Starting phenix.real_space_refine on Sun Feb 18 01:16:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyt_26194/02_2024/7tyt_26194_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyt_26194/02_2024/7tyt_26194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyt_26194/02_2024/7tyt_26194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyt_26194/02_2024/7tyt_26194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyt_26194/02_2024/7tyt_26194_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyt_26194/02_2024/7tyt_26194_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 28 5.49 5 S 93 5.16 5 C 13171 2.51 5 N 3452 2.21 5 O 3604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20349 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2535 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 16, 'TRANS': 339} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 9, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 13, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 164 Chain: "B" Number of atoms: 2349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2349 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 9, 'ASN:plan1': 2, 'HIS:plan': 4, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 147 Chain: "C" Number of atoms: 2370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2370 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 153 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 138 Chain: "D" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2395 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 13, 'TRANS': 312} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 102 Chain: "E" Number of atoms: 10003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1425, 10003 Classifications: {'peptide': 1425} Incomplete info: {'truncation_to_alanine': 366} Link IDs: {'PTRANS': 48, 'TRANS': 1376} Chain breaks: 6 Unresolved non-hydrogen bonds: 1285 Unresolved non-hydrogen angles: 1612 Unresolved non-hydrogen dihedrals: 1025 Unresolved non-hydrogen chiralities: 129 Planarities with less than four sites: {'GLN:plan1': 21, 'ASP:plan': 37, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 2, 'HIS:plan': 7, 'PHE:plan': 15, 'GLU:plan': 39, 'ARG:plan': 29} Unresolved non-hydrogen planarities: 687 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: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 68 Unusual residues: {' K': 1, 'ATP': 1, 'POV': 1} Classifications: {'undetermined': 3} 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: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 152 Unusual residues: {'ATP': 2, '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: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} 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: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'ATP': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 346 Unusual residues: {'ATP': 1, 'BJX': 1, 'POV': 1, 'PTY': 6} Classifications: {'peptide': 1, 'undetermined': 9} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 124 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 11.57, per 1000 atoms: 0.57 Number of scatterers: 20349 At special positions: 0 Unit cell: (163.02, 107.635, 149.435, 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 93 16.00 P 28 15.00 O 3604 8.00 N 3452 7.00 C 13171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG F 1 " - " ASN E 10 " Time building additional restraints: 9.94 Conformation dependent library (CDL) restraints added in 4.6 seconds 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 23 sheets defined 47.7% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.02 Creating SS restraints... Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.529A pdb=" N THR A 28 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 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 176 removed outlier: 3.569A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A 175 " --> pdb=" O THR A 171 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ARG A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 removed outlier: 3.996A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' 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 355 removed outlier: 3.623A pdb=" N ASP A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 64 removed outlier: 3.960A pdb=" N THR B 61 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 96 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 143 through 176 removed outlier: 3.560A pdb=" N GLN B 173 " --> pdb=" O MET B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 269 removed outlier: 4.047A pdb=" N ASP B 269 " --> pdb=" O PRO B 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 269' Processing helix chain 'B' and resid 346 through 355 removed outlier: 4.025A pdb=" N SER B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 355 " --> pdb=" O GLU B 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 64 removed outlier: 4.959A pdb=" N THR C 61 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR C 62 " --> pdb=" O VAL C 59 " (cutoff:3.500A) 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 175 removed outlier: 3.923A pdb=" N HIS C 175 " --> pdb=" O THR C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 269 removed outlier: 4.380A 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 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'D' and resid 56 through 64 Processing helix chain 'D' and resid 68 through 96 Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 143 through 176 removed outlier: 3.896A pdb=" N ARG D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 269 removed outlier: 4.152A 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 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 346 through 355 removed outlier: 4.245A pdb=" N ASP D 350 " --> pdb=" O ARG D 347 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU D 351 " --> pdb=" O GLN D 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG D 353 " --> pdb=" O ASP D 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 11 No H-bonds generated for 'chain 'E' and resid 9 through 11' Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 25 through 50 removed outlier: 3.543A pdb=" N VAL E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Proline residue: E 35 - end of helix Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 71 through 95 removed outlier: 4.161A pdb=" N TRP E 75 " --> pdb=" O HIS E 71 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (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 Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 138 through 159 removed outlier: 3.779A pdb=" N LEU E 145 " --> pdb=" O ILE E 141 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS E 150 " --> pdb=" O ALA E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 193 removed outlier: 3.701A pdb=" N ILE E 177 " --> pdb=" O GLY E 173 " (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 229 Processing helix chain 'E' and resid 231 through 240 removed outlier: 3.722A pdb=" N ALA E 235 " --> pdb=" O TRP E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 275 Processing helix chain 'E' and resid 284 through 328 removed outlier: 5.346A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE E 314 " --> pdb=" O ASP E 310 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA E 315 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 4.005A 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 