Starting phenix.real_space_refine on Sun Jun 30 11:41:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1q_26303/06_2024/7u1q_26303_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1q_26303/06_2024/7u1q_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_26303/06_2024/7u1q_26303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1q_26303/06_2024/7u1q_26303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1q_26303/06_2024/7u1q_26303_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u1q_26303/06_2024/7u1q_26303_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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 dihedrals: 6 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: 10.69, per 1000 atoms: 0.51 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: 8.62 Conformation dependent library (CDL) restraints added in 4.1 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: 5.05 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: 7.46 Time building geometry restraints manager: 9.46 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 - 34.77: 12482 34.77 - 69.53: 352 69.53 - 104.30: 54 104.30 - 139.06: 25 139.06 - 173.83: 23 Dihedral angle restraints: 12936 sinusoidal: 4830 harmonic: 8106 Sorted by residual: dihedral pdb=" C17 P5S D 402 " pdb=" C20 P5S D 402 " pdb=" C21 P5S D 402 " pdb=" C22 P5S D 402 " ideal model delta sinusoidal sigma weight residual 71.45 -102.38 173.83 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 P5S D 402 " pdb=" C22 P5S D 402 " pdb=" C23 P5S D 402 " pdb=" C24 P5S D 402 " ideal model delta sinusoidal sigma weight residual 295.37 122.41 172.96 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C17 P5S E1610 " pdb=" C20 P5S E1610 " pdb=" C21 P5S E1610 " pdb=" C22 P5S E1610 " ideal model delta sinusoidal sigma weight residual 71.45 -101.43 172.88 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3162 0.074 - 0.147: 325 0.147 - 0.221: 3 0.221 - 0.294: 5 0.294 - 0.368: 2 Chirality restraints: 3497 Sorted by residual: chirality pdb=" C2 P5S B 403 " pdb=" C1 P5S B 403 " pdb=" C3 P5S B 403 " pdb=" O37 P5S B 403 " both_signs ideal model delta sigma weight residual False 2.59 2.23 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C2 P5S E1610 " pdb=" C1 P5S E1610 " pdb=" C3 P5S E1610 " pdb=" O37 P5S E1610 " both_signs ideal model delta sigma weight residual False 2.59 2.29 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" C2 P5S A 403 " pdb=" C1 P5S A 403 " pdb=" C3 P5S A 403 " pdb=" O37 P5S A 403 " both_signs ideal model delta sigma weight residual False 2.59 2.33 0.27 2.00e-01 2.50e+01 1.80e+00 ... (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: 0.140 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: 1.420 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 56.810 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.820 ------------------------------------------------------------------------------- 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= 0.211 Angle : 0.580 9.895 29222 Z= 0.271 Chirality : 0.043 0.368 3497 Planarity : 0.004 0.059 3591 Dihedral : 19.076 173.828 7649 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 % Allowed : 5.84 % Favored : 94.16 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 998 HIS 0.003 0.000 HIS E1024 PHE 0.020 0.001 PHE D 168 TYR 0.016 0.001 TYR E 230 ARG 0.004 0.000 ARG E 248 *********************** 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 : 2.154 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 48 ASN cc_start: 0.8403 (m110) cc_final: 0.8120 (m110) REVERT: A 67 LYS cc_start: 0.8391 (mppt) cc_final: 0.8130 (mppt) REVERT: A 93 ILE cc_start: 0.9286 (tt) cc_final: 0.9029 (mp) REVERT: A 314 ARG cc_start: 0.7393 (ptp-170) cc_final: 0.7114 (ptm-80) REVERT: B 77 MET cc_start: 0.6654 (mmm) cc_final: 0.5964 (tmm) REVERT: B 88 MET cc_start: 0.7162 (tpp) cc_final: 0.6909 (tpp) REVERT: B 158 MET cc_start: 0.7577 (mmm) cc_final: 0.7040 (mmm) REVERT: B 180 THR cc_start: 0.8702 (p) cc_final: 0.8402 (p) REVERT: B 221 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7377 (mtp-110) REVERT: B 311 TRP cc_start: 0.8859 (t-100) cc_final: 0.8506 (t-100) REVERT: C 77 MET cc_start: 0.6759 (mmm) cc_final: 0.5943 (tmm) REVERT: C 86 PHE cc_start: 0.7928 (m-80) cc_final: 0.7383 (m-80) REVERT: D 43 ASN cc_start: 0.8733 (t0) cc_final: 0.8531 (t0) REVERT: D 67 LYS cc_start: 0.7988 (mppt) cc_final: 0.7438 (mtmt) REVERT: D 158 MET cc_start: 0.8031 (mmm) cc_final: 0.7725 (tpp) REVERT: D 240 MET cc_start: 0.8293 (ttp) cc_final: 0.8084 (ttp) REVERT: E 17 VAL cc_start: 0.8299 (m) cc_final: 0.7750 (t) REVERT: E 42 ILE cc_start: 0.8671 (tt) cc_final: 0.8437 (tt) REVERT: E 82 LEU cc_start: 0.9088 (mp) cc_final: 0.8813 (mt) REVERT: E 134 LYS cc_start: 0.8740 (mttt) cc_final: 0.8326 (mtpt) REVERT: E 158 TYR cc_start: 0.6343 (t80) cc_final: 0.5986 (t80) REVERT: E 230 TYR cc_start: 0.8596 (m-80) cc_final: 0.7672 (m-80) REVERT: E 232 TRP cc_start: 0.8494 (p-90) cc_final: 0.8257 (p-90) REVERT: E 252 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7935 (pttp) REVERT: E 264 GLN cc_start: 0.8017 (mm110) cc_final: 0.7701 (tp-100) REVERT: E 289 ARG cc_start: 