Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 9 04:05:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1q_26303/05_2023/7u1q_26303_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1q_26303/05_2023/7u1q_26303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1q_26303/05_2023/7u1q_26303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1q_26303/05_2023/7u1q_26303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1q_26303/05_2023/7u1q_26303_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1q_26303/05_2023/7u1q_26303_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians K 1 8.98 5 P 31 5.49 5 S 112 5.16 5 C 13591 2.51 5 N 3557 2.21 5 O 3721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 21013 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2608 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 69} Link IDs: {'PTRANS': 16, 'TRANS': 344} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 157 Chain: "B" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2511 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 13, 'TRANS': 319} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 10, 'HIS:plan': 1, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 2461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2461 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 13, 'TRANS': 318} Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2512 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 317} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 2, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 67 Chain: "E" Number of atoms: 10040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1434, 10040 Classifications: {'peptide': 1434} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 371} Link IDs: {'PTRANS': 48, 'TRANS': 1385} Chain breaks: 4 Unresolved non-hydrogen bonds: 1306 Unresolved non-hydrogen angles: 1637 Unresolved non-hydrogen dihedrals: 1045 Unresolved non-hydrogen chiralities: 132 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 34, 'TYR:plan': 5, 'ASN:plan1': 7, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 18, 'GLU:plan': 37, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 696 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 122 Unusual residues: {' K': 1, 'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 368 Unusual residues: {'ATP': 1, 'BJX': 1, 'POV': 1, 'PTY': 5} Classifications: {'peptide': 2, 'undetermined': 8} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 11.63, per 1000 atoms: 0.55 Number of scatterers: 21013 At special positions: 0 Unit cell: (164.065, 104.5, 144.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 1 19.00 S 112 16.00 P 31 15.00 O 3721 8.00 N 3557 7.00 C 13591 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN E 10 " Time building additional restraints: 9.46 Conformation dependent library (CDL) restraints added in 3.4 seconds 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 21 sheets defined 48.1% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 23 through 29 removed outlier: 3.911A pdb=" N ARG A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.651A pdb=" N VAL A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 96 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 Processing helix chain 'A' and resid 175 through 180 removed outlier: 4.028A pdb=" N GLU A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 175 through 180' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'B' and resid 54 through 57 No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 68 through 97 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 143 through 171 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 346 through 361 Processing helix chain 'C' and resid 54 through 57 No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 68 through 97 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 171 Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 266 through 269 removed outlier: 4.044A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 269' Processing helix chain 'C' and resid 272 through 274 No H-bonds generated for 'chain 'C' and resid 272 through 274' Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 346 through 360 Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 68 through 97 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 143 through 171 Processing helix chain 'D' and resid 175 through 180 removed outlier: 3.623A