353 removed outlier: 4.501A pdb=" N GLY E 353 " --> pdb=" O GLN E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 401 Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 414 through 456 Proline residue: E 436 - end of helix removed outlier: 3.523A 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 504 removed outlier: 3.542A pdb=" N ILE E 462 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL E 466 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE E 467 " --> pdb=" O GLY E 463 " (cutoff:3.500A) Proline residue: E 472 - end of helix Processing helix chain 'E' and resid 506 through 511 Processing helix chain 'E' and resid 515 through 563 removed outlier: 3.638A pdb=" N THR E 531 " --> pdb=" O ARG E 527 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER E 532 " --> pdb=" O LYS E 528 " (cutoff:3.500A) Proline residue: E 551 - end of helix Processing helix chain 'E' and resid 573 through 615 removed outlier: 3.591A pdb=" N THR E 588 " --> pdb=" O HIS E 584 " (cutoff:3.500A) Proline residue: E 589 - end of helix removed outlier: 5.254A pdb=" N SER E 594 " --> pdb=" O LEU E 590 " (cutoff:3.500A) removed outlier: 4.898A 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 806 removed outlier: 3.515A pdb=" N ILE E 803 " --> pdb=" O TYR E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 814 Processing helix chain 'E' and resid 832 through 846 removed outlier: 3.557A pdb=" N ALA E 843 " --> pdb=" O SER E 839 " (cutoff:3.500A) Processing helix chain 'E' and resid 865 through 880 Processing helix chain 'E' and resid 914 through 920 removed outlier: 4.000A pdb=" N GLN E 918 " --> pdb=" O LEU E 914 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARG E 919 " --> pdb=" O LYS E 915 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER E 920 " --> pdb=" O ASP E 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 914 through 920' Processing helix chain 'E' and resid 924 through 927 No H-bonds generated for 'chain 'E' and resid 924 through 927' Processing helix chain 'E' and resid 987 through 992 Processing helix chain 'E' and resid 997 through 1008 Processing helix chain 'E' and resid 1011 through 1041 removed outlier: 3.709A pdb=" N LEU E1016 " --> pdb=" O LEU E1012 " (cutoff:3.500A) Processing helix chain 'E' and resid 1065 through 1107 removed outlier: 3.562A pdb=" N ARG E1099 " --> pdb=" O LYS E1095 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU E1107 " --> pdb=" O ASN E1103 " (cutoff:3.500A) Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1118 through 1160 removed outlier: 4.287A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE E1136 " --> pdb=" O ILE E1132 " (cutoff:3.500A) Proline residue: E1137 - end of helix Processing helix chain 'E' and resid 1162 through 1209 Proline residue: E1170 - end of helix removed outlier: 4.209A pdb=" N CYS E1175 " --> pdb=" O ALA E1172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR E1181 " --> pdb=" O ILE E1178 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG E1187 " --> pdb=" O VAL E1184 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP E1188 " --> pdb=" O ALA E1185 " (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 1273 Processing helix chain 'E' and resid 1278 through 1320 removed outlier: 3.727A pdb=" N MET E1290 " --> pdb=" O THR E1286 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN E1293 " --> pdb=" O LEU E1289 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY E1310 " --> pdb=" O GLU E1306 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA E1311 " --> pdb=" O ILE E1307 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1387 through 1391 Processing helix chain 'E' and resid 1415 through 1421 removed outlier: 3.973A pdb=" N ARG E1421 " --> pdb=" O THR E1417 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1440 Processing helix chain 'E' and resid 1449 through 1458 Processing helix chain 'E' and resid 1461 through 1465 Processing helix chain 'E' and resid 1477 through 1479 No H-bonds generated for 'chain 'E' and resid 1477 through 1479' Processing helix chain 'E' and resid 1486 through 1498 removed outlier: 3.683A pdb=" N ARG E1494 " --> pdb=" O PHE E1490 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ALA E1495 " --> pdb=" O CYS E1491 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE E1496 " --> pdb=" O LEU E1492 " (cutoff:3.500A) Processing helix chain 'E' and resid 1513 through 1529 Processing helix chain 'E' and resid 1540 through 1544 Processing helix chain 'E' and resid 1573 through 1577 Processing sheet with id= A, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.516A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.604A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 282 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= D, first strand: chain 'A' and resid 319 through 321 Processing sheet with id= E, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'B' and resid 309 through 311 removed outlier: 6.588A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.189A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= I, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= J, first strand: chain 'C' and resid 187 through 189 Processing sheet with id= K, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.364A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 214 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= M, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= N, first strand: chain 'D' and resid 188 through 192 Processing sheet with id= O, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.040A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= Q, first strand: chain 'D' and resid 319 through 321 Processing sheet with id= R, first strand: chain 'E' and resid 678 through 681 Processing sheet with id= S, first strand: chain 'E' and resid 709 through 712 removed outlier: 6.001A pdb=" N TRP E 899 " --> pdb=" O MET E 710 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL E 712 " --> pdb=" O TRP E 899 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE E 901 " --> pdb=" O VAL E 712 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 850 through 854 removed outlier: 5.853A pdb=" N THR E 883 " --> pdb=" O VAL E 851 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU E 853 " --> pdb=" O THR E 883 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL E 885 " --> pdb=" O LEU E 853 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 1345 through 1347 Processing sheet with id= V, first strand: chain 'E' and resid 1374 through 1377 removed outlier: 8.036A pdb=" N VAL E1533 " --> pdb=" O ILE E1375 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N ILE E1377 " --> pdb=" O VAL E1533 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR E1535 " --> pdb=" O ILE E1377 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E1536 " --> pdb=" O MET E1505 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU E1507 " --> pdb=" O ILE E1536 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 685 through 687 removed outlier: 6.455A pdb=" N THR E 687 " --> pdb=" O LYS E 732 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS E 732 " --> pdb=" O THR E 687 " (cutoff:3.500A) 1033 hydrogen bonds defined for protein. 