0.5863 (mpt-90) cc_final: 0.5055 (tpt-90) REVERT: E 323 ILE cc_start: 0.8943 (mt) cc_final: 0.8708 (mt) REVERT: E 547 ASN cc_start: 0.8925 (t0) cc_final: 0.8695 (m-40) REVERT: E 604 LEU cc_start: 0.8797 (mt) cc_final: 0.8588 (mt) REVERT: E 708 LEU cc_start: 0.6151 (tt) cc_final: 0.5622 (mp) REVERT: E 807 SER cc_start: 0.8301 (m) cc_final: 0.7516 (p) REVERT: E 1012 LEU cc_start: 0.7117 (mt) cc_final: 0.6912 (tp) REVERT: E 1234 ASN cc_start: 0.8723 (t0) cc_final: 0.8456 (t0) outliers start: 0 outliers final: 0 residues processed: 755 average time/residue: 0.3212 time to fit residues: 373.5758 Evaluate side-chains 593 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 593 time to evaluate : 2.142 ------------------------------------------------------------------------------- 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: 0.7980 chunk 112 optimal weight: 8.9990 chunk 217 optimal weight: 30.0000 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: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 E1020 GLN E1245 ASN E1416 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 21443 Z= 0.293 Angle : 0.648 11.962 29222 Z= 0.327 Chirality : 0.046 0.444 3497 Planarity : 0.005 0.055 3591 Dihedral : 20.778 177.184 3783 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.84 % Allowed : 14.63 % Favored : 79.53 % 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: -0.70 (0.16), residues: 2773 helix: 1.17 (0.14), residues: 1353 sheet: -2.62 (0.32), residues: 230 loop : -1.99 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 83 HIS 0.008 0.001 HIS E1024 PHE 0.024 0.002 PHE C 75 TYR 0.014 0.002 TYR B 268 ARG 0.013 0.001 ARG C 192 *********************** 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 720 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 609 time to evaluate : 2.076 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 48 ASN cc_start: 0.8500 (m110) cc_final: 0.8242 (m110) REVERT: A 93 ILE cc_start: 0.9107 (tt) cc_final: 0.8898 (mp) REVERT: A 200 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8789 (tt) REVERT: A 314 ARG cc_start: 0.7377 (ptp-170) cc_final: 0.7069 (ptt90) REVERT: B 77 MET cc_start: 0.6782 (mmm) cc_final: 0.6066 (tmm) REVERT: B 88 MET cc_start: 0.7176 (tpp) cc_final: 0.6963 (tpp) REVERT: B 169 MET cc_start: 0.8042 (mtp) cc_final: 0.7601 (mtp) REVERT: B 177 ARG cc_start: 0.8213 (tpt170) cc_final: 0.7753 (tpt170) REVERT: B 311 TRP cc_start: 0.9095 (t-100) cc_final: 0.8624 (t-100) REVERT: B 313 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: B 325 ARG cc_start: 0.8450 (mtp85) cc_final: 0.7944 (mtp180) REVERT: C 77 MET cc_start: 0.6800 (mmm) cc_final: 0.5603 (tmm) REVERT: C 186 HIS cc_start: 0.7861 (OUTLIER) cc_final: 0.7563 (p-80) REVERT: C 347 ARG cc_start: 0.8710 (ttm-80) cc_final: 0.8505 (ttm-80) REVERT: D 67 LYS cc_start: 0.8073 (mppt) cc_final: 0.7507 (mtmt) REVERT: D 158 MET cc_start: 0.8065 (mmm) cc_final: 0.7824 (tpp) REVERT: D 173 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7710 (mt0) REVERT: D 240 MET cc_start: 0.8454 (ttp) cc_final: 0.8243 (ttp) REVERT: D 276 HIS cc_start: 0.7597 (p-80) cc_final: 0.7219 (p90) REVERT: E 17 VAL cc_start: 0.8418 (m) cc_final: 0.8026 (t) REVERT: E 38 PHE cc_start: 0.7616 (t80) cc_final: 0.7390 (t80) REVERT: E 39 LEU cc_start: 0.8912 (tt) cc_final: 0.8562 (tp) REVERT: E 130 SER cc_start: 0.7913 (OUTLIER) cc_final: 0.7600 (p) REVERT: E 134 LYS cc_start: 0.8790 (mttt) cc_final: 0.8318 (mtpt) REVERT: E 158 TYR cc_start: 0.6628 (t80) cc_final: 0.6143 (t80) REVERT: E 230 TYR cc_start: 0.8642 (m-80) cc_final: 0.7674 (m-80) REVERT: E 232 TRP cc_start: 0.8541 (p-90) cc_final: 0.8314 (p-90) REVERT: E 242 LYS cc_start: 0.8037 (mmtm) cc_final: 0.7697 (mmtp) REVERT: E 247 LEU cc_start: 0.9005 (mt) cc_final: 0.8722 (mt) REVERT: E 252 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8095 (pttp) REVERT: E 264 GLN cc_start: 0.8113 (mm110) cc_final: 0.7756 (tp-100) REVERT: E 265 ARG cc_start: 0.7934 (ttm110) cc_final: 0.7726 (ttm110) REVERT: E 358 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8766 (mt) REVERT: E 441 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7505 (mtm) REVERT: E 604 LEU cc_start: 0.8721 (mt) cc_final: 0.8479 (mt) REVERT: E 1073 SER cc_start: 0.8315 (m) cc_final: 0.8068 (p) REVERT: E 1154 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8096 (mm) REVERT: E 1234 ASN cc_start: 0.8734 (t0) cc_final: 0.8509 (t0) outliers start: 111 outliers final: 70 residues processed: 656 average time/residue: 0.3049 time to fit residues: 312.7095 Evaluate side-chains 644 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 567 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 519 CYS Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1271 SER Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1431 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 210 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 273 optimal weight: 50.0000 chunk 225 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 202 optimal weight: 0.4980 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN B 235 GLN B 264 ASN B 313 GLN C 335 ASN D 175 HIS D 235 GLN D 299 