 (tm-30) cc_final: 0.7698 (tt0) REVERT: A 542 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8817 (p) REVERT: A 564 LEU cc_start: 0.7878 (tp) cc_final: 0.7573 (mt) REVERT: A 606 LYS cc_start: 0.7247 (pttp) cc_final: 0.6914 (ptpt) REVERT: A 624 MET cc_start: 0.8644 (mmt) cc_final: 0.8365 (mmt) REVERT: A 640 TYR cc_start: 0.7709 (m-80) cc_final: 0.7400 (m-80) REVERT: A 643 ASP cc_start: 0.6713 (t70) cc_final: 0.6433 (t0) REVERT: A 647 ARG cc_start: 0.6388 (ptt-90) cc_final: 0.5871 (ptm160) REVERT: A 653 LYS cc_start: 0.8412 (pttp) cc_final: 0.7699 (tmtt) REVERT: A 655 ASP cc_start: 0.6515 (t70) cc_final: 0.6073 (t70) REVERT: A 688 ARG cc_start: 0.6772 (tpt170) cc_final: 0.6497 (mmm-85) REVERT: A 711 LYS cc_start: 0.7177 (tttt) cc_final: 0.6488 (ttpp) REVERT: A 713 ASN cc_start: 0.8474 (p0) cc_final: 0.7616 (p0) REVERT: A 714 MET cc_start: 0.8533 (ptt) cc_final: 0.8200 (ptt) REVERT: A 728 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: A 753 PHE cc_start: 0.8593 (m-80) cc_final: 0.8185 (m-10) REVERT: A 760 GLN cc_start: 0.6643 (pt0) cc_final: 0.6311 (pm20) REVERT: A 786 MET cc_start: 0.7738 (ptp) cc_final: 0.7171 (ptp) REVERT: A 939 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6679 (p0) REVERT: A 1002 LYS cc_start: 0.8341 (mtmt) cc_final: 0.7765 (mmtt) REVERT: A 1074 LYS cc_start: 0.8102 (mttt) cc_final: 0.7622 (mtpt) REVERT: A 1081 GLU cc_start: 0.7938 (tt0) cc_final: 0.7496 (tp30) REVERT: A 1083 VAL cc_start: 0.7327 (m) cc_final: 0.6984 (p) REVERT: A 1130 ASP cc_start: 0.8009 (t0) cc_final: 0.7603 (m-30) REVERT: A 1144 MET cc_start: 0.8602 (ptm) cc_final: 0.8247 (ptm) REVERT: A 1157 TYR cc_start: 0.8519 (m-80) cc_final: 0.8115 (m-10) REVERT: A 1162 LEU cc_start: 0.8744 (mt) cc_final: 0.8523 (mt) REVERT: A 1168 LYS cc_start: 0.8581 (pttp) cc_final: 0.8110 (mtmm) REVERT: A 1182 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6881 (t0) REVERT: A 1189 ASP cc_start: 0.7927 (m-30) cc_final: 0.7547 (m-30) REVERT: A 1222 SER cc_start: 0.8706 (t) cc_final: 0.8452 (m) REVERT: A 1233 ASN cc_start: 0.7714 (t0) cc_final: 0.7351 (t0) REVERT: A 1250 GLN cc_start: 0.8775 (mm110) cc_final: 0.7959 (mt0) REVERT: A 1279 ARG cc_start: 0.7450 (mtt-85) cc_final: 0.7047 (mtp85) REVERT: A 1281 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8299 (pp) REVERT: A 1295 ASN cc_start: 0.7128 (t0) cc_final: 0.6700 (m110) REVERT: A 1321 ILE cc_start: 0.7786 (tt) cc_final: 0.7574 (tp) REVERT: A 1347 GLU cc_start: 0.8127 (tp30) cc_final: 0.7844 (tp30) REVERT: B 31 ARG cc_start: 0.7783 (ptt-90) cc_final: 0.7549 (ptt-90) REVERT: B 48 ARG cc_start: 0.6686 (mtt90) cc_final: 0.6377 (mtm-85) REVERT: B 63 ASN cc_start: 0.7612 (t0) cc_final: 0.7288 (m110) REVERT: B 68 ARG cc_start: 0.7344 (mtt-85) cc_final: 0.6388 (mmm160) REVERT: B 72 ARG cc_start: 0.6775 (mtm-85) cc_final: 0.6406 (mtp180) REVERT: B 79 ASP cc_start: 0.7864 (t70) cc_final: 0.7053 (t70) REVERT: B 86 GLU cc_start: 0.8120 (tt0) cc_final: 0.7526 (tt0) REVERT: D 58 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6943 (tm-30) REVERT: D 106 ARG cc_start: 0.8306 (ttp80) cc_final: 0.8088 (ttp80) REVERT: D 132 GLN cc_start: 0.6865 (tt0) cc_final: 0.6441 (tm-30) REVERT: D 163 GLN cc_start: 0.8408 (mt0) cc_final: 0.7881 (mt0) REVERT: D 168 MET cc_start: 0.7555 (ptp) cc_final: 0.7119 (tmm) REVERT: D 183 MET cc_start: 0.8348 (mmp) cc_final: 0.7998 (mpp) REVERT: D 200 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8735 (tt) REVERT: D 201 LEU cc_start: 0.8119 (mp) cc_final: 0.7784 (mt) REVERT: D 273 LYS cc_start: 0.8530 (mmpt) cc_final: 0.7908 (mtpt) REVERT: D 283 ASP cc_start: 0.7123 (t70) cc_final: 0.6758 (t70) REVERT: D 297 GLU cc_start: 0.8760 (pt0) cc_final: 0.7620 (tt0) REVERT: D 328 SER cc_start: 0.8626 (m) cc_final: 0.7971 (p) REVERT: D 337 ASN cc_start: 0.7463 (m-40) cc_final: 0.7096 (t0) REVERT: D 340 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6710 (mm-30) REVERT: D 359 ASN cc_start: 0.8282 (p0) cc_final: 0.7933 (p0) REVERT: D 370 LYS cc_start: 0.7513 (ptpt) cc_final: 0.6724 (mtpp) REVERT: D 388 TYR cc_start: 0.6196 (m-80) cc_final: 0.5632 (m-80) outliers start: 107 outliers