2895 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: 7.39 Time building geometry restraints manager: 10.31 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: 3339 1.32 - 1.44: 5361 1.44 - 1.57: 11884 1.57 - 1.69: 53 1.69 - 1.81: 142 Bond restraints: 20779 Sorted by residual: bond pdb=" N BJX E1602 " pdb=" C6 BJX E1602 " ideal model delta sigma weight residual 1.412 1.532 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" C16 BJX E1602 " pdb=" N1 BJX E1602 " ideal model delta sigma weight residual 1.344 1.455 -0.111 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C21 BJX E1602 " pdb=" O1 BJX E1602 " ideal model delta sigma weight residual 1.347 1.422 -0.075 2.00e-02 2.50e+03 1.39e+01 bond pdb=" C5 BJX E1602 " pdb=" N1 BJX E1602 " ideal model delta sigma weight residual 1.446 1.516 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C5 BJX E1602 " pdb=" C8 BJX E1602 " ideal model delta sigma weight residual 1.536 1.601 -0.065 2.00e-02 2.50e+03 1.04e+01 ... (remaining 20774 not shown) Histogram of bond angle deviations from ideal: 92.06 - 101.65: 67 101.65 - 111.23: 9481 111.23 - 120.81: 12538 120.81 - 130.40: 6185 130.40 - 139.98: 130 Bond angle restraints: 28401 Sorted by residual: angle pdb=" C16 BJX E1602 " pdb=" N1 BJX E1602 " pdb=" C5 BJX E1602 " ideal model delta sigma weight residual 123.13 134.16 -11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C VAL E 33 " pdb=" N VAL E 34 " pdb=" CA VAL E 34 " ideal model delta sigma weight residual 120.33 122.94 -2.61 8.00e-01 1.56e+00 1.07e+01 angle pdb=" CA GLN C 313 " pdb=" CB GLN C 313 " pdb=" CG GLN C 313 " ideal model delta sigma weight residual 114.10 119.29 -5.19 2.00e+00 2.50e-01 6.73e+00 angle pdb=" N ILE E 423 " pdb=" CA ILE E 423 " pdb=" C ILE E 423 " ideal model delta sigma weight residual 110.82 113.25 -2.43 9.70e-01 1.06e+00 6.27e+00 angle pdb=" O2 BJX E1602 " pdb=" C24 BJX E1602 " pdb=" O3 BJX E1602 " ideal model delta sigma weight residual 126.98 119.85 7.13 3.00e+00 1.11e-01 5.65e+00 ... (remaining 28396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.52: 11915 34.52 - 69.05: 393 69.05 - 103.57: 32 103.57 - 138.09: 1 138.09 - 172.62: 2 Dihedral angle restraints: 12343 sinusoidal: 4337 harmonic: 8006 Sorted by residual: dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 142 " pdb=" CB CYS B 142 " ideal model delta sinusoidal sigma weight residual 93.00 138.49 -45.49 1 1.00e+01 1.00e-02 2.87e+01 dihedral pdb=" O16 P5S E1607 " pdb=" C2 P5S E1607 " pdb=" C3 P5S E1607 " pdb=" O37 P5S E1607 " ideal model delta sinusoidal sigma weight residual -57.33 115.29 -172.62 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O BJX E1602 " pdb=" C16 BJX E1602 " pdb=" C17 BJX E1602 " pdb=" C18 BJX E1602 " ideal model delta sinusoidal sigma weight residual 10.31 -151.35 161.66 1 3.00e+01 1.11e-03 2.08e+01 ... (remaining 12340 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2549 0.045 - 0.090: 661 0.090 - 0.135: 216 0.135 - 0.179: 3 0.179 - 0.224: 2 Chirality restraints: 3431 Sorted by residual: chirality pdb=" C5 BJX E1602 " pdb=" C7 BJX E1602 " pdb=" C8 BJX E1602 " pdb=" N1 BJX E1602 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN E 10 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 189 " pdb=" N ILE A 189 " pdb=" C ILE A 189 " pdb=" CB ILE A 189 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 3428 not shown) Planarity restraints: 3508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY E 316 " -0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO E 317 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO E 317 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 317 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 280 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO E 281 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 281 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 281 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 253 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO B 254 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 254 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 254 " -0.027 5.00e-02 4.00e+02 ... (remaining 3505 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 4867 2.79 - 3.38: 22924 3.38 - 3.96: 36919 3.96 - 4.55: 50593 4.55 - 5.14: 73408 Nonbonded interactions: 188711 Sorted by model distance: nonbonded pdb=" OH TYR E 123 " pdb=" O LEU E 135 " model vdw 2.202 2.440 nonbonded pdb=" O ILE A 74 " pdb=" OG SER A 78 " model vdw 2.205 2.440 nonbonded pdb=" O PHE C 168 " pdb=" OG1 THR C 171 " model vdw 2.209 2.440 nonbonded pdb=" ND2 ASN E 781 " pdb=" OE2 GLU E1206 " model vdw 2.216 2.520 nonbonded pdb=" O ILE E 544 " pdb=" OG1 THR E 548 " model vdw 2.233 2.440 ... (remaining 188706 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 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 42 or (resid 43 and (n \ ame N or name CA or name C or name O or name CB )) or resid 44 through 48 or (re \ sid 49 and (name N or name CA or name C or name O or name CB )) or resid 50 thro \ ugh 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 58 and (name N or name CA or name C or name O or n \ ame CB )) or resid 59 through 72 or (resid 73 through 74 and (name N or name CA \ or name C or name O or name CB )) or resid 75 through 81 or (resid 82 and (name \ N or name CA or name C or name O or name CB )) or resid 83 through 91 or (resid \ 92 and (name N or name CA or name C or name O or name CB )) or resid 93 through \ 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) or re \ sid 119 through 139 or (resid 140 through 141 and (name N or name CA or name C o \ r name O or name CB )) or resid 142 through 147 or (resid 148 and (name N or nam \ e CA or name C or name O or name CB )) or resid 149 through 151 or (resid 152 an \ d (name N or name CA or name C or name O or name CB )) or resid 153 through 168 \ or (resid 169 and (name N or name CA or name C or name O or name CB )) or resid \ 170 through 179 or (resid 180 and (name N or name CA or name C or name O or name \ CB )) or resid 181 or (resid 182 and (name N or name CA or name C or name O or \ name CB )) or resid 183 through 187 or (resid 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 through 192 or (resid 193 and (name N or \ name CA or name C or name O or name CB )) or resid 194 or (resid 195 and (name \ N or name CA or name C or name O or name CB )) or resid 196 through 203 or (resi \ d 204 and (name N or name CA or name C or name O or name CB )) or resid 205 thro \ ugh 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) o \ r resid 208 through 209 or (resid 210 through 211 and (name N or name CA or name \ C or name O or name CB )) or resid 212 through 221 or (resid 222 and (name N or \ name CA or name C or name O or name CB )) or resid 223 through 268 or (resid 26 \ 9 through 271 and (name N or name CA or name C or name O or name CB )) or resid \ 272 through 274 or (resid 275 through 276 and (name N or name CA or name C or na \ me O or name CB )) or resid 277 through 278 or (resid 279 through 282 and (name \ N or name CA or name C or name O or name CB )) or resid 283 through 291 or (resi \ d 292 and (name N or name CA or name C or name O or name CB )) or resid 293 thro \ ugh 302 or (resid 303 and (name N or name CA or name C or name O or name CB )) o \ r resid 304 or (resid 305 through 308 and (name N or name CA or name C or name O \ or name CB )) or resid 309 through 317 or (resid 318 and (name N or name CA or \ name C or name O or name CB )) or resid 319 through 328 or (resid 329 and (name \ N or name CA or name C or name O or name CB )) or resid 330 through 343 or (resi \ d 344 and (name N or name CA or name C or name O