GLN E1416 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21443 Z= 0.261 Angle : 0.622 10.927 29222 Z= 0.311 Chirality : 0.045 0.396 3497 Planarity : 0.005 0.057 3591 Dihedral : 19.740 174.224 3783 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.84 % Allowed : 17.05 % Favored : 77.11 % 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: -0.43 (0.16), residues: 2773 helix: 1.35 (0.14), residues: 1345 sheet: -2.49 (0.33), residues: 224 loop : -1.79 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 83 HIS 0.018 0.001 HIS E1416 PHE 0.024 0.002 PHE C 95 TYR 0.017 0.002 TYR C 326 ARG 0.007 0.001 ARG E 168 *********************** 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 696 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 585 time to evaluate : 2.144 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 48 ASN cc_start: 0.8488 (m110) cc_final: 0.8186 (m110) REVERT: A 93 ILE cc_start: 0.9158 (tt) cc_final: 0.8888 (mp) REVERT: A 200 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8882 (tt) REVERT: A 292 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6311 (pp20) REVERT: B 58 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6815 (t0) REVERT: B 77 MET cc_start: 0.6812 (mmm) cc_final: 0.6071 (tmm) REVERT: B 169 MET cc_start: 0.8066 (mtp) cc_final: 0.7631 (mtp) REVERT: B 177 ARG cc_start: 0.8155 (tpt170) cc_final: 0.7685 (tpt170) REVERT: B 278 HIS cc_start: 0.7113 (m90) cc_final: 0.6814 (m90) REVERT: B 325 ARG cc_start: 0.8483 (mtp85) cc_final: 0.7744 (mtp180) REVERT: C 77 MET cc_start: 0.6781 (mmm) cc_final: 0.5768 (tmm) REVERT: C 186 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7635 (p-80) REVERT: D 67 LYS cc_start: 0.8168 (mppt) cc_final: 0.7494 (mtmt) REVERT: D 112 THR cc_start: 0.8825 (p) cc_final: 0.8523 (t) REVERT: D 152 GLN cc_start: 0.9169 (tp40) cc_final: 0.8529 (tp40) REVERT: D 173 GLN cc_start: 0.8162 (mm-40) cc_final: 0.7604 (mt0) REVERT: D 276 HIS cc_start: 0.7795 (p-80) cc_final: 0.7454 (p-80) REVERT: D 304 TYR cc_start: 0.8556 (m-80) cc_final: 0.8089 (m-10) REVERT: D 305 LEU cc_start: 0.8121 (mm) cc_final: 0.7919 (mt) REVERT: E 39 LEU cc_start: 0.8976 (tt) cc_final: 0.8763 (tp) REVERT: E 130 SER cc_start: 0.8007 (OUTLIER) cc_final: 0.7641 (p) REVERT: E 134 LYS cc_start: 0.8788 (mttt) cc_final: 0.8369 (mtpt) REVERT: E 230 TYR cc_start: 0.8620 (m-80) cc_final: 0.7646 (m-80) REVERT: E 247 LEU cc_start: 0.9001 (mt) cc_final: 0.8751 (mt) REVERT: E 252 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8047 (pttp) REVERT: E 264 GLN cc_start: 0.8027 (mm110) cc_final: 0.7722 (tp-100) REVERT: E 358 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8737 (mt) REVERT: E 604 LEU cc_start: 0.8702 (mt) cc_final: 0.8451 (mt) REVERT: E 1073 SER cc_start: 0.8273 (m) cc_final: 0.8042 (p) REVERT: E 1154 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8079 (mm) outliers start: 111 outliers final: 78 residues processed: 635 average time/residue: 0.2992 time to fit residues: 299.3868 Evaluate side-chains 639 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 554 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1103 ASN Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1196 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1271 SER Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1431 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 9.9990 chunk 190 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 169 optimal weight: 8.9990 chunk 253 optimal weight: 0.6980 chunk 268 optimal weight: 40.0000 chunk 132 optimal weight: 9.9990 chunk 240 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1197 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21443 Z= 0.211 Angle : 0.602 10.840 29222 Z= 0.295 Chirality : 0.044 0.377 3497 Planarity : 0.004 0.047 3591 Dihedral : 18.607 178.281 3783 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 6.16 % Allowed : 18.47 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2773 helix: 1.54 (0.14), residues: 1346 sheet: -2.22 (0.33), residues: 233 loop : -1.72 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 83 HIS 0.009 0.001 HIS E 36 PHE 0.024 0.001 PHE C 95 TYR 0.020 0.001 TYR E 475 ARG 0.006 0.001 ARG C 347 *********************** 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 700 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 583 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8485 (m110) cc_final: 0.8182 (m110) REVERT: A 75 PHE cc_start: 0.8173 (t80) cc_final: 0.7761 (t80) REVERT: A 200 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8790 (tt) REVERT: B 169 MET cc_start: 0.8061 (mtp) cc_final: 0.7622 (mtp) REVERT: B 177 ARG cc_start: 0.8096 (tpt170) cc_final: 0.7619 (tpt170) REVERT: B 278 HIS cc_start: 0.7127 (m90) cc_final: 0.6887 (m90) REVERT: C 77 MET cc_start: 0.6725 (mmm) cc_final: 0.5890 (tmm) REVERT: C 186 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7392 (p-80) REVERT: D 67 LYS cc_start: 0.8150 (mppt) cc_final: 0.7489 (mtmt) REVERT: D 112 THR cc_start: 0.8797 (p) cc_final: 0.8550 (t) REVERT: D 152 GLN cc_start: 0.9178 (tp40) cc_final: 0.8486 (tp40) REVERT: D 173 GLN cc_start: 0.8240 (mm-40) cc_final: 0.7641 (mt0) REVERT: D 177 ARG cc_start: 0.8357 (tpt170) cc_final: 0.8115 (tpt170) REVERT: D 304 TYR cc_start: 0.8499 (m-80) cc_final: 0.8042 (m-10) REVERT: D 307 ASP cc_start: 0.8470 (p0) cc_final: 0.8112 (p0) REVERT: E 130 SER cc_start: 0.7964 (OUTLIER) cc_final: 0.7562 (p) REVERT: E 134 LYS cc_start: 0.8771 (mttt) cc_final: 0.8569 (mttm) REVERT: E 158 TYR cc_start: 0.6494 (t80) cc_final: 0.6108 (t80) REVERT: E 230 TYR cc_start: 0.8536 (m-80) cc_final: 0.7600 (m-80) REVERT: E 247 LEU cc_start: 0.8953 (mt) cc_final: 0.8703 (mt) REVERT: E 252 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7898 (pttp) REVERT: E 264 GLN cc_start: 0.8004 (mm110) cc_final: 0.7680 (tp-100) REVERT: E 358 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8665 (mt) REVERT: E 604 LEU cc_start: 0.8667 (mt) cc_final: 0.8426 (mt) REVERT: E 1095 LYS cc_start: 0.7248 (tttp) cc_final: 0.6791 (ttpt) REVERT: E 1154 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8020 (mm) outliers start: 117 outliers final: 85 residues processed: 640 average time/residue: 0.3003 time to fit residues: 301.9285 Evaluate side-chains 642 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 552 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1038 THR Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1196 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1269 SER Chi-restraints excluded: chain E residue 1271 SER Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1431 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 200 optimal weight: 30.0000 chunk 110 optimal weight: 0.0980 chunk 229 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN B 313 GLN C 186 HIS ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 21443 Z= 0.325 Angle : 0.665 10.410 29222 Z= 0.331 Chirality : 0.046 0.386 3497 Planarity : 0.005 0.053 3591 Dihedral : 18.096 178.590 3783 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 7.11 % Allowed : 18.58 % Favored : 74.32 % 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: -0.33 (0.16), residues: 2773 helix: 1.43 (0.14), residues: 1342 sheet: -2.27 (0.33), residues: 240 loop : -1.75 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 83 HIS 0.020 0.001 HIS C 186 PHE 0.025 0.002 PHE C 95 TYR 0.019 0.002 TYR E 772 ARG 0.005 0.001 ARG E1300 *********************** 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 695 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 560 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7202 (mtt-85) cc_final: 0.6978 (mtt-85) REVERT: A 48 ASN cc_start: 0.8492 (m110) cc_final: 0.8257 (m110) REVERT: A 75 PHE cc_start: 0.8196 (t80) cc_final: 0.7925 (t80) REVERT: A 325 ARG cc_start: 0.7761 (ptm-80) cc_final: 0.7443 (ptm-80) REVERT: B 169 MET cc_start: 0.8130 (mtp) cc_final: 0.7659 (mtp) REVERT: B 177 ARG cc_start: 0.8084 (tpt170) cc_final: 0.7571 (tpt170) REVERT: B 325 ARG cc_start: 0.8529 (mtp180) cc_final: 0.7801 (mtp180) REVERT: C 37 SER cc_start: 0.9037 (t) cc_final: 0.8641 (m) REVERT: C 77 MET cc_start: 0.6894 (mmm) cc_final: 0.5809 (tmm) REVERT: D 67 LYS cc_start: 0.8188 (mppt) cc_final: 0.7557 (mtmt) REVERT: D 112 THR cc_start: 0.8869 (p) cc_final: 0.8622 (t) REVERT: D 173 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7775 (mt0) REVERT: D 177 ARG cc_start: 0.8383 (tpt170) cc_final: 0.8082 (tpt170) REVERT: D 186 HIS cc_start: 0.7416 (p-80) cc_final: 0.6985 (p90) REVERT: D 304 TYR cc_start: 0.8547 (m-80) cc_final: 0.8112 (m-10) REVERT: D 325 ARG cc_start: 0.7629 (ptp90) cc_final: 0.7427 (ptp90) REVERT: E 44 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7462 (t80) REVERT: E 81 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7331 (pp) REVERT: E 134 LYS cc_start: 0.8761 (mttt) cc_final: 0.8326 (mtpt) REVERT: E 158 TYR cc_start: 0.6660 (t80) cc_final: 0.6229 (t80) REVERT: E 176 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8284 (t) REVERT: E 230 TYR cc_start: 0.8675 (m-80) cc_final: 0.7718 (m-80) REVERT: E 252 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8014 (pttp) REVERT: E 264 GLN cc_start: 0.7997 (mm110) cc_final: 0.7734 (tp-100) REVERT: E 289 ARG cc_start: 0.7407 (ttm170) cc_final: 0.7174 (ttp-170) REVERT: E 604 LEU cc_start: 0.8655 (mt) cc_final: 0.8385 (mt) REVERT: E 1154 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8060 (mm) outliers start: 135 outliers final: 107 residues processed: 625 average time/residue: 0.3018 time to fit residues: 296.9011 Evaluate side-chains 654 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 543 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1038 THR Chi-restraints excluded: chain E residue 1103 ASN Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1196 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1260 VAL Chi-restraints excluded: chain E residue 1269 SER Chi-restraints excluded: chain E residue 1271 SER Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1431 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 6.9990 chunk 241 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 268 optimal weight: 40.0000 chunk 223 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 22 optimal weight: 0.0770 chunk 88 optimal weight: 9.9990 chunk 141 optimal weight: 0.2980 overall best weight: 3.