final: 58 residues processed: 446 average time/residue: 0.2544 time to fit residues: 165.8137 Evaluate side-chains 406 residues out of total 1557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 338 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASN Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 691 LEU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 792 HIS Chi-restraints excluded: chain A residue 822 TYR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 826 THR Chi-restraints excluded: chain A residue 879 SER Chi-restraints excluded: chain A residue 915 THR Chi-restraints excluded: chain A residue 917 THR Chi-restraints excluded: chain A residue 939 ASP Chi-restraints excluded: chain A residue 955 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 994 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1037 ILE Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1099 ILE Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1133 SER Chi-restraints excluded: chain A residue 1173 SER Chi-restraints excluded: chain A residue 1177 LEU Chi-restraints excluded: chain A residue 1182 ASP Chi-restraints excluded: chain A residue 1185 PHE Chi-restraints excluded: chain A residue 1213 VAL Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1281 LEU Chi-restraints excluded: chain A residue 1312 VAL Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 144 SER Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 211 GLN Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 286 CYS Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 352 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 69.8938 > 50: distance: 59 - 64: 35.829 distance: 64 - 65: 23.831 distance: 64 - 187: 32.955 distance: 65 - 66: 47.304 distance: 65 - 68: 47.165 distance: 66 - 67: 40.279 distance: 66 - 72: 45.910 distance: 67 - 184: 36.054 distance: 68 - 69: 33.544 distance: 69 - 70: 31.203 distance: 69 - 71: 31.753 distance: 72 - 73: 47.483 distance: 73 - 74: 11.852 distance: 73 - 76: 45.678 distance: 74 - 75: 28.782 distance: 74 - 80: 33.143 distance: 76 - 77: 13.147 distance: 76 - 78: 10.211 distance: 77 - 79: 22.227 distance: 80 - 81: 34.272 distance: 81 - 82: 19.386 distance: 81 - 84: 12.531 distance: 82 - 83: 57.657 distance: 82 - 89: 27.719 distance: 83 - 172: 33.868 distance: 84 - 85: 50.185 distance: 85 - 86: 17.802 distance: 86 - 87: 35.941 distance: 86 - 88: 32.133 distance: 89 - 90: 23.960 distance: 90 - 91: 42.060 distance: 90 - 93: 60.584 distance: 91 - 100: 39.033 distance: 93 - 94: 54.860 distance: 94 - 95: 48.704 distance: 94 - 96: 40.022 distance: 95 - 97: 51.270 distance: 96 - 98: 49.440 distance: 97 - 99: 20.870 distance: 98 - 99: 5.947 distance: 100 - 101: 41.343 distance: 100 - 162: 32.087 distance: 101 - 102: 39.419 distance: 101 - 104: 39.065 distance: 102 - 103: 56.190 distance: 102 - 108: 57.005 distance: 104 - 105: 41.036 distance: 105 - 106: 38.724 distance: 105 - 107: 59.510 distance: 108 - 109: 68.243 distance: 109 - 110: 40.017 distance: 109 - 112: 40.466 distance: 110 - 111: 22.240 distance: 110 - 117: 69.574 distance: 112 - 113: 56.945 distance: 113 - 114: 39.853 distance: 114 - 115: 16.070 distance: 115 - 116: 49.229 distance: 118 - 119: 45.640 distance: 118 - 121: 39.291 distance: 119 - 120: 57.637 distance: 119 - 125: 13.653 distance: 121 - 122: 25.760 distance: 122 - 123: 13.554 distance: 122 - 124: 14.270 distance: 125 - 126: 23.865 distance: 126 - 127: 59.818 distance: 126 - 129: 57.690 distance: 127 - 128: 4.245 distance: 127 - 136: 54.023 distance: 129 - 130: 7.943 distance: 130 - 131: 22.155 distance: 130 - 132: 40.431 distance: 131 - 133: 47.401 distance: 134 - 135: 56.764 distance: 136 - 137: 47.958 distance: 137 - 138: 44.143 distance: 137 - 140: 38.778 distance: 138 - 139: 44.936 distance: 138 - 143: 27.095 distance: 140 - 141: 39.726 distance: 140 - 142: 43.805 distance: 143 - 144: 29.056 distance: 144 - 145: 30.289 distance: 144 - 147: 26.451 distance: 145 - 146: 40.975 distance: 145 - 152: 29.986 distance: 147 - 148: 34.012 distance: 148 - 149: 33.267 distance: 149 - 150: 56.301 distance: 150 - 151: 56.735