or name CB )) or resid 345 thro \ ugh 346 or (resid 347 through 348 and (name N or name CA or name C or name O or \ name CB )) or resid 349 through 350 or (resid 351 through 356 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 31 through 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 54 or (resid 55 throug \ h 58 and (name N or name CA or name C or name O or name CB )) or resid 59 throug \ h 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or re \ sid 67 through 70 or (resid 71 and (name N or name CA or name C or name O or nam \ e CB )) or resid 72 through 76 or (resid 77 and (name N or name CA or name C or \ name O or name CB )) or resid 78 through 91 or (resid 92 and (name N or name CA \ or name C or name O or name CB )) or resid 93 through 99 or (resid 100 through 1 \ 01 and (name N or name CA or name C or name O or name CB )) or resid 102 through \ 117 or (resid 118 and (name N or name CA or name C or name O or name CB )) or r \ esid 119 through 147 or (resid 148 and (name N or name CA or name C or name O or \ name CB )) or resid 149 through 153 or (resid 154 and (name N or name CA or nam \ e C or name O or name CB )) or resid 155 through 187 or (resid 188 and (name N o \ r name CA or name C or name O or name CB )) or resid 189 through 191 or (resid 1 \ 92 through 193 and (name N or name CA or name C or name O or name CB )) or resid \ 194 or (resid 195 and (name N or name CA or name C or name O or name CB )) or r \ esid 196 through 206 or (resid 207 and (name N or name CA or name C or name O or \ name CB )) or resid 208 through 209 or (resid 210 through 211 and (name N or na \ me CA or name C or name O or name CB )) or resid 212 through 221 or (resid 222 a \ nd (name N or name CA or name C or name O or name CB )) or resid 223 through 250 \ or (resid 251 and (name N or name CA or name C or name O or name CB )) or resid \ 252 through 259 or (resid 260 through 262 and (name N or name CA or name C or n \ ame O or name CB )) or resid 263 through 264 or (resid 265 and (name N or name C \ A or name C or name O or name CB )) or resid 266 through 269 or (resid 270 throu \ gh 271 and (name N or name CA or name C or name O or name CB )) or resid 272 thr \ ough 280 or (resid 281 through 282 and (name N or name CA or name C or name O or \ name CB )) or resid 283 through 302 or (resid 303 and (name N or name CA or nam \ e C or name O or name CB )) or resid 304 or (resid 305 through 308 and (name N o \ r name CA or name C or name O or name CB )) or resid 309 through 317 or (resid 3 \ 18 and (name N or name CA or name C or name O or name CB )) or resid 319 through \ 328 or (resid 329 and (name N or name CA or name C or name O or name CB )) or r \ esid 330 through 353 or (resid 354 through 356 and (name N or name CA or name C \ or name O or name CB )))) selection = (chain 'C' and (resid 31 through 35 or (resid 36 through 39 and (name N or name \ CA or name C or name O or name CB )) or resid 40 through 42 or (resid 43 and (na \ me N or name CA or name C or name O or name CB )) or resid 44 through 48 or (res \ id 49 and (name N or name CA or name C or name O or name CB )) or resid 50 throu \ gh 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or r \ esid 67 through 70 or (resid 71 and (name N or name CA or name C or name O or na \ me CB )) or resid 72 or (resid 73 through 74 and (name N or name CA or name C or \ name O or name CB )) or resid 75 through 76 or (resid 77 and (name N or name CA \ or name C or name O or name CB )) or resid 78 through 81 or (resid 82 and (name \ N or name CA or name C or name O or name CB )) or resid 83 through 99 or (resid \ 100 through 101 and (name N or name CA or name C or name O or name CB )) or res \ id 102 through 139 or (resid 140 through 141 and (name N or name CA or name C or \ name O or name CB )) or resid 142 through 153 or (resid 154 and (name N or name \ CA or name C or name O or name CB )) or resid 155 through 168 or (resid 169 and \ (name N or name CA or name C or name O or name CB )) or resid 170 through 181 o \ r (resid 182 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 83 through 191 or (resid 192 through 193 and (name N or name CA or name C or nam \ e O or name CB )) or resid 194 through 206 or (resid 207 and (name N or name CA \ or name C or name O or name CB )) or resid 208 through 209 or (resid 210 through \ 211 and (name N or name CA or name C or name O or name CB )) or resid 212 throu \ gh 221 or (resid 222 and (name N or name CA or name C or name O or name CB )) or \ resid 223 through 250 or (resid 251 and (name N or name CA or name C or name O \ or name CB )) or resid 252 through 254 or (resid 255 and (name N or name CA or n \ ame C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 2 \ 64 or (resid 265 and (name N or name CA or name C or name O or name CB )) or res \ id 266 through 268 or (resid 269 through 271 and (name N or name CA or name C or \ name O or name CB )) or resid 272 through 273 or (resid 274 through 276 and (na \ me N or name CA or name C or name O or name CB )) or resid 277 through 278 or (r \ esid 279 through 282 and (name N or name CA or name C or name O or name CB )) or \ resid 283 through 291 or (resid 292 and (name N or name CA or name C or name O \ or name CB )) or resid 293 through 306 or (resid 307 through 308 and (name N or \ name CA or name C or name O or name CB )) or resid 309 through 317 or (resid 318 \ and (name N or name CA or name C or name O or name CB )) or resid 319 through 3 \ 31 or (resid 332 and (name N or name CA or name C or name O or name CB )) or res \ id 333 through 343 or (resid 344 and (name N or name CA or name C or name O or n \ ame CB )) or resid 345 through 346 or (resid 347 through 348 and (name N or name \ CA or name C or name O or name CB )) or resid 349 through 356)) selection = (chain 'D' and (resid 31 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 48 or (resid 49 and (name N or nam \ e CA or name C or name O or name CB )) or resid 50 through 54 or (resid 55 throu \ gh 58 and (name N or name CA or name C or name O or name CB )) or resid 59 throu \ gh 72 or (resid 73 through 74 and (name N or name CA or name C or name O or name \ CB )) or resid 75 through 76 or (resid 77 and (name N or name CA or name C or n \ ame O or name CB )) or resid 78 through 81 or (resid 82 and (name N or name CA o \ r name C or name O or name CB )) or resid 83 through 91 or (resid 92 and (name N \ or name CA or name C or name O or name CB )) or resid 93 through 99 or (resid 1 \ 00 through 101 and (name N or name CA or name C or name O or name CB )) or resid \ 102 through 114 or (resid 115 and (name N or name CA or name C or name O or nam \ e CB )) or resid 116 through 117 or (resid 118 and (name N or name CA or name C \ or name O or name CB )) or resid 119 through 139 or (resid 140 through 141 and ( \ name N or name CA or name C or name O or name CB )) or resid 142 through 147 or \ (resid 148 and (name N or name CA or name C or name O or name CB )) or resid 149 \ through 151 or (resid 152 and (name N or name CA or name C or name O or name CB \ )) or resid 153 or (resid 154 and (name N or name CA or name C or name O or nam \ e CB )) or resid 155 through 179 or (resid 180 and (name N or name CA or name C \ or name O or name CB )) or resid 181 or (resid 182 and (name N or name CA or nam \ e C or name O or name CB )) or resid 183 through 192 or (resid 193 and (name N o \ r name CA or name C or name O or name CB )) or resid 