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 186 HIS ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7519 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 21443 Z= 0.227 Angle : 0.618 11.768 29222 Z= 0.304 Chirality : 0.045 0.351 3497 Planarity : 0.004 0.050 3591 Dihedral : 17.485 177.129 3783 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 6.16 % Allowed : 20.63 % Favored : 73.21 % 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: -0.16 (0.16), residues: 2773 helix: 1.61 (0.14), residues: 1332 sheet: -2.11 (0.33), residues: 241 loop : -1.71 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 83 HIS 0.009 0.001 HIS C 186 PHE 0.021 0.002 PHE C 95 TYR 0.017 0.001 TYR E 123 ARG 0.008 0.001 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 6 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 679 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 562 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7195 (mtt-85) cc_final: 0.6931 (mtt-85) REVERT: A 48 ASN cc_start: 0.8459 (m110) cc_final: 0.8179 (m110) REVERT: A 75 PHE cc_start: 0.8174 (t80) cc_final: 0.7825 (t80) REVERT: A 84 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8604 (tt) REVERT: B 77 MET cc_start: 0.6777 (mmm) cc_final: 0.5770 (mtp) REVERT: B 158 MET cc_start: 0.7934 (mmm) cc_final: 0.7570 (mmm) REVERT: B 169 MET cc_start: 0.8070 (mtp) cc_final: 0.7684 (mtp) REVERT: C 77 MET cc_start: 0.6845 (mmm) cc_final: 0.5849 (tmm) REVERT: C 84 LEU cc_start: 0.9058 (mt) cc_final: 0.8813 (mt) REVERT: D 67 LYS cc_start: 0.8232 (mppt) cc_final: 0.7628 (mtmt) REVERT: D 152 GLN cc_start: 0.9252 (tp40) cc_final: 0.8611 (tp40) REVERT: D 173 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7790 (mt0) REVERT: D 177 ARG cc_start: 0.8327 (tpt170) cc_final: 0.8083 (tpt170) REVERT: D 186 HIS cc_start: 0.7409 (p-80) cc_final: 0.6950 (p90) REVERT: D 240 MET cc_start: 0.8048 (ttm) cc_final: 0.7793 (ttm) REVERT: D 247 ASN cc_start: 0.7760 (m-40) cc_final: 0.7139 (p0) REVERT: D 304 TYR cc_start: 0.8505 (m-80) cc_final: 0.8072 (m-10) REVERT: E 44 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7354 (t80) REVERT: E 48 PHE cc_start: 0.7882 (m-80) cc_final: 0.7402 (m-10) REVERT: E 134 LYS cc_start: 0.8739 (mttt) cc_final: 0.8321 (mtpt) REVERT: E 158 TYR cc_start: 0.6643 (t80) cc_final: 0.6282 (t80) REVERT: E 176 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8223 (t) REVERT: E 230 TYR cc_start: 0.8647 (m-80) cc_final: 0.7696 (m-80) REVERT: E 252 LYS cc_start: 0.8229 (ttmt) cc_final: 0.7884 (pttp) REVERT: E 264 GLN cc_start: 0.7980 (mm110) cc_final: 0.7723 (tp-100) REVERT: E 547 ASN cc_start: 0.8912 (t0) cc_final: 0.8632 (t0) REVERT: E 604 LEU cc_start: 0.8635 (mt) cc_final: 0.8359 (mt) REVERT: E 775 GLN cc_start: 0.8391 (tp40) cc_final: 0.8132 (mm-40) REVERT: E 1154 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7977 (mm) outliers start: 117 outliers final: 102 residues processed: 618 average time/residue: 0.2932 time to fit residues: 289.9300 Evaluate side-chains 655 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 549 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 175 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1103 ASN Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1196 THR Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1269 SER Chi-restraints excluded: chain E residue 1271 SER Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1286 THR Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1431 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 226 optimal weight: 50.0000 chunk 150 optimal weight: 4.9990 chunk 267 optimal weight: 40.0000 chunk 167 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN C 128 GLN C 186 HIS D 235 GLN ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 21443 Z= 0.383 Angle : 0.707 10.325 29222 Z= 0.353 Chirality : 0.048 0.374 3497 Planarity : 0.005 0.055 3591 Dihedral : 17.340 175.472 3783 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 7.16 % Allowed : 20.47 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2773 helix: 1.32 (0.14), residues: 1342 sheet: -2.25 (0.33), residues: 235 loop : -1.82 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 83 HIS 0.008 0.001 HIS E 125 PHE 0.025 0.002 PHE C 75 TYR 0.022 0.002 TYR E 772 ARG 0.006 0.001 ARG E1300 *********************** REFINEMENT MACRO_CYCLE 7 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 693 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 557 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8609 (tt) REVERT: A 164 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8775 (tt) REVERT: B 77 MET cc_start: 0.6830 (mmm) cc_final: 0.5854 (mtp) REVERT: B 169 MET cc_start: 0.8138 (mtp) cc_final: 0.7735 (mtp) REVERT: B 199 MET cc_start: 0.8224 (mmm) cc_final: 0.8007 (mmm) REVERT: C 37 SER cc_start: 0.9029 (t) cc_final: 0.8625 (m) REVERT: C 77 MET cc_start: 0.6996 (mmm) cc_final: 0.5835 (tmm) REVERT: D 67 LYS cc_start: 0.8160 (mppt) cc_final: 0.7530 (mtmt) REVERT: D 173 GLN cc_start: 0.8488 (mm-40) cc_final: 0.7879 (mt0) REVERT: D 177 ARG cc_start: 0.8446 (tpt170) cc_final: 