Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 04:05:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v05_20969/07_2023/6v05_20969.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v05_20969/07_2023/6v05_20969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v05_20969/07_2023/6v05_20969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v05_20969/07_2023/6v05_20969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v05_20969/07_2023/6v05_20969.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v05_20969/07_2023/6v05_20969.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 8518 2.51 5 N 2407 2.21 5 O 2742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 176": "OE1" <-> "OE2" Residue "A PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A TYR 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A ASP 358": "OD1" <-> "OD2" Residue "A ASP 383": "OD1" <-> "OD2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 404": "NH1" <-> "NH2" Residue "A ARG 421": "NH1" <-> "NH2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 447": "OD1" <-> "OD2" Residue "A TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 503": "OD1" <-> "OD2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A PHE 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 623": "OD1" <-> "OD2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 734": "NH1" <-> "NH2" Residue "A ARG 767": "NH1" <-> "NH2" Residue "A PHE 785": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ASP 271": "OD1" <-> "OD2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B ASP 303": "OD1" <-> "OD2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "C TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 74": "OD1" <-> "OD2" Residue "D ASP 84": "OD1" <-> "OD2" Residue "D ASP 93": "OD1" <-> "OD2" Residue "D ARG 94": "NH1" <-> "NH2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 120": "OD1" <-> "OD2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ASP 213": "OD1" <-> "OD2" Residue "E ARG 78": "NH1" <-> "NH2" Residue "E ASP 105": "OD1" <-> "OD2" Residue "F ASP 464": "OD1" <-> "OD2" Residue "F TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 470": "OE1" <-> "OE2" Residue "F PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 521": "OE1" <-> "OE2" Residue "F ASP 568": "OD1" <-> "OD2" Residue "F PHE 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 605": "OD1" <-> "OD2" Residue "F TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F ASP 639": "OD1" <-> "OD2" Residue "F TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 703": "OD1" <-> "OD2" Residue "F ASP 704": "OD1" <-> "OD2" Residue "F PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 750": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 13705 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5429 Classifications: {'peptide': 758} Incomplete info: {'backbone_only': 138} Link IDs: {'PTRANS': 28, 'TRANS': 729} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 571 Unresolved non-hydrogen angles: 830 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 188 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 13, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 7, 'GLU:plan': 9, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 257 Chain: "B" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2522 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 329} Chain breaks: 4 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'ARG%COO:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 919 Classifications: {'peptide': 181} Incomplete info: {'backbone_only': 112} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 169} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 149 Planarities with less than four sites: {'GLN:plan1': 13, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 236 Chain: "D" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1722 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "E" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 645 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "F" Number of atoms: 2468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2468 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 15, 'TRANS': 293} Chain breaks: 2 Time building chain proxies: 6.89, per 1000 atoms: 0.50 Number of scatterers: 13705 At special positions: 0 Unit cell: (145.35, 125.8, 139.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 2742 8.00 N 2407 7.00 C 8518 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 804 " - pdb=" SG CYS F 467 " 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 Time building additional restraints: 5.35 Conformation dependent library (CDL) restraints added in 2.0 seconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2938 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 18 sheets defined 21.3% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.634A pdb=" N ALA A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 67 Processing helix chain 'A' and resid 68 through 70 No H-bonds generated for 'chain 'A' and resid 68 through 70' Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.620A pdb=" N LEU A 193 " --> pdb=" O THR A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 232 removed outlier: 3.589A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 298 through 314 removed outlier: 4.189A pdb=" N THR A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 369 removed outlier: 4.185A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.796A pdb=" N GLY A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 552 removed outlier: 3.723A pdb=" N SER A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'B' and resid 319 through 323 removed outlier: 3.999A pdb=" N LEU B 322 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.942A pdb=" N GLU C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 39 through 44' Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.634A pdb=" N GLN C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 209 removed outlier: 3.871A pdb=" N MET C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.793A pdb=" N ALA D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 removed outlier: 3.785A pdb=" N GLN D 72 " --> pdb=" O SER D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 4.129A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 4.025A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.798A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.619A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 