194 or (resid 195 and (name \ N or name CA or name C or name O or name CB )) or resid 196 through 198 or (res \ id 199 through 200 and (name N or name CA or name C or name O or name CB )) or r \ esid 201 through 210 or (resid 211 and (name N or name CA or name C or name O or \ name CB )) or resid 212 through 250 or (resid 251 and (name N or name CA or nam \ e C or name O or name CB )) or resid 252 through 254 or (resid 255 and (name N o \ r name CA or name C or name O or name CB )) or resid 256 through 259 or (resid 2 \ 60 through 262 and (name N or name CA or name C or name O or name CB )) or resid \ 263 through 264 or (resid 265 and (name N or name CA or name C or name O or nam \ e CB )) or resid 266 through 268 or (resid 269 through 271 and (name N or name C \ A or name C or name O or name CB )) or resid 272 through 273 or (resid 274 throu \ gh 276 and (name N or name CA or name C or name O or name CB )) or resid 277 thr \ ough 278 or (resid 279 through 282 and (name N or name CA or name C or name O or \ name CB )) or resid 283 through 287 or (resid 288 and (name N or name CA or nam \ e C or name O or name CB )) or resid 289 through 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 through 302 or (resid 3 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 304 or (res \ id 305 through 308 and (name N or name CA or name C or name O or name CB )) or r \ esid 309 through 328 or (resid 329 and (name N or name CA or name C or name O or \ name CB )) or resid 330 through 343 or (resid 344 and (name N or name CA or nam \ e C or name O or name CB )) or resid 345 through 346 or (resid 347 through 348 a \ nd (name N or name CA or name C or name O or name CB )) or resid 349 through 351 \ or (resid 352 through 356 and (name N or name CA or name C or name O or name CB \ )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.970 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 60.120 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 : 0.004 0.120 20779 Z= 0.270 Angle : 0.551 11.028 28401 Z= 0.298 Chirality : 0.043 0.224 3431 Planarity : 0.004 0.063 3507 Dihedral : 17.000 172.617 7124 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.67 % Allowed : 25.35 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2737 helix: 2.25 (0.14), residues: 1300 sheet: -1.28 (0.29), residues: 315 loop : -0.96 (0.19), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 65 HIS 0.009 0.001 HIS E1098 PHE 0.021 0.001 PHE B 60 TYR 0.014 0.001 TYR E 123 ARG 0.007 0.000 ARG E1145 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 510 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8518 (tt) REVERT: B 186 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6386 (p-80) REVERT: C 74 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8334 (mp) REVERT: C 84 LEU cc_start: 0.8720 (tt) cc_final: 0.8490 (tt) REVERT: C 191 LEU cc_start: 0.7171 (mp) cc_final: 0.6822 (mp) REVERT: C 230 VAL cc_start: 0.8541 (OUTLIER) cc_final: 0.8238 (m) REVERT: D 70 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7637 (m90) REVERT: E 416 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8026 (tm-30) REVERT: E 427 GLN cc_start: 0.8193 (mt0) cc_final: 0.7973 (mt0) REVERT: E 529 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7519 (tm-30) REVERT: E 1004 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6315 (m-80) REVERT: E 1036 LYS cc_start: 0.8110 (tppt) cc_final: 0.7837 (mmtp) outliers start: 30 outliers final: 9 residues processed: 523 average time/residue: 0.2995 time to fit residues: 246.8238 Evaluate side-chains 486 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 471 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1316 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 213 optimal weight: 30.0000 chunk 82 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 247 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN D 235 GLN E 166 GLN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 822 GLN E 836 GLN E1135 HIS E1270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20779 Z= 0.347 Angle : 0.587 11.048 28401 Z= 0.302 Chirality : 0.045 0.344 3431 Planarity : 0.005 0.053 3507 Dihedral : 13.696 173.051 3529 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 7.00 % Allowed : 22.62 % Favored : 70.37 % 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: 0.48 (0.16), residues: 2737 helix: 1.84 (0.14), residues: 1311 sheet: -1.23 (0.31), residues: 282 loop : -1.09 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 430 HIS 0.008 0.001 HIS E1024 PHE 0.025 0.002 PHE E 577 TYR 0.023 0.002 TYR E 123 ARG 0.007 0.000 ARG C 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 508 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9492 (OUTLIER) cc_final: 0.9263 (t) REVERT: A 168 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6475 (t80) REVERT: B 186 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.6386 (p-80) REVERT: C 84 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8471 (tt) REVERT: D 70 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7634 (m90) REVERT: D 252 VAL cc_start: 0.8906 (t) cc_final: 0.8411 (p) REVERT: D 308 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: E 136 LEU cc_start: 0.8671 (mt) cc_final: 0.8459 (mt) REVERT: E 168 ARG cc_start: 0.8482 (tpp80) cc_final: 0.8012 (tpp80) REVERT: E 427 GLN cc_start: 0.8157 (mt0) cc_final: 0.7936 (mt0) REVERT: E 781 ASN cc_start: 0.7074 (OUTLIER) cc_final: 0.6766 (p0) REVERT: E 1004 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.6528 (m-80) REVERT: E 1092 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8041 (tttp) outliers start: 126 outliers final: 82 residues processed: 572 average time/residue: 0.3043 time to fit residues: 274.1406 Evaluate side-chains 575 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 484 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 190 ILE Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 439 TRP Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 483 GLN Chi-restraints excluded: chain E residue 542 ILE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 781 ASN Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1081 VAL Chi-restraints excluded: chain E residue 1089 THR Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1195 THR Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1316 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 206 optimal weight: 20.0000 chunk 168 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 248 optimal weight: 0.8980 chunk 268 optimal weight: 50.0000 chunk 221 optimal weight: 9.9990 chunk 246 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 199 optimal weight: 0.0570 overall best weight: 2.