0.8068 (tpt170) REVERT: D 186 HIS cc_start: 0.7500 (p-80) cc_final: 0.7064 (p90) REVERT: D 240 MET cc_start: 0.8096 (ttm) cc_final: 0.7874 (ttm) REVERT: D 304 TYR cc_start: 0.8527 (m-80) cc_final: 0.8126 (m-10) REVERT: D 307 ASP cc_start: 0.8503 (p0) cc_final: 0.8064 (p0) REVERT: E 44 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7515 (t80) REVERT: E 81 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7553 (pp) REVERT: E 134 LYS cc_start: 0.8726 (mttt) cc_final: 0.8347 (mtpt) REVERT: E 154 PHE cc_start: 0.8746 (t80) cc_final: 0.8389 (t80) REVERT: E 158 TYR cc_start: 0.6860 (t80) cc_final: 0.6427 (t80) REVERT: E 176 VAL cc_start: 0.8501 (OUTLIER) cc_final: 0.8294 (t) REVERT: E 230 TYR cc_start: 0.8713 (m-80) cc_final: 0.7779 (m-80) REVERT: E 264 GLN cc_start: 0.8062 (mm110) cc_final: 0.7750 (tp-100) REVERT: E 604 LEU cc_start: 0.8643 (mt) cc_final: 0.8353 (mt) REVERT: E 781 ASN cc_start: 0.7961 (p0) cc_final: 0.7529 (p0) REVERT: E 1104 ARG cc_start: 0.7182 (tpp80) cc_final: 0.6968 (tpt-90) REVERT: E 1154 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8101 (mm) outliers start: 136 outliers final: 108 residues processed: 622 average time/residue: 0.2928 time to fit residues: 288.6792 Evaluate side-chains 665 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 551 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 234 HIS Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 105 HIS Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 522 VAL Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1030 ILE Chi-restraints excluded: chain E residue 1038 THR Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1103 ASN Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1173 VAL Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1196 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1271 SER Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1431 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 182 optimal weight: 0.3980 chunk 132 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 210 optimal weight: 30.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS C 128 GLN C 186 HIS ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21443 Z= 0.255 Angle : 0.643 10.541 29222 Z= 0.318 Chirality : 0.045 0.340 3497 Planarity : 0.005 0.056 3591 Dihedral : 16.812 175.377 3783 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 6.42 % Allowed : 21.95 % Favored : 71.63 % 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: -0.32 (0.16), residues: 2773 helix: 1.49 (0.14), residues: 1331 sheet: -2.30 (0.32), residues: 240 loop : -1.77 (0.18), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 83 HIS 0.008 0.001 HIS C 186 PHE 0.049 0.002 PHE E 351 TYR 0.033 0.002 TYR C 258 ARG 0.006 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 8 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 682 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 560 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8428 (m110) cc_final: 0.8212 (m110) REVERT: A 149 LEU cc_start: 0.9239 (tp) cc_final: 0.8947 (tt) REVERT: A 164 LEU cc_start: 0.8907 (mt) cc_final: 0.8670 (tt) REVERT: A 251 LEU cc_start: 0.8945 (tp) cc_final: 0.8540 (tp) REVERT: B 77 MET cc_start: 0.6668 (mmm) cc_final: 0.5689 (mtp) REVERT: B 158 MET cc_start: 0.7960 (mmm) cc_final: 0.7557 (mmm) REVERT: B 169 MET cc_start: 0.8035 (mtp) cc_final: 0.7699 (mtp) REVERT: B 177 ARG cc_start: 0.8080 (tpt170) cc_final: 0.7563 (tpt170) REVERT: B 199 MET cc_start: 0.8115 (mmm) cc_final: 0.7841 (mmm) REVERT: B 325 ARG cc_start: 0.8548 (mtp180) cc_final: 0.7781 (mtp180) REVERT: C 77 MET cc_start: 0.6960 (mmm) cc_final: 0.5877 (tmm) REVERT: D 52 GLN cc_start: 0.7752 (mp10) cc_final: 0.7306 (mp10) REVERT: D 67 LYS cc_start: 0.8087 (mppt) cc_final: 0.7460 (mtmt) REVERT: D 152 GLN cc_start: 0.9276 (tp40) cc_final: 0.8582 (tp40) REVERT: D 173 GLN cc_start: 0.8470 (mm-40) cc_final: 0.7790 (mt0) REVERT: D 177 ARG cc_start: 0.8382 (tpt170) cc_final: 0.8135 (tpt170) REVERT: D 186 HIS cc_start: 0.7499 (p-80) cc_final: 0.7055 (p90) REVERT: D 304 TYR cc_start: 0.8488 (m-80) cc_final: 0.8091 (m-10) REVERT: E 44 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7470 (t80) REVERT: E 48 PHE cc_start: 0.7930 (m-80) cc_final: 0.7378 (m-10) REVERT: E 134 LYS cc_start: 0.8668 (mttt) cc_final: 0.8290 (mtpt) REVERT: E 158 TYR cc_start: 0.6707 (t80) cc_final: 0.6345 (t80) REVERT: E 230 TYR cc_start: 0.8690 (m-80) cc_final: 0.7758 (m-80) REVERT: E 437 ASN cc_start: 0.7936 (m-40) cc_final: 0.7694 (t0) REVERT: E 604 LEU cc_start: 0.8636 (mt) cc_final: 0.8345 (mt) REVERT: E 781 ASN cc_start: 0.7988 (p0) cc_final: 0.7555 (p0) REVERT: E 1148 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7879 (tp) REVERT: E 1154 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7992 (mm) outliers start: 122 outliers final: 103 residues processed: 621 average time/residue: 0.3153 time to fit residues: 307.5510 Evaluate side-chains 650 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 544 time to evaluate : 2.