pdb=" N GLU D 179 " --> pdb=" O HIS D 175 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 175 through 180' Processing helix chain 'D' and resid 266 through 269 removed outlier: 4.135A pdb=" N ASP D 269 " --> pdb=" O PRO D 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 269' Processing helix chain 'D' and resid 272 through 274 No H-bonds generated for 'chain 'D' and resid 272 through 274' Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'E' and resid 9 through 12 No H-bonds generated for 'chain 'E' and resid 9 through 12' Processing helix chain 'E' and resid 21 through 23 No H-bonds generated for 'chain 'E' and resid 21 through 23' Processing helix chain 'E' and resid 27 through 56 Proline residue: E 35 - end of helix removed outlier: 4.025A pdb=" N PHE E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Proline residue: E 45 - end of helix removed outlier: 3.688A pdb=" N SER E 55 " --> pdb=" O TRP E 51 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 98 removed outlier: 4.086A pdb=" N VAL E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY E 97 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 108 through 129 removed outlier: 3.743A pdb=" N MET E 115 " --> pdb=" O GLY E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 159 removed outlier: 3.656A pdb=" N ILE E 137 " --> pdb=" O LYS E 134 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA E 138 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 193 removed outlier: 3.855A pdb=" N ILE E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 211 No H-bonds generated for 'chain 'E' and resid 208 through 211' Processing helix chain 'E' and resid 224 through 226 No H-bonds generated for 'chain 'E' and resid 224 through 226' Processing helix chain 'E' and resid 231 through 242 removed outlier: 3.937A pdb=" N ALA E 235 " --> pdb=" O TRP E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 276 Processing helix chain 'E' and resid 284 through 327 removed outlier: 5.654A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLY E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Proline residue: E 317 - end of helix Processing helix chain 'E' and resid 348 through 352 removed outlier: 3.895A pdb=" N LEU E 352 " --> pdb=" O SER E 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 348 through 352' Processing helix chain 'E' and resid 355 through 400 removed outlier: 4.476A pdb=" N GLN E 374 " --> pdb=" O ARG E 370 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR E 396 " --> pdb=" O GLN E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 455 removed outlier: 3.998A pdb=" N THR E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) Proline residue: E 436 - end of helix removed outlier: 3.697A pdb=" N TRP E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) Proline residue: E 442 - end of helix Processing helix chain 'E' and resid 458 through 511 Proline residue: E 472 - end of helix removed outlier: 3.784A pdb=" N GLY E 505 " --> pdb=" O GLU E 501 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET E 506 " --> pdb=" O MET E 502 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LYS E 507 " --> pdb=" O LEU E 503 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU E 508 " --> pdb=" O ARG E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 563 Proline residue: E 551 - end of helix Processing helix chain 'E' and resid 573 through 615 removed outlier: 3.842A pdb=" N ALA E 578 " --> pdb=" O SER E 574 " (cutoff:3.500A) Proline residue: E 589 - end of helix removed outlier: 3.886A pdb=" N LEU E 592 " --> pdb=" O THR E 588 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER E 594 " --> pdb=" O LEU E 590 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER E 595 " --> pdb=" O PHE E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 727 Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 796 through 805 Processing helix chain 'E' and resid 808 through 811 No H-bonds generated for 'chain 'E' and resid 808 through 811' Processing helix chain 'E' and resid 818 through 820 No H-bonds generated for 'chain 'E' and resid 818 through 820' Processing helix chain 'E' and resid 832 through 846 removed outlier: 4.267A pdb=" N GLN E 846 " --> pdb=" O ARG E 842 " (cutoff:3.500A) Processing helix chain 'E' and resid 863 through 879 removed outlier: 3.697A pdb=" N ASP E 879 " --> pdb=" O GLU E 875 " (cutoff:3.500A) Processing helix chain 'E' and resid 914 through 920 Processing