241 removed outlier: 3.606A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 51 through 60 removed outlier: 3.742A pdb=" N VAL E 55 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 553 removed outlier: 3.945A pdb=" N LEU F 549 " --> pdb=" O MET F 545 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET F 552 " --> pdb=" O TYR F 548 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.517A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP A 74 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.348A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 4.889A pdb=" N ILE A 177 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 256 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN A 179 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL A 258 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASN A 181 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.364A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.750A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 11.874A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 12.197A pdb=" N ALA A 343 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 9.870A pdb=" N GLY A 275 " --> pdb=" O ALA A 343 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 334 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 329 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A 336 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 338 " --> pdb=" O MET A 325 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 325 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 355 removed outlier: 5.967A pdb=" N VAL A 412 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS A 351 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 399 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 419 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 805 removed outlier: 3.535A pdb=" N ASP A 740 " --> pdb=" O SER A 769 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 710 " --> pdb=" O TRP A 745 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN A 506 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 440 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN A 445 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 425 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL F 784 " --> pdb=" O TRP F 776 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TRP F 776 " --> pdb=" O VAL F 784 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER F 786 " --> pdb=" O LEU F 774 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU F 774 " --> pdb=" O SER F 786 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA F 788 " --> pdb=" O ILE F 772 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ILE F 772 " --> pdb=" O ALA F 788 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA F 770 " --> pdb=" O PRO F 790 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR F 735 " --> pdb=" O THR F 720 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 716 " --> pdb=" O TRP F 739 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 628 " --> pdb=" O ILE F 719 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS F 610 " --> pdb=" O LYS F 598 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY F 590 " --> pdb=" O TYR F 618 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR F 567 " --> pdb=" O ASN F 534 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS F 467 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.586A pdb=" N VAL B 71 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 74 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL B 81 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL B 95 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.537A pdb=" N SER B 118 " --> pdb=" O HIS B 121 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS B 121 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B 131 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 145 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP B 143 " --> pdb=" O ALA B 133 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 158 Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.646A pdb=" N VAL B 216 " --> pdb=" O GLN B 230 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 230 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 218 " --> pdb=" O TRP B 228 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.911A pdb=" N VAL B 252 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE B 259 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 290 through 291 removed outlier: 3.815A pdb=" N TYR B 297 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 330 through 333 Processing sheet with id=AB5, first strand: chain 'B' and resid 372 through 374 Processing sheet with id=AB6, first strand: chain 'C' and resid 95 through 100 removed outlier: 5.334A pdb=" N VAL C 174 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS C 166 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL C 176 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N SER C 164 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU C 178 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLN C 162 " --> pdb=" O LEU C 178 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 131 through 133 removed outlier: 4.362A pdb=" N TYR C 161 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLN C 162 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LEU C 178 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N SER C 164 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL C 176 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS C 166 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL C 174 " --> pdb=" O LYS C 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.575A pdb=" N THR E 94 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 654 through 655 removed outlier: 7.445A pdb=" N ALA F 654 " --> pdb=" O THR F 667 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1788 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: 4.89 Time building geometry restraints manager: 5.