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN D 235 GLN E 32 ASN E 166 GLN ** E 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20779 Z= 0.176 Angle : 0.511 10.583 28401 Z= 0.259 Chirality : 0.043 0.299 3431 Planarity : 0.004 0.047 3507 Dihedral : 13.462 172.115 3527 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.67 % Allowed : 25.51 % Favored : 68.82 % 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: 0.61 (0.17), residues: 2737 helix: 2.04 (0.14), residues: 1316 sheet: -1.41 (0.29), residues: 324 loop : -1.05 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1452 HIS 0.005 0.001 HIS E1024 PHE 0.018 0.001 PHE E 577 TYR 0.014 0.001 TYR E 123 ARG 0.006 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 482 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9491 (OUTLIER) cc_final: 0.9254 (t) REVERT: A 168 PHE cc_start: 0.7192 (OUTLIER) cc_final: 0.6375 (t80) REVERT: B 186 HIS cc_start: 0.7046 (OUTLIER) cc_final: 0.6457 (p-80) REVERT: D 70 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7551 (m90) REVERT: D 128 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8148 (tp40) REVERT: D 308 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: E 168 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7355 (mmm-85) REVERT: E 427 GLN cc_start: 0.8147 (mt0) cc_final: 0.7920 (mt0) REVERT: E 429 MET cc_start: 0.7869 (ttp) cc_final: 0.7610 (ttt) REVERT: E 433 PHE cc_start: 0.8851 (m-10) cc_final: 0.8543 (m-80) REVERT: E 781 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6817 (p0) REVERT: E 1004 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: E 1092 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7965 (tttp) REVERT: E 1132 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8700 (mt) REVERT: E 1149 LEU cc_start: 0.8858 (mt) cc_final: 0.8585 (mt) REVERT: E 1272 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7381 (mp) outliers start: 102 outliers final: 60 residues processed: 536 average time/residue: 0.2914 time to fit residues: 249.3311 Evaluate side-chains 540 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 469 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 PHE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 781 ASN Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1502 ILE Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 27 optimal weight: 40.0000 chunk 118 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 263 optimal weight: 0.0570 chunk 130 optimal weight: 0.9980 chunk 236 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 overall best weight: 3.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN D 235 GLN E 437 ASN ** E 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20779 Z= 0.218 Angle : 0.519 10.173 28401 Z= 0.263 Chirality : 0.043 0.309 3431 Planarity : 0.004 0.045 3507 Dihedral : 13.263 172.225 3523 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 6.50 % Allowed : 26.18 % Favored : 67.32 % 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: 0.59 (0.17), residues: 2737 helix: 2.06 (0.14), residues: 1309 sheet: -1.51 (0.28), residues: 324 loop : -1.07 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 232 HIS 0.013 0.001 HIS E 11 PHE 0.018 0.001 PHE E 577 TYR 0.016 0.001 TYR E 123 ARG 0.004 0.000 ARG E1145 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 483 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9505 (OUTLIER) cc_final: 0.9275 (t) REVERT: A 168 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6391 (t80) REVERT: A 314 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6054 (ttm-80) REVERT: B 186 HIS cc_start: 0.7062 (OUTLIER) cc_final: 0.6545 (p-80) REVERT: C 314 ARG cc_start: 0.6501 (ptt180) cc_final: 0.6192 (ptp-170) REVERT: D 70 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7610 (m90) REVERT: D 128 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8145 (tp40) REVERT: D 308 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: D 347 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8150 (tpp80) REVERT: E 168 ARG cc_start: 0.8414 (tpp80) cc_final: 0.7410 (mmm-85) REVERT: E 233 MET cc_start: 0.8497 (tpp) cc_final: 0.7862 (tpp) REVERT: E 427 GLN cc_start: 0.8161 (mt0) cc_final: 0.7933 (mt0) REVERT: E 433 PHE cc_start: 0.8873 (m-10) cc_final: 0.8565 (m-80) REVERT: E 781 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6735 (p0) REVERT: E 1004 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.6368 (m-80) REVERT: E 1092 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7985 (tttp) REVERT: E 1132 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8709 (mt) REVERT: E 1149 LEU cc_start: 0.8891 (mt) cc_final: 0.8591 (mt) REVERT: E 1272 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7336 (mp) outliers start: 117 outliers final: 83 residues processed: 547 average time/residue: 0.2943 time to fit residues: 254.1736 Evaluate side-chains 565 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 470 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 PHE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 781 ASN Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1102 LEU Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1502 ILE Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 196 optimal weight: 0.5980 chunk 108 optimal weight: 0.8980 chunk 225 optimal weight: 7.9990 chunk 182 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 134 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** E 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20779 Z= 0.203 Angle : 0.510 10.041 28401 Z= 0.258 Chirality : 0.043 0.299 3431 Planarity : 0.004 0.044 3507 Dihedral : 13.064 171.914 3522 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.78 % Allowed : 26.51 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2737 helix: 2.15 (0.14), residues: 1303 sheet: -1.51 (0.28), residues: 324 loop : -1.03 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E1452 HIS 0.009 0.001 HIS E 11 PHE 0.018 0.001 PHE E 790 TYR 0.015 0.001 TYR E 123 ARG 0.004 0.000 ARG E1145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 483 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9468 (OUTLIER) cc_final: 0.9217 (t) REVERT: A 168 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.6410 (t80) REVERT: A 314 ARG cc_start: 0.6792 (OUTLIER) cc_final: 0.6060 (ttm-80) REVERT: B 186 HIS cc_start: 0.7068 (OUTLIER) cc_final: 0.6539 (p-80) REVERT: D 70 HIS cc_start: 0.7824 (OUTLIER) cc_final: 0.7552 (m90) REVERT: D 128 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8084 (tp40) REVERT: D 308 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: D 347 ARG cc_start: 0.8394 (tpp80) cc_final: 0.8062 (tpp80) REVERT: E 168 ARG cc_start: 0.8411 (tpp80) cc_final: 0.8040 (tpp80) REVERT: E 175 LEU cc_start: 0.9171 (tp) cc_final: 0.8911 (mt) REVERT: E 233 MET cc_start: 0.8483 (tpp) cc_final: 0.7917 (tpp) REVERT: E 427 GLN cc_start: 0.8143 (mt0) cc_final: 0.7895 (mt0) REVERT: E 433 PHE cc_start: 0.8868 (m-10) cc_final: 0.8563 (m-80) REVERT: E 781 ASN cc_start: 0.7034 (OUTLIER) cc_final: 0.6788 (p0) REVERT: E 1004 TYR cc_start: 0.7678 (OUTLIER) cc_final: 0.6398 (m-80) REVERT: E 1092 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7941 (tttp) REVERT: E 1132 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8702 (mt) REVERT: E 1149 LEU cc_start: 0.8876 (mt) cc_final: 0.8570 (mt) REVERT: E 1272 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7324 (mp) outliers start: 122 outliers final: 87 residues processed: 549 average time/residue: 0.3002 time to fit residues: 261.0809 Evaluate side-chains 576 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 477 time to evaluate : 2.