helix chain 'E' and resid 987 through 992 Processing helix chain 'E' and resid 997 through 1008 removed outlier: 3.723A pdb=" N SER E1006 " --> pdb=" O THR E1002 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER E1007 " --> pdb=" O LYS E1003 " (cutoff:3.500A) Processing helix chain 'E' and resid 1012 through 1041 removed outlier: 3.954A pdb=" N PHE E1018 " --> pdb=" O SER E1014 " (cutoff:3.500A) Processing helix chain 'E' and resid 1065 through 1106 Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1120 through 1134 removed outlier: 4.557A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1136 through 1160 Processing helix chain 'E' and resid 1162 through 1209 removed outlier: 3.619A pdb=" N LEU E1165 " --> pdb=" O PRO E1162 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU E1169 " --> pdb=" O VAL E1166 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 4.174A pdb=" N ARG E1187 " --> pdb=" O VAL E1184 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU E1198 " --> pdb=" O THR E1195 " (cutoff:3.500A) Proline residue: E1199 - end of helix Processing helix chain 'E' and resid 1211 through 1216 Processing helix chain 'E' and resid 1220 through 1274 Processing helix chain 'E' and resid 1278 through 1320 removed outlier: 4.166A pdb=" N MET E1290 " --> pdb=" O THR E1286 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASN E1293 " --> pdb=" O LEU E1289 " (cutoff:3.500A) Processing helix chain 'E' and resid 1381 through 1392 removed outlier: 4.321A pdb=" N LYS E1385 " --> pdb=" O THR E1381 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER E1386 " --> pdb=" O GLY E1382 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER E1387 " --> pdb=" O SER E1383 " (cutoff:3.500A) Processing helix chain 'E' and resid 1410 through 1412 No H-bonds generated for 'chain 'E' and resid 1410 through 1412' Processing helix chain 'E' and resid 1415 through 1418 No H-bonds generated for 'chain 'E' and resid 1415 through 1418' Processing helix chain 'E' and resid 1436 through 1440 Processing helix chain 'E' and resid 1451 through 1457 Processing helix chain 'E' and resid 1461 through 1465 removed outlier: 4.010A pdb=" N LYS E1465 " --> pdb=" O LYS E1461 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1461 through 1465' Processing helix chain 'E' and resid 1486 through 1497 Processing helix chain 'E' and resid 1513 through 1529 Processing helix chain 'E' and resid 1540 through 1544 Processing helix chain 'E' and resid 1564 through 1569 removed outlier: 3.618A pdb=" N SER E1568 " --> pdb=" O GLU E1564 " (cutoff:3.500A) Processing helix chain 'E' and resid 1571 through 1577 removed outlier: 4.087A pdb=" N PHE E1577 " --> pdb=" O VAL E1573 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 189 through 192 Processing sheet with id= C, first strand: chain 'A' and resid 214 through 219 Processing sheet with id= D, first strand: chain 'A' and resid 287 through 290 removed outlier: 3.716A pdb=" N LEU A 287 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= F, first strand: chain 'A' and resid 319 through 321 Processing sheet with id= G, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= H, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.740A pdb=" N ARG B 195 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 282 through 288 Processing sheet with id= J, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= K, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= L, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.334A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 195 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 219 through 221 Processing sheet with id= N, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= O, first strand: chain 'C' and resid 319 through 321 Processing sheet with id= P, first strand: chain 'D' and resid 189 through 191 Processing sheet with id= Q, first strand: chain 'D' and resid 283 through 288 removed outlier: 3.913A pdb=" N THR D 214 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= S, first strand: chain 'D' and resid 319 through 321 Processing sheet with id= T, first strand: chain 'E' and resid 685 through 687 removed outlier: 6.503A pdb=" N THR E 687 " --> pdb=" O LYS E 732 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LYS E 732 " --> pdb=" O THR E 687 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 1551 through 1553 removed outlier: 5.502A pdb=" N LYS E1553 " --> pdb=" O ILE E1557 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE E1557 " --> pdb=" O LYS E1553 " (cutoff:3.500A) 1004 hydrogen bonds defined for protein. 