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4349 1.33 - 1.45: 2234 1.45 - 1.57: 7347 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 14004 Sorted by residual: bond pdb=" N ILE A 254 " pdb=" CA ILE A 254 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" N VAL A 173 " pdb=" CA VAL A 173 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.31e+00 bond pdb=" N GLU A 176 " pdb=" CA GLU A 176 " ideal model delta sigma weight residual 1.455 1.493 -0.039 1.27e-02 6.20e+03 9.20e+00 bond pdb=" N GLN A 179 " pdb=" CA GLN A 179 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.23e-02 6.61e+03 8.88e+00 bond pdb=" CA TRP C 117 " pdb=" C TRP C 117 " ideal model delta sigma weight residual 1.521 1.556 -0.034 1.17e-02 7.31e+03 8.55e+00 ... (remaining 13999 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.68: 268 105.68 - 112.83: 6850 112.83 - 119.98: 4775 119.98 - 127.14: 6893 127.14 - 134.29: 132 Bond angle restraints: 18918 Sorted by residual: angle pdb=" CA ILE A 177 " pdb=" C ILE A 177 " pdb=" O ILE A 177 " ideal model delta sigma weight residual 122.63 118.33 4.30 8.70e-01 1.32e+00 2.44e+01 angle pdb=" N SER C 198 " pdb=" CA SER C 198 " pdb=" C SER C 198 " ideal model delta sigma weight residual 111.14 106.01 5.13 1.08e+00 8.57e-01 2.26e+01 angle pdb=" CA GLN A 178 " pdb=" C GLN A 178 " pdb=" O GLN A 178 " ideal model delta sigma weight residual 120.82 116.08 4.74 1.05e+00 9.07e-01 2.04e+01 angle pdb=" C LEU C 58 " pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 119.84 114.46 5.38 1.25e+00 6.40e-01 1.85e+01 angle pdb=" C ILE C 67 " pdb=" N PRO C 68 " pdb=" CA PRO C 68 " ideal model delta sigma weight residual 119.84 124.94 -5.10 1.25e+00 6.40e-01 1.66e+01 ... (remaining 18913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7034 17.93 - 35.86: 682 35.86 - 53.78: 89 53.78 - 71.71: 15 71.71 - 89.64: 11 Dihedral angle restraints: 7831 sinusoidal: 2928 harmonic: 4903 Sorted by residual: dihedral pdb=" CA GLN F 466 " pdb=" C GLN F 466 " pdb=" N CYS F 467 " pdb=" CA CYS F 467 " ideal model delta harmonic sigma weight residual 180.00 143.70 36.30 0 5.00e+00 4.00e-02 5.27e+01 dihedral pdb=" CA ALA D 83 " pdb=" C ALA D 83 " pdb=" N ASP D 84 " pdb=" CA ASP D 84 " ideal model delta harmonic sigma weight residual 180.00 144.31 35.69 0 5.00e+00 4.00e-02 5.10e+01 dihedral pdb=" CA MET B 221 " pdb=" C MET B 221 " pdb=" N GLU B 222 " pdb=" CA GLU B 222 " ideal model delta harmonic sigma weight residual 180.00 147.31 32.69 0 5.00e+00 4.00e-02 4.27e+01 ... (remaining 7828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1514 0.062 - 0.124: 315 0.124 - 0.186: 40 0.186 - 0.249: 6 0.249 - 0.311: 4 Chirality restraints: 1879 Sorted by residual: chirality pdb=" CA ILE A 177 " pdb=" N ILE A 177 " pdb=" C ILE A 177 " pdb=" CB ILE A 177 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ILE A 180 " pdb=" N ILE A 180 " pdb=" C ILE A 180 " pdb=" CB ILE A 180 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1876 not shown) Planarity restraints: 2579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 173 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ARG D 173 " -0.058 2.00e-02 2.50e+03 pdb=" O ARG D 173 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU D 174 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 306 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C ASP A 306 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP A 306 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP A 307 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 302 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.56e+00 pdb=" C THR A 302 " 0.048 2.00e-02 2.50e+03 pdb=" O THR A 302 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS A 303 " -0.016 2.00e-02 2.50e+03 ... (remaining 2576 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 139 2.62 - 3.19: 11725 3.19 - 3.76: 19423 3.76 - 4.33: 25478 4.33 - 4.90: 42608 Nonbonded interactions: 99373 Sorted by model distance: nonbonded pdb=" OD1 ASP D 45 " pdb=" N GLY D 46 " model vdw 2.054 2.520 nonbonded pdb=" O GLN D 41 " pdb=" OD1 ASP D 45 " model vdw 2.087 3.040 nonbonded pdb=" OH TYR D 110 " pdb=" OD2 ASP D 162 " model vdw 2.178 2.440 nonbonded pdb=" OH TYR F 531 " pdb=" OD1 ASP F 568 " model vdw 2.204 2.440 nonbonded pdb=" OH TYR F 548 " pdb=" ND2 ASN F 606 " model vdw 2.214 2.520 ... (remaining 99368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 10.820 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 36.520 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 14004 Z= 0.206 Angle : 0.655 9.286 18918 Z= 0.421 Chirality : 0.053 0.311 1879 Planarity : 0.004 0.054 2579 Dihedral : 13.874 89.638 4890 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.61 % Favored : 96.34 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.17), residues: 1856 helix: -1.75 (0.22), residues: 352 sheet: -0.76 (0.20), residues: 602 loop : -2.82 (0.17), residues: 902 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 246 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 251 average time/residue: 0.2930 time to fit residues: 102.2171 Evaluate side-chains 154 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 152 time to evaluate : 1.615 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1184 time to fit residues: 2.6206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS A 371 GLN A 411 GLN A 523 ASN A 666 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN B 334 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN D 241 ASN E 33 ASN F 459 ASN F 563 ASN F 731 ASN F 748 ASN F 765 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 14004 Z= 0.349 Angle : 0.655 7.245 18918 Z= 0.357 Chirality : 0.047 0.196 1879 Planarity : 0.004 0.054 2579 Dihedral : 5.519 31.497 2037 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.18), residues: 1856 helix: 0.52 (0.26), residues: 371 sheet: -0.51 (0.19), residues: 638 loop : -2.48 (0.19), residues: 847 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 182 average time/residue: 0.2630 time to fit residues: 69.9688 Evaluate side-chains 139 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 1.696 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1218 time to fit residues: 2.6944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 182 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 167 optimal weight: 0.0570 chunk 57 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 329 ASN A 666 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN F 606 ASN ** F 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 14004 Z= 0.160 Angle : 0.552 7.954 18918 Z= 0.293 Chirality : 0.044 0.148 1879 Planarity : 0.003 0.060 2579 Dihedral : 4.837 34.952 2037 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 1856 helix: 1.50 (0.27), residues: 365 sheet: -0.10 (0.20), residues: 614 loop : -2.13 (0.19), residues: 877 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.2515 time to fit residues: 70.7462 Evaluate side-chains 137 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.583 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 0.6980 chunk 127 optimal weight: 0.0980 chunk 87 optimal weight: 0.2980 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 113 optimal weight: 0.0020 chunk 169 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN B 62 ASN ** B 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 14004 Z= 0.150 Angle : 0.537 7.143 18918 Z= 0.283 Chirality : 0.044 0.263 1879 Planarity : 0.003 0.048 2579 Dihedral : 4.472 30.801 2037 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.66 (0.19), residues: 1856 helix: 1.76 (0.27), residues: 367 sheet: 0.11 (0.20), residues: 630 loop : -1.91 (0.20), residues: 859 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2455 time to fit residues: 70.7539 Evaluate side-chains 144 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.562 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 124 optimal weight: 20.0000 chunk 0 optimal weight: 80.0000 chunk 91 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN B 264 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN F 664 GLN F 789 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 14004 Z= 0.171 Angle : 0.538 6.339 18918 Z= 0.283 Chirality : 0.044 0.262 1879 Planarity : 0.003 0.041 2579 Dihedral : 4.363 32.286 2037 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1856 helix: 1.88 (0.27), residues: 366 sheet: 0.21 (0.20), residues: 652 loop : -1.79 (0.21), residues: 838 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.2556 time to fit residues: 70.0711 Evaluate side-chains 136 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.698 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 50.0000 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN F 731 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 14004 Z= 0.439 Angle : 0.717 8.450 18918 Z= 0.385 Chirality : 0.050 0.239 1879 Planarity : 0.005 0.042 2579 Dihedral : 5.336 32.821 2037 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.96 (0.19), residues: 1856 helix: 1.19 (0.27), residues: 374 sheet: -0.11 (0.19), residues: 653 loop : -1.97 (0.21), residues: 829 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 173 average time/residue: 0.2517 time to fit residues: 65.6264 Evaluate side-chains 137 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.495 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 151 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 112 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 82 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN B 62 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 14004 Z= 0.153 Angle : 0.561 7.785 18918 Z= 0.292 Chirality : 0.044 0.153 1879 Planarity : 0.003 0.047 2579 Dihedral : 4.543 31.131 2037 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.49 (0.20), residues: 1856 helix: 1.81 (0.27), residues: 365 sheet: 0.12 (0.20), residues: 651 loop : -1.69 (0.21), residues: 840 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.637 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2721 time to fit residues: 74.7447 Evaluate side-chains 141 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.833 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 50.0000 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN B 62 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 14004 Z= 0.192 Angle : 0.572 7.661 18918 Z= 0.299 Chirality : 0.044 0.183 1879 Planarity : 0.004 0.044 2579 Dihedral : 4.489 29.538 2037 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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 (0.20), residues: 1856 helix: 1.82 (0.28), residues: 366 sheet: 0.08 (0.20), residues: 655 loop : -1.60 (0.22), residues: 835 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.731 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2255 time to fit residues: 62.9780 Evaluate side-chains 140 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.662 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN B 62 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 495 GLN ** F 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 14004 Z= 0.297 Angle : 0.641 11.022 18918 Z= 0.337 Chirality : 0.046 0.177 1879 Planarity : 0.004 0.045 2579 Dihedral : 4.822 33.329 2037 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1856 helix: 1.58 (0.28), residues: 364 sheet: -0.02 (0.20), residues: 656 loop : -1.65 (0.21), residues: 836 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 1.578 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.2379 time to fit residues: 63.9569 Evaluate side-chains 142 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.7980 chunk 176 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 40.0000 chunk 185 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 14004 Z= 0.193 Angle : 0.590 8.022 18918 Z= 0.309 Chirality : 0.044 0.184 1879 Planarity : 0.004 0.054 2579 Dihedral : 4.532 32.384 2037 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.54 (0.20), residues: 1856 helix: 1.66 (0.28), residues: 370 sheet: 0.00 (0.20), residues: 655 loop : -1.62 (0.21), residues: 831 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.731 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2325 time to fit residues: 62.7745 Evaluate side-chains 141 residues out of total 1580 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 50.0000 chunk 157 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 136 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 147 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 666 ASN ** B 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 731 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.127902 restraints weight = 24893.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127717 restraints weight = 51846.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128360 restraints weight = 45077.816| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 14004 Z= 0.187 Angle : 0.579 8.932 18918 Z= 0.302 Chirality : 0.044 0.182 1879 Planarity : 0.004 0.057 2579 Dihedral : 4.441 31.551 2037 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.46 (0.20), residues: 1856 helix: 1.69 (0.28), residues: 369 sheet: 0.05 (0.20), residues: 656 loop : -1.54 (0.22), residues: 831 =============================================================================== Job complete usr+sys time: 2550.17 seconds wall clock time: 47 minutes 14.64 seconds (2834.64 seconds total)