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 372 PHE Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 781 ASN Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1092 LYS Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1126 SER Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1195 THR Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1502 ILE Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 20.0000 chunk 237 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 264 optimal weight: 50.0000 chunk 219 optimal weight: 20.0000 chunk 122 optimal weight: 0.0010 chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1270 ASN E1293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20779 Z= 0.148 Angle : 0.495 10.612 28401 Z= 0.249 Chirality : 0.042 0.292 3431 Planarity : 0.004 0.057 3507 Dihedral : 12.707 171.722 3522 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.61 % Allowed : 28.13 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.17), residues: 2737 helix: 2.23 (0.14), residues: 1309 sheet: -1.43 (0.29), residues: 322 loop : -1.01 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E1452 HIS 0.009 0.001 HIS E1098 PHE 0.015 0.001 PHE E 577 TYR 0.013 0.001 TYR E 123 ARG 0.003 0.000 ARG E1145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 491 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9510 (OUTLIER) cc_final: 0.9261 (t) REVERT: A 168 PHE cc_start: 0.7161 (OUTLIER) cc_final: 0.6182 (t80) REVERT: C 274 ASP cc_start: 0.7466 (t70) cc_final: 0.5973 (t70) REVERT: C 279 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7064 (tp40) REVERT: D 70 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7487 (m90) REVERT: D 92 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7902 (tt) REVERT: D 128 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8027 (tp40) REVERT: D 269 ASP cc_start: 0.8064 (m-30) cc_final: 0.7852 (m-30) REVERT: D 347 ARG cc_start: 0.8379 (tpp80) cc_final: 0.8010 (tpp80) REVERT: E 233 MET cc_start: 0.8412 (tpp) cc_final: 0.7831 (tpp) REVERT: E 427 GLN cc_start: 0.8099 (mt0) cc_final: 0.7849 (mt0) REVERT: E 433 PHE cc_start: 0.8805 (m-10) cc_final: 0.8469 (m-80) REVERT: E 1004 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.6392 (m-80) REVERT: E 1132 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8658 (mt) REVERT: E 1272 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7235 (mp) REVERT: E 1535 THR cc_start: 0.7611 (m) cc_final: 0.7251 (p) outliers start: 101 outliers final: 69 residues processed: 548 average time/residue: 0.2924 time to fit residues: 255.7599 Evaluate side-chains 552 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 474 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1102 LEU Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 150 optimal weight: 9.9990 chunk 192 optimal weight: 30.0000 chunk 149 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 263 optimal weight: 0.0030 chunk 164 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN ** C 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20779 Z= 0.158 Angle : 0.497 10.909 28401 Z= 0.250 Chirality : 0.043 0.293 3431 Planarity : 0.004 0.060 3507 Dihedral : 12.487 171.329 3518 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.89 % Allowed : 27.90 % Favored : 66.20 % 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: 0.83 (0.17), residues: 2737 helix: 2.28 (0.14), residues: 1312 sheet: -1.40 (0.29), residues: 322 loop : -0.98 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 439 HIS 0.009 0.001 HIS E1098 PHE 0.024 0.001 PHE B 168 TYR 0.013 0.001 TYR E 123 ARG 0.004 0.000 ARG E1145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 479 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8758 (mt) cc_final: 0.8293 (mp) REVERT: A 314 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6207 (ttm-80) REVERT: B 186 HIS cc_start: 0.6958 (OUTLIER) cc_final: 0.6480 (p-80) REVERT: C 77 MET cc_start: 0.7342 (tpt) cc_final: 0.7009 (tpt) REVERT: C 274 ASP cc_start: 0.7448 (t70) cc_final: 0.5921 (t70) REVERT: C 279 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7055 (tp40) REVERT: D 70 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7462 (m90) REVERT: D 92 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7936 (tt) REVERT: D 128 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8098 (tp40) REVERT: E 233 MET cc_start: 0.8410 (tpp) cc_final: 0.8042 (tpp) REVERT: E 427 GLN cc_start: 0.8089 (mt0) cc_final: 0.7870 (mt0) REVERT: E 433 PHE cc_start: 0.8806 (m-10) cc_final: 0.8466 (m-80) REVERT: E 1004 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.6473 (m-80) REVERT: E 1132 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8659 (mt) REVERT: E 1272 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7276 (mp) REVERT: E 1535 THR cc_start: 0.7613 (m) cc_final: 0.7278 (p) outliers start: 106 outliers final: 80 residues processed: 541 average time/residue: 0.3097 time to fit residues: 267.5042 Evaluate side-chains 559 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 470 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 270 PHE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1102 LEU Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1126 SER Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1242 THR Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 167 optimal weight: 0.9990 chunk 179 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 206 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN C 234 HIS ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 870 GLN E1270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20779 Z= 0.339 Angle : 0.587 11.136 28401 Z= 0.299 Chirality : 0.046 0.308 3431 Planarity : 0.004 0.062 3507 Dihedral : 12.742 170.574 3518 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 6.67 % Allowed : 27.13 % Favored : 66.20 % 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: 0.47 (0.16), residues: 2737 helix: 1.93 (0.14), residues: 1309 sheet: -1.60 (0.28), residues: 323 loop : -1.08 (0.19), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 439 HIS 0.011 0.001 HIS E1098 PHE 0.025 0.002 PHE C 60 TYR 0.019 0.002 TYR E 123 ARG 0.007 0.001 ARG D 347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 495 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9476 (OUTLIER) cc_final: 0.9234 (t) REVERT: A 314 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6250 (ttm-80) REVERT: B 186 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.6682 (p-80) REVERT: C 279 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7245 (tp40) REVERT: C 313 GLN cc_start: 0.7316 (mm-40) cc_final: 0.6876 (mm-40) REVERT: D 92 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8125 (tt) REVERT: D 128 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8145 (tp40) REVERT: E 168 ARG cc_start: 0.8528 (tpp80) cc_final: 0.7632 (mmm-85) REVERT: E 427 GLN cc_start: 0.8188 (mt0) cc_final: 0.7940 (mt0) REVERT: E 433 PHE cc_start: 0.8962 (m-10) cc_final: 0.8640 (m-80) REVERT: E 1004 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.6582 (m-80) REVERT: E 1132 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8767 (mp) REVERT: E 1272 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7469 (mp) outliers start: 120 outliers final: 92 residues processed: 557 average time/residue: 0.3036 time to fit residues: 266.4455 Evaluate side-chains 584 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 483 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 195 ARG Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 39 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 208 SER Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 305 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 210 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 404 THR Chi-restraints excluded: chain E residue 439 TRP Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1102 LEU Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1120 SER Chi-restraints excluded: chain E residue 1126 