2787 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: 6.71 Time building geometry restraints manager: 9.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3459 1.32 - 1.45: 5455 1.45 - 1.57: 12296 1.57 - 1.69: 59 1.69 - 1.81: 174 Bond restraints: 21443 Sorted by residual: bond pdb=" C16 BJX E1603 " pdb=" N1 BJX E1603 " ideal model delta sigma weight residual 1.344 1.478 -0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" N BJX E1603 " pdb=" C6 BJX E1603 " ideal model delta sigma weight residual 1.412 1.509 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C5 BJX E1603 " pdb=" N1 BJX E1603 " ideal model delta sigma weight residual 1.446 1.542 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C5 BJX E1603 " pdb=" C7 BJX E1603 " ideal model delta sigma weight residual 1.518 1.607 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C21 BJX E1603 " pdb=" O1 BJX E1603 " ideal model delta sigma weight residual 1.347 1.425 -0.078 2.00e-02 2.50e+03 1.53e+01 ... (remaining 21438 not shown) Histogram of bond angle deviations from ideal: 92.91 - 102.31: 92 102.31 - 111.72: 11051 111.72 - 121.12: 12365 121.12 - 130.53: 5578 130.53 - 139.93: 136 Bond angle restraints: 29222 Sorted by residual: angle pdb=" C17 BJX E1603 " pdb=" C16 BJX E1603 " pdb=" N1 BJX E1603 " ideal model delta sigma weight residual 113.90 122.77 -8.87 3.00e+00 1.11e-01 8.75e+00 angle pdb=" C16 BJX E1603 " pdb=" N1 BJX E1603 " pdb=" C5 BJX E1603 " ideal model delta sigma weight residual 123.13 131.64 -8.51 3.00e+00 1.11e-01 8.04e+00 angle pdb=" N GLN E 219 " pdb=" CA GLN E 219 " pdb=" C GLN E 219 " ideal model delta sigma weight residual 109.81 115.50 -5.69 2.21e+00 2.05e-01 6.63e+00 angle pdb=" CA LEU A 191 " pdb=" CB LEU A 191 " pdb=" CG LEU A 191 " ideal model delta sigma weight residual 116.30 124.72 -8.42 3.50e+00 8.16e-02 5.79e+00 angle pdb=" O2 BJX E1603 " pdb=" C24 BJX E1603 " pdb=" O3 BJX E1603 " ideal model delta sigma weight residual 126.98 119.81 7.17 3.00e+00 1.11e-01 5.71e+00 ... (remaining 29217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.56: 12280 32.56 - 65.12: 221 65.12 - 97.67: 20 97.67 - 130.23: 3 130.23 - 162.79: 7 Dihedral angle restraints: 12531 sinusoidal: 4425 harmonic: 8106 Sorted by residual: dihedral pdb=" C41 P5S A 403 " pdb=" C42 P5S A 403 " pdb=" C43 P5S A 403 " pdb=" C44 P5S A 403 " ideal model delta sinusoidal sigma weight residual 181.47 18.68 162.79 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O BJX E1603 " pdb=" C16 BJX E1603 " pdb=" C17 BJX E1603 " pdb=" C18 BJX E1603 " ideal model delta sinusoidal sigma weight residual 10.31 -151.43 161.74 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C53 P5S E1610 " pdb=" C54 P5S E1610 " pdb=" C55 P5S E1610 " pdb=" C56 P5S E1610 " ideal model delta sinusoidal sigma weight residual 180.05 23.74 156.31 1 3.00e+01 1.11e-03 2.04e+01 ... (remaining 12528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2896 0.053 - 0.107: 516 0.107 - 0.160: 82 0.160 - 0.214: 2 0.214 - 0.267: 1 Chirality restraints: 3497 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 10 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BJX E1603 " pdb=" C7 BJX E1603 " pdb=" C8 BJX E1603 " pdb=" N1 BJX E1603 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.37 -0.16 2.00e-01 2.50e+01 6.58e-01 ... (remaining 3494 not shown) Planarity restraints: 3592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 265 " -0.039 5.00e-02 4.00e+02 5.91e-02 5.58e+00 pdb=" N PRO B 266 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 266 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 266 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 588 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO E 589 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO E 589 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 589 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E1335 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO E1336 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO E1336 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E1336 " -0.028 5.00e-02 4.00e+02 ... (remaining 3589 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 5563 2.81 - 3.39: 23843 3.39 - 3.98: 38015 3.98 - 4.56: 51475 4.56 - 5.14: 76347 Nonbonded interactions: 195243 Sorted by model distance: nonbonded pdb=" OD1 ASP C 329 " pdb=" OG SER C 331 " model vdw 2.228 2.440 nonbonded pdb=" O VAL A 138 " pdb=" NH2 ARG B 136 " model vdw 2.237 2.520 nonbonded pdb=" O SER B 116 " pdb=" OG SER B 119 " model vdw 2.241 2.440 nonbonded pdb=" NH1 ARG D 177 " pdb=" OG SER D 208 " model vdw 2.241 2.520 nonbonded pdb=" NH1 ARG B 177 " pdb=" OG SER B 208 " model vdw 2.253 2.520 ... (remaining 195238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 30 through 51 or (resid 52 and (name N or name CA or name \ C or name O or name CB )) or resid 53 or (resid 54 through 59 and (name N or nam \ e CA or name C or name O or name CB )) or resid 60 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 205 o \ r (resid 206 through 207 and (name N or name CA or name C or name O or name CB ) \ ) or resid 208 through 261 or (resid 262 through 265 and (name N or name CA or n \ ame C or name O or name CB )) or resid 266 through 285 or (resid 286 and (name N \ or name CA or name C or name O or name CB )) or resid 287 or (resid 288 and (na \ me N or name CA or name C or name O or name CB )) or resid 289 through 290 or (r \ esid 291 and (name N or name CA or name C or name O or name CB )) or resid 292 t \ hrough 320 or (resid 321 through 323 and (name N or name CA or name C or name O \ or name CB )) or resid 324 through 328 or (resid 329 and (name N or name CA or n \ ame C or name O or name CB )) or resid 330 through 331 or (resid 332 and (name N \ or name CA or name C or name O or name CB )) or resid 333 through 348 or (resid \ 349 through 360 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 51 or (resid 52 and \ (name N or name CA or name C or name O or name CB )) or resid 53 or (resid 54 th \ rough 59 and (name N or name CA or name C or name O or name CB )) or resid 60 th \ rough 64 or (resid 65 and (name N or name CA or name C or name O or name CB )) o \ r resid 66 through 98 or (resid 99 and (name N or name CA or name C or name O or \ name CB )) or resid 100 through 125 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB )) or resid 127 through 175 or (resid 176 and (name N o \ r name CA or name C or name O or name CB )) or resid 177 through 259 or (resid 2 \ 60 and (name N or name CA or name C or name O or name CB )) or resid 261 or (res \ id 262 through 265 and (name N or name CA or name C or name O or name CB )) or r \ esid 266 through 273 or (resid 274 through 275 and (name N or name CA or name C \ or name O or name CB )) or resid 276 or (resid 277 and (name N or name CA or nam \ e C or name O or name CB )) or resid 278 through 279 or (resid 280 through 281 a \ nd (name N or name CA or name C or name O or name CB )) or resid 282 through 285 \ or (resid 286 and (name N or name CA or name C or name O or name CB )) or resid \ 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) or r \ esid 289 through 290 or (resid 291 and (name N or name CA or name C or name O or \ name CB )) or resid 292 through 304 or (resid 305 through 306 and (name N or na \ me CA or name C or name O or name CB )) or resid 307 through 331 or (resid 332 a \ nd (name N or name CA or name C or name O or name CB )) or resid 333 through 335 \ or (resid 336 through 337 and (name N or name CA or name C or name O or name CB \ )) or resid 338 or (resid 339 and (name N or name CA or name C or name O or nam \ e CB )) or resid 340 or (resid 341 and (name N or name CA or name C or name O or \ name CB )) or resid 342 through 347 or (resid 348 through 360 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 58 or (resid 59 and (name N or na \ me CA or name C or name O or name CB )) or resid 60 through 98 or (resid 99 and \ (name N or name CA or name C or name O or name CB )) or resid 100 through 125 or \ (resid 126 and (name N or name CA or name C or name O or name CB )) or resid 12 \ 7 through 205 or (resid 206 through 207 and (name N or name CA or name C or name \ O or name CB )) or resid 208 through 243 or (resid 244 and (name N or name CA o \ r name C or name O or name CB )) or resid 245 through 259 or (resid 260 and (nam \ e N or name CA or name C or name O or name CB )) or resid 261 through 273 or (re \ sid 274 through 275 and (name N or name CA or name C or name O or name CB )) or \ resid 276 or (resid 277 and (name N or name CA or name C or name O or name CB )) \ or resid 278 through 279 or (resid 280 through 281 and (name N or name CA or na \ me C or name O or name CB )) or resid 282 through 304 or (resid 305 through 