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain C residue 42 CYS Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain D residue 36 VAL Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1042 LEU Chi-restraints excluded: chain E residue 1103 ASN Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1148 LEU Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1151 VAL Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1196 THR Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1271 SER Chi-restraints excluded: chain E residue 1277 SER Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Chi-restraints excluded: chain E residue 1431 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 7.9990 chunk 256 optimal weight: 0.3980 chunk 234 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 196 optimal weight: 7.9990 chunk 76 optimal weight: 0.0000 chunk 225 optimal weight: 0.4980 chunk 236 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 GLN C 186 HIS ** C 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 HIS E 234 ASN E 273 GLN ** E 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 21443 Z= 0.160 Angle : 0.607 9.969 29222 Z= 0.296 Chirality : 0.044 0.334 3497 Planarity : 0.004 0.048 3591 Dihedral : 16.039 177.661 3783 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.37 % Allowed : 24.16 % Favored : 71.47 % 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: -0.02 (0.17), residues: 2773 helix: 1.74 (0.15), residues: 1338 sheet: -2.14 (0.32), residues: 250 loop : -1.63 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 83 HIS 0.021 0.001 HIS C 186 PHE 0.041 0.001 PHE E 351 TYR 0.023 0.001 TYR E 772 ARG 0.007 0.001 ARG E 168 *********************** REFINEMENT MACRO_CYCLE 9 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 658 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 575 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8410 (m110) cc_final: 0.8111 (m110) REVERT: B 158 MET cc_start: 0.7816 (mmm) cc_final: 0.7562 (mmm) REVERT: B 169 MET cc_start: 0.7921 (mtp) cc_final: 0.7543 (mtp) REVERT: B 199 MET cc_start: 0.8022 (mmm) cc_final: 0.7753 (mmm) REVERT: B 297 THR cc_start: 0.9486 (m) cc_final: 0.9218 (p) REVERT: B 305 LEU cc_start: 0.7793 (mm) cc_final: 0.7226 (mp) REVERT: B 311 TRP cc_start: 0.9053 (t-100) cc_final: 0.8531 (t60) REVERT: C 77 MET cc_start: 0.6706 (mmm) cc_final: 0.5930 (tmm) REVERT: C 299 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: D 52 GLN cc_start: 0.7689 (mp10) cc_final: 0.7280 (mp10) REVERT: D 67 LYS cc_start: 0.8021 (mppt) cc_final: 0.7414 (mtmt) REVERT: D 170 LYS cc_start: 0.8497 (mtpp) cc_final: 0.8102 (ttmm) REVERT: D 173 GLN cc_start: 0.8349 (mm-40) cc_final: 0.7689 (mt0) REVERT: D 177 ARG cc_start: 0.8228 (tpt170) cc_final: 0.7972 (tpt170) REVERT: D 186 HIS cc_start: 0.7401 (p-80) cc_final: 0.6962 (p90) REVERT: D 247 ASN cc_start: 0.7620 (m-40) cc_final: 0.7181 (p0) REVERT: D 276 HIS cc_start: 0.7671 (p-80) cc_final: 0.7200 (p-80) REVERT: D 304 TYR cc_start: 0.8414 (m-80) cc_final: 0.8051 (m-10) REVERT: E 44 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.7435 (t80) REVERT: E 48 PHE cc_start: 0.7874 (m-80) cc_final: 0.7462 (m-10) REVERT: E 134 LYS cc_start: 0.8663 (mttt) cc_final: 0.8223 (mtpt) REVERT: E 154 PHE cc_start: 0.8567 (t80) cc_final: 0.8316 (t80) REVERT: E 158 TYR cc_start: 0.6531 (t80) cc_final: 0.6180 (t80) REVERT: E 230 TYR cc_start: 0.8542 (m-80) cc_final: 0.7611 (m-80) REVERT: E 437 ASN cc_start: 0.7893 (m-40) cc_final: 0.7689 (t0) REVERT: E 604 LEU cc_start: 0.8652 (mt) cc_final: 0.8361 (mt) REVERT: E 714 GLN cc_start: 0.7219 (mm110) cc_final: 0.6570 (tp40) REVERT: E 1037 TRP cc_start: 0.8212 (t60) cc_final: 0.7790 (t60) REVERT: E 1248 LEU cc_start: 0.9157 (tp) cc_final: 0.8701 (tp) outliers start: 83 outliers final: 72 residues processed: 617 average time/residue: 0.3099 time to fit residues: 305.6461 Evaluate side-chains 631 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 557 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 611 SER Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1196 THR Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1271 SER Chi-restraints excluded: chain E residue 1416 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 183 optimal weight: 30.0000 chunk 276 optimal weight: 1.9990 chunk 254 optimal weight: 0.3980 chunk 220 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 chunk 170 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 HIS C 235 GLN D 235 GLN E 273 GLN ** E 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21443 Z= 0.169 Angle : 0.612 11.131 29222 Z= 0.297 Chirality : 0.044 0.339 3497 Planarity : 0.004 0.047 3591 Dihedral : 15.651 178.369 3783 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.05 % Allowed : 25.11 % Favored : 70.84 % 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: 0.06 (0.17), residues: 2773 helix: 1.79 (0.15), residues: 1339 sheet: -2.03 (0.32), residues: 242 loop : -1.61 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 83 HIS 0.014 0.001 HIS C 186 PHE 0.040 0.001 PHE E 351 TYR 0.022 0.001 TYR E 772 ARG 0.005 0.000 ARG B 195 ********************** REFINEMENT MACRO_CYCLE 10 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 638 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 561 