SER Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1502 ILE Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 0.9990 chunk 252 optimal weight: 40.0000 chunk 229 optimal weight: 0.0040 chunk 245 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 192 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1270 ASN E1293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20779 Z= 0.144 Angle : 0.521 12.696 28401 Z= 0.263 Chirality : 0.043 0.288 3431 Planarity : 0.004 0.063 3507 Dihedral : 12.417 169.552 3516 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.06 % Allowed : 29.91 % Favored : 66.04 % 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: 0.78 (0.17), residues: 2737 helix: 2.25 (0.14), residues: 1307 sheet: -1.48 (0.28), residues: 322 loop : -0.99 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 232 HIS 0.012 0.001 HIS E1098 PHE 0.025 0.001 PHE C 60 TYR 0.014 0.001 TYR E1159 ARG 0.011 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 479 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9285 (t) REVERT: A 314 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6224 (ttm-80) REVERT: B 186 HIS cc_start: 0.6973 (OUTLIER) cc_final: 0.6489 (p-80) REVERT: B 229 GLU cc_start: 0.7980 (mp0) cc_final: 0.7774 (mp0) REVERT: C 77 MET cc_start: 0.7328 (tpt) cc_final: 0.6984 (tpt) REVERT: C 274 ASP cc_start: 0.7513 (t70) cc_final: 0.5989 (t70) REVERT: C 279 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7091 (tp40) REVERT: D 92 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7920 (tt) REVERT: D 128 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8027 (tp40) REVERT: E 233 MET cc_start: 0.8015 (tpp) cc_final: 0.7730 (tpp) REVERT: E 433 PHE cc_start: 0.8816 (m-10) cc_final: 0.8482 (m-80) REVERT: E 1004 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.6374 (m-80) REVERT: E 1132 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8640 (mt) REVERT: E 1272 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7285 (mp) REVERT: E 1535 THR cc_start: 0.7593 (m) cc_final: 0.7199 (p) outliers start: 73 outliers final: 62 residues processed: 522 average time/residue: 0.2963 time to fit residues: 242.9711 Evaluate side-chains 540 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 469 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 278 HIS Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1102 LEU Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1126 SER Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 4.9990 chunk 259 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 123 optimal weight: 0.0670 chunk 180 optimal weight: 30.0000 chunk 271 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 167 optimal weight: 3.9990 chunk 132 optimal weight: 0.1980 overall best weight: 2.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1270 ASN E1293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20779 Z= 0.174 Angle : 0.517 12.729 28401 Z= 0.261 Chirality : 0.043 0.293 3431 Planarity : 0.004 0.063 3507 Dihedral : 12.259 169.158 3516 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.34 % Allowed : 29.91 % Favored : 65.76 % 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: 0.82 (0.17), residues: 2737 helix: 2.27 (0.14), residues: 1308 sheet: -1.46 (0.28), residues: 323 loop : -0.96 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 311 HIS 0.011 0.001 HIS E1098 PHE 0.028 0.001 PHE B 168 TYR 0.014 0.001 TYR E 123 ARG 0.009 0.000 ARG B 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5474 Ramachandran restraints generated. 2737 Oldfield, 0 Emsley, 2737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 475 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.9511 (OUTLIER) cc_final: 0.9258 (t) REVERT: A 314 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6192 (ttm-80) REVERT: B 186 HIS cc_start: 0.6969 (OUTLIER) cc_final: 0.6479 (p-80) REVERT: C 77 MET cc_start: 0.7351 (tpt) cc_final: 0.7016 (tpt) REVERT: C 221 ARG cc_start: 0.7698 (ptt180) cc_final: 0.6977 (ptt90) REVERT: D 92 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7964 (tt) REVERT: D 128 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8133 (tp40) REVERT: E 233 MET cc_start: 0.8207 (tpp) cc_final: 0.7910 (tpp) REVERT: E 427 GLN cc_start: 0.8092 (mt0) cc_final: 0.7859 (mt0) REVERT: E 433 PHE cc_start: 0.8827 (m-10) cc_final: 0.8499 (m-80) REVERT: E 1004 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.6477 (m-80) REVERT: E 1132 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8653 (mt) REVERT: E 1272 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7328 (mp) REVERT: E 1535 THR cc_start: 0.7585 (m) cc_final: 0.7205 (p) outliers start: 78 outliers final: 65 residues processed: 522 average time/residue: 0.3066 time to fit residues: 250.9144 Evaluate side-chains 541 residues out of total 2408 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 468 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 259 HIS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 387 LEU Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 518 PHE Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 555 VAL Chi-restraints excluded: chain E residue 575 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 776 LYS Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain E residue 785 GLU Chi-restraints excluded: chain E residue 821 THR Chi-restraints excluded: chain E residue 823 ILE Chi-restraints excluded: chain E residue 894 LEU Chi-restraints excluded: chain E residue 1004 TYR Chi-restraints excluded: chain E residue 1102 LEU Chi-restraints excluded: chain E residue 1105 ILE Chi-restraints excluded: chain E residue 1126 SER Chi-restraints excluded: chain E residue 1132 ILE Chi-restraints excluded: chain E residue 1150 CYS Chi-restraints excluded: chain E residue 1154 LEU Chi-restraints excluded: chain E residue 1228 LEU Chi-restraints excluded: chain E residue 1272 LEU Chi-restraints excluded: chain E residue 1291 VAL Chi-restraints excluded: chain E residue 1306 GLU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain E residue 1367 THR Chi-restraints excluded: chain E residue 1533 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 199 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 chunk 216 optimal weight: 40.0000 chunk 90 optimal weight: 5.9990 chunk 222 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1270 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.170885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.142817 restraints weight = 26183.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.143331 restraints weight = 16521.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.143742 restraints weight = 12222.718| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 20779 Z= 0.344 Angle : 0.608 12.377 28401 Z= 0.310 Chirality : 0.046 0.316 3431 Planarity : 0.005 0.065 3507 Dihedral : 12.515 168.414 3516 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.95 % Allowed : 29.18 % Favored : 65.87 % 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: 2737 helix: 1.89 (0.14), residues: 1313 sheet: -1.57 (0.29), residues: 301 loop : -1.09 (0.19), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 439 HIS 0.012 0.001 HIS E1098 PHE 0.033 0.002 PHE B 168 TYR 0.019 0.002 TYR E 123 ARG 0.008 0.001 ARG D 347 =============================================================================== Job complete usr+sys time: 4745.42 seconds wall clock time: 86 minutes 28.71 seconds (5188.71 seconds total)