306 \ and (name N or name CA or name C or name O or name CB )) or resid 307 through 32 \ 0 or (resid 321 through 323 and (name N or name CA or name C or name O or name C \ B )) or resid 324 through 328 or (resid 329 and (name N or name CA or name C or \ name O or name CB )) or resid 330 through 331 or (resid 332 and (name N or name \ CA or name C or name O or name CB )) or resid 333 through 335 or (resid 336 thro \ ugh 337 and (name N or name CA or name C or name O or name CB )) or resid 338 or \ (resid 339 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 0 or (resid 341 and (name N or name CA or name C or name O or name CB )) or resi \ d 342 through 360)) selection = (chain 'D' and ((resid 30 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 46 or (resid 47 and (name N or na \ me CA or name C or name O or name CB )) or resid 48 through 50 or (resid 51 thro \ ugh 52 and (name N or name CA or name C or name O or name CB )) or resid 53 or ( \ resid 54 through 59 and (name N or name CA or name C or name O or name CB )) or \ resid 60 through 125 or (resid 126 and (name N or name CA or name C or name O or \ name CB )) or resid 127 through 175 or (resid 176 and (name N or name CA or nam \ e C or name O or name CB )) or resid 177 through 205 or (resid 206 through 207 a \ nd (name N or name CA or name C or name O or name CB )) or resid 208 through 243 \ or (resid 244 and (name N or name CA or name C or name O or name CB )) or resid \ 245 through 258 or (resid 259 through 260 and (name N or name CA or name C or n \ ame O or name CB )) or resid 261 or (resid 262 through 265 and (name N or name C \ A or name C or name O or name CB )) or resid 266 through 273 or (resid 274 throu \ gh 275 and (name N or name CA or name C or name O or name CB )) or resid 276 or \ (resid 277 and (name N or name CA or name C or name O or name CB )) or resid 278 \ through 279 or (resid 280 through 281 and (name N or name CA or name C or name \ O or name CB )) or resid 282 through 285 or (resid 286 and (name N or name CA or \ name C or name O or name CB )) or resid 287 or (resid 288 and (name N or name C \ A or name C or name O or name CB )) or resid 289 through 290 or (resid 291 and ( \ name N or name CA or name C or name O or name CB )) or resid 292 through 304 or \ (resid 305 through 306 and (name N or name CA or name C or name O or name CB )) \ or resid 307 through 320 or (resid 321 through 323 and (name N or name CA or nam \ e C or name O or name CB )) or resid 324 through 328 or (resid 329 and (name N o \ r name CA or name C or name O or name CB )) or resid 330 through 335 or (resid 3 \ 36 through 337 and (name N or name CA or name C or name O or name CB )) or resid \ 338 or (resid 339 and (name N or name CA or name C or name O or name CB )) or r \ esid 340 or (resid 341 and (name N or name CA or name C or name O or name CB )) \ or resid 342 through 360)) } 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.820 Check model and map are aligned: 0.370 Set scattering table: 0.190 Process input model: 56.290 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.080 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 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 : 0.003 0.134 21443 Z= 0.192 Angle : 0.543 9.895 29222 Z= 0.262 Chirality : 0.041 0.267 3497 Planarity : 0.004 0.059 3591 Dihedral : 13.667 162.788 7244 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 0.00 % 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: -1.11 (0.16), residues: 2773 helix: 0.89 (0.14), residues: 1340 sheet: -2.96 (0.30), residues: 246 loop : -2.19 (0.17), residues: 1187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 755 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 755 average time/residue: 0.3624 time to fit residues: 421.1531 Evaluate side-chains 583 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 583 time to evaluate : 2.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 0.8980 chunk 210 optimal weight: 30.0000 chunk 116 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 217 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 132 optimal weight: 1.9990 chunk 162 optimal weight: 30.0000 chunk 252 optimal weight: 20.0000 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS A 279 GLN B 173 GLN C 335 ASN D 247 ASN D 276 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN E 160 HIS E 282 GLN E 562 HIS E 584 HIS E 817 HIS E 846 GLN E1245 ASN E1416 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 21443 Z= 0.262 Angle : 0.633 11.968 29222 Z= 0.319 Chirality : 0.045 0.427 3497 Planarity : 0.005 0.053 3591 Dihedral : 13.124 172.885 3378 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 5.