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8413 (m110) cc_final: 0.8087 (m110) REVERT: A 75 PHE cc_start: 0.7992 (t80) cc_final: 0.7679 (t80) REVERT: A 84 LEU cc_start: 0.8764 (tt) cc_final: 0.8553 (tt) REVERT: B 77 MET cc_start: 0.6778 (mmm) cc_final: 0.5823 (mtp) REVERT: B 199 MET cc_start: 0.8079 (mmm) cc_final: 0.7800 (mmm) REVERT: B 297 THR cc_start: 0.9472 (m) cc_final: 0.9267 (p) REVERT: B 311 TRP cc_start: 0.9033 (t-100) cc_final: 0.8546 (t60) REVERT: C 77 MET cc_start: 0.6708 (mmm) cc_final: 0.5995 (tmm) REVERT: C 152 GLN cc_start: 0.9015 (tp40) cc_final: 0.8353 (tp40) REVERT: C 217 MET cc_start: 0.7586 (mtp) cc_final: 0.7194 (mtm) REVERT: C 299 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: D 67 LYS cc_start: 0.7923 (mppt) cc_final: 0.7348 (mtmt) REVERT: D 152 GLN cc_start: 0.9132 (tp40) cc_final: 0.8472 (tp40) REVERT: D 170 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8099 (ttmm) REVERT: D 173 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7642 (mt0) REVERT: D 186 HIS cc_start: 0.7340 (p-80) cc_final: 0.6887 (p90) REVERT: D 276 HIS cc_start: 0.7653 (p-80) cc_final: 0.7324 (p-80) REVERT: D 279 GLN cc_start: 0.6917 (mm-40) cc_final: 0.6640 (mm-40) REVERT: D 304 TYR cc_start: 0.8401 (m-80) cc_final: 0.7998 (m-10) REVERT: E 44 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7500 (t80) REVERT: E 48 PHE cc_start: 0.7835 (m-80) cc_final: 0.7416 (m-10) REVERT: E 134 LYS cc_start: 0.8671 (mttt) cc_final: 0.8216 (mtpt) REVERT: E 154 PHE cc_start: 0.8576 (t80) cc_final: 0.8333 (t80) REVERT: E 158 TYR cc_start: 0.6481 (t80) cc_final: 0.6153 (t80) REVERT: E 230 TYR cc_start: 0.8563 (m-80) cc_final: 0.7616 (m-80) REVERT: E 604 LEU cc_start: 0.8633 (mt) cc_final: 0.8359 (mt) REVERT: E 800 LYS cc_start: 0.7748 (tttt) cc_final: 0.7420 (tptt) REVERT: E 1037 TRP cc_start: 0.8180 (t60) cc_final: 0.7781 (t60) REVERT: E 1104 ARG cc_start: 0.6964 (tpt-90) cc_final: 0.6723 (tpt-90) REVERT: E 1154 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7912 (mm) REVERT: E 1248 LEU cc_start: 0.9162 (tp) cc_final: 0.8722 (tp) outliers start: 77 outliers final: 66 residues processed: 599 average time/residue: 0.3037 time to fit residues: 290.3913 Evaluate side-chains 617 residues out of total 2435 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 548 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 299 GLN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 321 GLU Chi-restraints excluded: chain E residue 6 CYS Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 546 MET Chi-restraints excluded: chain E residue 550 ILE Chi-restraints excluded: chain E residue 580 LEU Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 607 VAL Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1025 MET Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1149 LEU Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1196 THR Chi-restraints excluded: chain E residue 1197 GLN Chi-restraints excluded: chain E residue 1252 MET Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1271 SER Chi-restraints excluded: chain E residue 1416 HIS Chi-restraints excluded: chain E residue 1425 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.1678 > 50: distance: 1 - 26: 23.032 distance: 21 - 26: 22.483 distance: 26 - 27: 34.236 distance: 27 - 28: 15.523 distance: 27 - 30: 8.363 distance: 28 - 29: 7.131 distance: 28 - 34: 39.284 distance: 30 - 31: 15.676 distance: 31 - 32: 30.309 distance: 32 - 33: 29.621 distance: 34 - 35: 32.215 distance: 35 - 36: 19.369 distance: 35 - 38: 30.094 distance: 36 - 37: 16.043 distance: 36 - 44: 33.470 distance: 38 - 39: 33.852 distance: 39 - 40: 19.660 distance: 39 - 41: 29.429 distance: 40 - 42: 17.294 distance: 41 - 43: 29.798 distance: 42 - 43: 18.813 distance: 44 - 45: 9.612 distance: 45 - 46: 19.486 distance: 45 - 48: 17.410 distance: 46 - 47: 4.929 distance: 46 - 52: 19.704 distance: 48 - 49: 20.619 distance: 49 - 50: 40.891 distance: 50 - 51: 20.614 distance: 52 - 53: 10.986 distance: 53 - 54: 35.643 distance: 53 - 56: 36.189 distance: 54 - 55: 14.566 distance: 54 - 57: 27.565 distance: 57 - 58: 5.514 distance: 58 - 59: 22.469 distance: 58 - 61: 17.735 distance: 59 - 60: 32.105 distance: 59 - 64: 30.984 distance: 61 - 62: 8.899 distance: 61 - 63: 22.477 distance: 64 - 65: 15.391 distance: 65 - 66: 12.843 distance: 65 - 68: 33.001 distance: 66 - 67: 22.227 distance: 66 - 70: 15.040 distance: 70 - 71: 19.223 distance: 71 - 72: 11.590 distance: 71 - 74: 4.268 distance: 72 - 73: 17.751 distance: 72 - 78: 16.519 distance: 74 - 75: 3.793 distance: 75 - 76: 22.947 distance: 75 - 77: 8.552 distance: 78 - 79: 23.699 distance: 79 - 80: 14.794 distance: 79 - 82: 15.694 distance: 80 - 81: 13.778 distance: 80 - 86: 9.819 distance: 82 - 83: 27.736 distance: 83 - 84: 36.969 distance: 83 - 85: 48.683 distance: 86 - 87: 13.935 distance: 87 - 88: 6.440 distance: 87 - 90: 19.107 distance: 88 - 89: 9.019 distance: 88 - 92: 3.806 distance: 90 - 91: 13.190 distance: 92 - 93: 13.491 distance: 93 - 94: 8.257 distance: 93 - 96: 8.609 distance: 94 - 95: 19.897 distance: 94 - 100: 7.521 distance: 96 - 97: 20.658 distance: 97 - 98: 22.301 distance: 98 - 99: 30.563