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.16), residues: 2773 helix: 1.18 (0.14), residues: 1354 sheet: -2.61 (0.32), residues: 230 loop : -1.97 (0.18), residues: 1189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 608 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 65 residues processed: 648 average time/residue: 0.3148 time to fit residues: 319.5397 Evaluate side-chains 632 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 567 time to evaluate : 2.358 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.2136 time to fit residues: 29.0056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 210 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 250 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS B 173 GLN B 235 GLN C 186 HIS C 335 ASN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 HIS D 299 GLN E 32 ASN E 273 GLN E1020 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.086 21443 Z= 0.355 Angle : 0.688 11.590 29222 Z= 0.345 Chirality : 0.047 0.402 3497 Planarity : 0.005 0.059 3591 Dihedral : 12.693 173.114 3378 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.16), residues: 2773 helix: 1.15 (0.14), residues: 1344 sheet: -2.62 (0.31), residues: 238 loop : -1.84 (0.18), residues: 1191 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 580 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 39 residues processed: 612 average time/residue: 0.3226 time to fit residues: 305.7829 Evaluate side-chains 602 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 563 time to evaluate : 2.146 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2025 time to fit residues: 17.2552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 169 optimal weight: 20.0000 chunk 253 optimal weight: 30.0000 chunk 268 optimal weight: 40.0000 chunk 132 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 GLN C 128 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 21443 Z= 0.220 Angle : 0.609 10.464 29222 Z= 0.302 Chirality : 0.044 0.355 3497 Planarity : 0.005 0.053 3591 Dihedral : 11.888 161.499 3378 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.16), residues: 2773 helix: 1.44 (0.14), residues: 1334 sheet: -2.30 (0.32), residues: 232 loop : -1.77 (0.18), residues: 1207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 585 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 47 residues processed: 614 average time/residue: 0.3273 time to fit residues: 313.9486 Evaluate side-chains 606 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 559 time to evaluate : 2.187 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.2040 time to fit residues: 20.9383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 200 optimal weight: 40.0000 chunk 110 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 241 optimal weight: 10.0000 chunk 67 optimal weight: 0.2980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 GLN B 313 GLN ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 21443 Z= 0.182 Angle : 0.588 10.184 29222 Z= 0.289 Chirality : 0.044 0.337 3497 Planarity : 0.004 0.054 3591 Dihedral : 11.140 155.567 3378 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2773 helix: 1.62 (0.14), residues: 1332 sheet: -1.98 (0.34), residues: 230 loop : -1.71 (0.18), residues: 1211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5546 Ramachandran restraints generated. 2773 Oldfield, 0 Emsley, 2773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 595 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 607 average time/residue: 0.3210 time to fit residues: 307.4496 Evaluate side-chains 581 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 564 time to evaluate : 2.495 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2091 time to fit residues: 10.1097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 0.0270 chunk 241 optimal weight: 10.0000 chunk 53 optimal weight: 0.1980 chunk 157 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 268 optimal weight: 30.0000 chunk 223 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 141 optimal weight: 0.0770 overall best weight: 2.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2828 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: