Starting phenix.real_space_refine on Sat Feb 17 09:47:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpv_22424/02_2024/7jpv_22424_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpv_22424/02_2024/7jpv_22424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpv_22424/02_2024/7jpv_22424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpv_22424/02_2024/7jpv_22424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpv_22424/02_2024/7jpv_22424_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpv_22424/02_2024/7jpv_22424_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Ca 1 9.91 5 P 10 5.49 5 S 107 5.16 5 C 11930 2.51 5 N 2940 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A GLU 54": "OE1" <-> "OE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 500": "OD1" <-> "OD2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 615": "OD1" <-> "OD2" Residue "A TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 656": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 794": "NH1" <-> "NH2" Residue "A PHE 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A GLU 966": "OE1" <-> "OE2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "A TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1022": "NH1" <-> "NH2" Residue "A ASP 1025": "OD1" <-> "OD2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1060": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1099": "NH1" <-> "NH2" Residue "A TYR 1101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1151": "OD1" <-> "OD2" Residue "A GLU 1164": "OE1" <-> "OE2" Residue "A PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1236": "NH1" <-> "NH2" Residue "A ARG 1242": "NH1" <-> "NH2" Residue "A GLU 1251": "OE1" <-> "OE2" Residue "A PHE 1279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1327": "OE1" <-> "OE2" Residue "A TYR 1334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1343": "OD1" <-> "OD2" Residue "A TYR 1344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1348": "OE1" <-> "OE2" Residue "A TYR 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1382": "OD1" <-> "OD2" Residue "A PHE 1384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1385": "OD1" <-> "OD2" Residue "A ARG 1389": "NH1" <-> "NH2" Residue "A ASP 1390": "OD1" <-> "OD2" Residue "A GLU 1401": "OE1" <-> "OE2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1428": "NH1" <-> "NH2" Residue "E PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 175": "OE1" <-> "OE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "F ASP 38": "OD1" <-> "OD2" Residue "F ASP 43": "OD1" <-> "OD2" Residue "F ASP 66": "OD1" <-> "OD2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ASP 202": "OD1" <-> "OD2" Residue "F TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 230": "NH1" <-> "NH2" Residue "F ASP 236": "OD1" <-> "OD2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 368": "OE1" <-> "OE2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F GLU 373": "OE1" <-> "OE2" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 427": "OE1" <-> "OE2" Residue "F ASP 441": "OD1" <-> "OD2" Residue "F GLU 497": "OE1" <-> "OE2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F GLU 587": "OE1" <-> "OE2" Residue "F ARG 591": "NH1" <-> "NH2" Residue "F GLU 599": "OE1" <-> "OE2" Residue "F TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 607": "NH1" <-> "NH2" Residue "F TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 639": "OE1" <-> "OE2" Residue "F PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 672": "OD1" <-> "OD2" Residue "F PHE 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 692": "NH1" <-> "NH2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 745": "NH1" <-> "NH2" Residue "F GLU 753": "OE1" <-> "OE2" Residue "F TYR 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 820": "OD1" <-> "OD2" Residue "F ASP 843": "OD1" <-> "OD2" Residue "F ARG 846": "NH1" <-> "NH2" Residue "F ASP 868": "OD1" <-> "OD2" Residue "F ASP 869": "OD1" <-> "OD2" Residue "F ASP 882": "OD1" <-> "OD2" Residue "F PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 998": "OD1" <-> "OD2" Residue "F ARG 1004": "NH1" <-> "NH2" Residue "F GLU 1038": "OE1" <-> "OE2" Residue "F ASP 1042": "OD1" <-> "OD2" Residue "F ASP 1048": "OD1" <-> "OD2" Residue "F PHE 1063": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1069": "OE1" <-> "OE2" Residue "F ASP 1070": "OD1" <-> "OD2" 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: 18288 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1115, 8987 Classifications: {'peptide': 1115} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 36, 'TRANS': 1078} Chain breaks: 10 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain breaks: 2 Chain: "F" Number of atoms: 7804 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 973, 7796 Classifications: {'peptide': 973} Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927} Chain breaks: 2 bond proxies already assigned to first conformer: 7954 Chain: "A" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 363 Unusual residues: {' CA': 1, '3PE': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.30, per 1000 atoms: 0.73 Number of scatterers: 18288 At special positions: 0 Unit cell: (144.82, 141.478, 158.188, 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) Ca 1 19.99 S 107 16.00 P 10 15.00 O 3300 8.00 N 2940 7.00 C 11930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 245 " - pdb=" SG CYS A 261 " distance=2.03 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 968 " distance=2.03 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.04 Simple disulfide: pdb=" SG CYS F 356 " - pdb=" SG CYS F1062 " distance=2.03 Simple disulfide: pdb=" SG CYS F 406 " - pdb=" SG CYS F1074 " distance=2.03 Simple disulfide: pdb=" SG CYS F 670 " - pdb=" SG CYS F 700 " distance=2.03 Simple disulfide: pdb=" SG CYS F 844 " - pdb=" SG CYS F 853 " distance=2.03 Simple disulfide: pdb=" SG CYS F 907 " - pdb=" SG CYS F 977 " distance=2.03 Simple disulfide: pdb=" SG CYS F 999 " - pdb=" SG CYS F1029 " distance=2.03 Simple disulfide: pdb=" SG CYS F1002 " - pdb=" SG CYS F1027 " 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.11 Conformation dependent library (CDL) restraints added in 4.2 seconds 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4218 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 13 sheets defined 47.7% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 81 through 105 removed outlier: 3.599A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 142 removed outlier: 3.849A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 178 removed outlier: 4.359A pdb=" N PHE A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ARG A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ARG A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Proline residue: A 172 - end of helix removed outlier: 4.178A pdb=" N LEU A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.595A pdb=" N VAL A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 217 Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 311 through 345 removed outlier: 4.576A pdb=" N PHE A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE A 325 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 449 removed outlier: 4.296A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 486 removed outlier: 3.788A pdb=" N ILE A 466 " --> pdb=" O HIS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 500 through 515 Processing helix chain 'A' and resid 521 through 541 removed outlier: 3.557A pdb=" N ARG A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 581 removed outlier: 5.719A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 611 Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.830A pdb=" N TYR A 621 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 622 " --> pdb=" O SER A 618 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 646 removed outlier: 4.052A pdb=" N LEU A 636 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL A 637 " --> pdb=" O PRO A 633 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N CYS A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N TYR A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N PHE A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 642 " --> pdb=" O CYS A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 656 removed outlier: 3.642A pdb=" N LEU A 652 " --> pdb=" O GLY A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 672 removed outlier: 3.692A pdb=" N GLU A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 810 removed outlier: 3.639A pdb=" N LEU A 807 " --> pdb=" O ASN A 803 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 809 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 817 removed outlier: 3.682A pdb=" N ALA A 817 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 851 removed outlier: 3.716A pdb=" N ALA A 838 " --> pdb=" O TYR A 834 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE A 843 " --> pdb=" O PHE A 839 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 846 " --> pdb=" O VAL A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 881 removed outlier: 4.176A pdb=" N SER A 879 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 880 " --> pdb=" O VAL A 876 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE A 881 " --> pdb=" O ALA A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 900 removed outlier: 3.642A pdb=" N VAL A 898 " --> pdb=" O LYS A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 911 No H-bonds generated for 'chain 'A' and resid 908 through 911' Processing helix chain 'A' and resid 914 through 927 removed outlier: 3.598A pdb=" N ARG A 926 " --> pdb=" O PHE A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 949 removed outlier: 4.044A pdb=" N VAL A 934 " --> pdb=" O ASN A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 978 No H-bonds generated for 'chain 'A' and resid 976 through 978' Processing helix chain 'A' and resid 1000 through 1011 Processing helix chain 'A' and resid 1016 through 1023 removed outlier: 3.749A pdb=" N ARG A1022 " --> pdb=" O GLN A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1047 No H-bonds generated for 'chain 'A' and resid 1044 through 1047' Processing helix chain 'A' and resid 1055 through 1071 removed outlier: 3.504A pdb=" N VAL A1064 " --> pdb=" O PHE A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1094 removed outlier: 4.392A pdb=" N CYS A1088 " --> pdb=" O GLN A1085 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL A1089 " --> pdb=" O ARG A1086 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A1093 " --> pdb=" O GLN A1090 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS A1094 " --> pdb=" O TYR A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 4.890A pdb=" N VAL A1111 " --> pdb=" O TYR A1107 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1136 Processing helix chain 'A' and resid 1153 through 1170 Processing helix chain 'A' and resid 1181 through 1205 Processing helix chain 'A' and resid 1233 through 1248 removed outlier: 3.870A pdb=" N PHE A1238 " --> pdb=" O PHE A1235 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET A1241 " --> pdb=" O PHE A1238 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A1243 " --> pdb=" O VAL A1240 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A1245 " --> pdb=" O ARG A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1261 removed outlier: 3.901A pdb=" N THR A1255 " --> pdb=" O GLU A1251 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A1256 " --> pdb=" O GLY A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1270 through 1288 removed outlier: 3.806A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A1275 " --> pdb=" O ALA A1271 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A1283 " --> pdb=" O PHE A1279 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A1284 " --> pdb=" O ILE A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1321 Processing helix chain 'A' and resid 1325 through 1331 removed outlier: 3.657A pdb=" N LEU A1330 " --> pdb=" O GLN A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1355 through 1380 removed outlier: 4.124A pdb=" N PHE A1361 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ILE A1362 " --> pdb=" O TYR A1359 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER A1363 " --> pdb=" O TYR A1360 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A1367 " --> pdb=" O PHE A1364 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N CYS A1368 " --> pdb=" O TYR A1365 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A1375 " --> pdb=" O ILE A1372 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA A1378 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A1379 " --> pdb=" O PHE A1376 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1387 No H-bonds generated for 'chain 'A' and resid 1384 through 1387' Processing helix chain 'A' and resid 1396 through 1409 removed outlier: 3.536A pdb=" N ALA A1407 " --> pdb=" O LYS A1403 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A1408 " --> pdb=" O ALA A1404 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1428 No H-bonds generated for 'chain 'A' and resid 1426 through 1428' Processing helix chain 'E' and resid 7 through 28 removed outlier: 3.577A pdb=" N VAL E 18 " --> pdb=" O PHE E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 126 removed outlier: 3.867A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 134 through 162 Proline residue: E 139 - end of helix removed outlier: 4.143A pdb=" N PHE E 152 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN E 160 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 203 removed outlier: 3.741A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 50 removed outlier: 3.570A pdb=" N THR F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 63 removed outlier: 3.617A pdb=" N GLU F 62 " --> pdb=" O VAL F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 110 removed outlier: 3.680A pdb=" N LEU F 97 " --> pdb=" O ARG F 93 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG F 99 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA F 110 " --> pdb=" O LYS F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 190 removed outlier: 3.506A pdb=" N ASN F 183 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU F 184 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALA F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 201 Processing helix chain 'F' and resid 240 through 242 No H-bonds generated for 'chain 'F' and resid 240 through 242' Processing helix chain 'F' and resid 244 through 249 Processing helix chain 'F' and resid 264 through 266 No H-bonds generated for 'chain 'F' and resid 264 through 266' Processing helix chain 'F' and resid 269 through 284 removed outlier: 3.542A pdb=" N THR F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU F 283 " --> pdb=" O SER F 279 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 4.383A pdb=" N ASN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 345 Processing helix chain 'F' and resid 372 through 378 Processing helix chain 'F' and resid 399 through 407 Processing helix chain 'F' and resid 418 through 421 removed outlier: 3.521A pdb=" N ILE F 421 " --> pdb=" O ILE F 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 418 through 421' Processing helix chain 'F' and resid 428 through 432 Processing helix chain 'F' and resid 434 through 439 removed outlier: 4.002A pdb=" N ALA F 439 " --> pdb=" O PRO F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 500 removed outlier: 3.655A pdb=" N LYS F 500 " --> pdb=" O LEU F 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 496 through 500' Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 563 through 565 No H-bonds generated for 'chain 'F' and resid 563 through 565' Processing helix chain 'F' and resid 573 through 581 Processing helix chain 'F' and resid 641 through 650 removed outlier: 3.870A pdb=" N THR F 650 " --> pdb=" O ARG F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 659 removed outlier: 3.700A pdb=" N PHE F 656 " --> pdb=" O PRO F 653 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLU F 657 " --> pdb=" O ASP F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 692 removed outlier: 3.545A pdb=" N ARG F 692 " --> pdb=" O GLU F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 702 through 721 Processing helix chain 'F' and resid 749 through 754 removed outlier: 3.936A pdb=" N GLU F 753 " --> pdb=" O LYS F 749 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN F 754 " --> pdb=" O GLU F 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 749 through 754' Processing helix chain 'F' and resid 765 through 772 Processing helix chain 'F' and resid 821 through 829 Processing helix chain 'F' and resid 878 through 881 No H-bonds generated for 'chain 'F' and resid 878 through 881' Processing helix chain 'F' and resid 883 through 891 Processing helix chain 'F' and resid 1046 through 1048 No H-bonds generated for 'chain 'F' and resid 1046 through 1048' Processing helix chain 'F' and resid 1050 through 1052 No H-bonds generated for 'chain 'F' and resid 1050 through 1052' Processing sheet with id= A, first strand: chain 'A' and resid 225 through 228 removed outlier: 3.916A pdb=" N THR A 225 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 262 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 971 through 975 Processing sheet with id= C, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= D, first strand: chain 'F' and resid 124 through 126 Processing sheet with id= E, first strand: chain 'F' and resid 167 through 169 removed outlier: 3.501A pdb=" N TYR F 219 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 411 through 415 removed outlier: 3.750A pdb=" N TYR F 411 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE F 290 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE F 258 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASN F 292 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N VAL F 260 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA F 294 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 513 through 517 removed outlier: 3.538A pdb=" N PHE F 515 " --> pdb=" O ALA F 623 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 586 through 592 removed outlier: 3.636A pdb=" N GLY F 586 " --> pdb=" O TRP F 611 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 661 through 663 removed outlier: 3.941A pdb=" N THR F 744 " --> pdb=" O PHE F 663 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE F 736 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 851 through 857 removed outlier: 6.033A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 895 through 897 Processing sheet with id= L, first strand: chain 'F' and resid 900 through 902 removed outlier: 4.527A pdb=" N ILE F 978 " --> pdb=" O SER F1041 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 905 through 907 727 hydrogen bonds defined for protein. 1976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.65 Time building geometry restraints manager: 7.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 1 1.20 - 1.36: 5702 1.36 - 1.51: 6507 1.51 - 1.67: 6312 1.67 - 1.83: 166 Bond restraints: 18688 Sorted by residual: bond pdb=" C ASN A1036 " pdb=" N ASN A1037 " ideal model delta sigma weight residual 1.334 1.044 0.290 1.27e-02 6.20e+03 5.21e+02 bond pdb=" C21 3PE A1908 " pdb=" O21 3PE A1908 " ideal model delta sigma weight residual 1.316 1.455 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C21 3PE A1902 " pdb=" O21 3PE A1902 " ideal model delta sigma weight residual 1.316 1.454 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" C21 3PE A1905 " pdb=" O21 3PE A1905 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C21 3PE A1906 " pdb=" O21 3PE A1906 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.69e+01 ... (remaining 18683 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.61: 470 106.61 - 113.48: 10275 113.48 - 120.35: 7139 120.35 - 127.22: 7217 127.22 - 134.09: 159 Bond angle restraints: 25260 Sorted by residual: angle pdb=" N GLY A1062 " pdb=" CA GLY A1062 " pdb=" C GLY A1062 " ideal model delta sigma weight residual 112.77 107.77 5.00 1.28e+00 6.10e-01 1.52e+01 angle pdb=" N ILE A1052 " pdb=" CA ILE A1052 " pdb=" C ILE A1052 " ideal model delta sigma weight residual 110.36 114.20 -3.84 1.05e+00 9.07e-01 1.34e+01 angle pdb=" N LEU A 937 " pdb=" CA LEU A 937 " pdb=" C LEU A 937 " ideal model delta sigma weight residual 112.45 107.54 4.91 1.39e+00 5.18e-01 1.25e+01 angle pdb=" N PHE A1060 " pdb=" CA PHE A1060 " pdb=" C PHE A1060 " ideal model delta sigma weight residual 112.23 107.80 4.43 1.26e+00 6.30e-01 1.24e+01 angle pdb=" C2 3PE A1903 " pdb=" O21 3PE A1903 " pdb=" C21 3PE A1903 " ideal model delta sigma weight residual 121.04 110.77 10.27 3.00e+00 1.11e-01 1.17e+01 ... (remaining 25255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.05: 10045 23.05 - 46.09: 962 46.09 - 69.14: 223 69.14 - 92.18: 38 92.18 - 115.23: 3 Dihedral angle restraints: 11271 sinusoidal: 4741 harmonic: 6530 Sorted by residual: dihedral pdb=" CB CYS F 999 " pdb=" SG CYS F 999 " pdb=" SG CYS F1029 " pdb=" CB CYS F1029 " ideal model delta sinusoidal sigma weight residual 93.00 -178.32 -88.68 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS F 670 " pdb=" SG CYS F 670 " pdb=" SG CYS F 700 " pdb=" CB CYS F 700 " ideal model delta sinusoidal sigma weight residual -86.00 -158.79 72.79 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS A 226 " pdb=" SG CYS A 226 " pdb=" SG CYS A 254 " pdb=" CB CYS A 254 " ideal model delta sinusoidal sigma weight residual 93.00 161.60 -68.60 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 11268 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1954 0.040 - 0.080: 682 0.080 - 0.121: 154 0.121 - 0.161: 24 0.161 - 0.201: 3 Chirality restraints: 2817 Sorted by residual: chirality pdb=" CA PHE A 314 " pdb=" N PHE A 314 " pdb=" C PHE A 314 " pdb=" CB PHE A 314 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA VAL A1034 " pdb=" N VAL A1034 " pdb=" C VAL A1034 " pdb=" CB VAL A1034 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CA GLU A 76 " pdb=" N GLU A 76 " pdb=" C GLU A 76 " pdb=" CB GLU A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 2814 not shown) Planarity restraints: 3153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 51 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO A 52 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 52 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 52 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 141 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO F 142 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO F 142 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 142 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 300 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C TRP A 300 " 0.035 2.00e-02 2.50e+03 pdb=" O TRP A 300 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 301 " -0.012 2.00e-02 2.50e+03 ... (remaining 3150 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 215 2.61 - 3.18: 16207 3.18 - 3.76: 26740 3.76 - 4.33: 38342 4.33 - 4.90: 63532 Nonbonded interactions: 145036 Sorted by model distance: nonbonded pdb=" O TYR A 210 " pdb=" OH TYR A 313 " model vdw 2.040 2.440 nonbonded pdb=" N 3PE A1910 " pdb=" O14 3PE A1910 " model vdw 2.079 2.520 nonbonded pdb=" N 3PE A1903 " pdb=" O14 3PE A1903 " model vdw 2.080 2.520 nonbonded pdb=" OD2 ASP F 154 " pdb=" OH TYR F 163 " model vdw 2.100 2.440 nonbonded pdb=" O TYR F 61 " pdb=" OH TYR F 68 " model vdw 2.135 2.440 ... (remaining 145031 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.520 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: 5.970 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 54.320 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.006 0.290 18688 Z= 0.369 Angle : 0.756 10.266 25260 Z= 0.385 Chirality : 0.042 0.201 2817 Planarity : 0.004 0.061 3153 Dihedral : 18.503 115.231 7017 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.57 % Favored : 93.25 % Rotamer: Outliers : 7.64 % Allowed : 20.88 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.15), residues: 2194 helix: -1.82 (0.13), residues: 1070 sheet: -2.70 (0.33), residues: 192 loop : -3.62 (0.17), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 187 HIS 0.003 0.001 HIS F 888 PHE 0.016 0.001 PHE F 157 TYR 0.016 0.001 TYR A1109 ARG 0.003 0.000 ARG F 769 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 282 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8495 (t80) cc_final: 0.8249 (t80) REVERT: A 343 LYS cc_start: 0.5271 (ptpp) cc_final: 0.5063 (pttt) REVERT: A 828 ARG cc_start: 0.4607 (ttp-170) cc_final: 0.4278 (tpp-160) REVERT: A 938 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8109 (mp) REVERT: A 1040 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: A 1060 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.6656 (t80) REVERT: A 1186 ASP cc_start: 0.8159 (t0) cc_final: 0.7872 (t0) REVERT: A 1205 PHE cc_start: 0.4638 (t80) cc_final: 0.4438 (t80) REVERT: A 1316 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8752 (mp) REVERT: A 1381 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6293 (tmm) REVERT: E 189 PHE cc_start: 0.7287 (t80) cc_final: 0.6984 (t80) REVERT: F 281 MET cc_start: 0.8844 (tpp) cc_final: 0.8426 (ttm) REVERT: F 348 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8271 (t0) REVERT: F 368 GLU cc_start: 0.7367 (pt0) cc_final: 0.7133 (pt0) REVERT: F 380 LYS cc_start: 0.8418 (ttpp) cc_final: 0.7895 (ttpt) REVERT: F 413 TYR cc_start: 0.9275 (m-80) cc_final: 0.8964 (m-80) REVERT: F 442 LYS cc_start: 0.8742 (ttpp) cc_final: 0.8386 (ttpt) REVERT: F 604 LYS cc_start: 0.8378 (mtmm) cc_final: 0.8132 (mttm) REVERT: F 858 ASP cc_start: 0.7959 (p0) cc_final: 0.7630 (p0) outliers start: 150 outliers final: 112 residues processed: 410 average time/residue: 0.3152 time to fit residues: 196.2570 Evaluate side-chains 361 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 243 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 792 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 935 THR Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1011 SER Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1038 ARG Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1040 GLU Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1047 ILE Chi-restraints excluded: chain A residue 1050 ILE Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1067 THR Chi-restraints excluded: chain A residue 1069 GLN Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1159 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1316 LEU Chi-restraints excluded: chain A residue 1380 ILE Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain E residue 27 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 552 ASN Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 729 ILE Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 798 SER Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 874 ILE Chi-restraints excluded: chain F residue 997 LEU Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1068 LEU Chi-restraints excluded: chain F residue 1074 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 3.9990 chunk 167 optimal weight: 0.2980 chunk 92 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 67 optimal weight: 0.0370 chunk 105 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 307 ASN A 327 ASN A 453 HIS A 599 ASN A 797 ASN A 999 ASN A1036 ASN A1085 GLN A1108 GLN A1138 GLN A1154 ASN F 65 GLN F 74 ASN F 299 ASN F 307 GLN ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 477 ASN F 484 GLN F 511 ASN F 644 GLN F 679 ASN F 685 ASN ** F 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 866 ASN F 872 ASN F 981 GLN F 983 GLN F1065 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18688 Z= 0.146 Angle : 0.523 8.111 25260 Z= 0.267 Chirality : 0.040 0.146 2817 Planarity : 0.004 0.059 3153 Dihedral : 14.770 87.169 3011 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 6.16 % Allowed : 23.78 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.17), residues: 2194 helix: -0.38 (0.16), residues: 1068 sheet: -2.05 (0.34), residues: 207 loop : -3.04 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 187 HIS 0.002 0.000 HIS A 453 PHE 0.018 0.001 PHE A1185 TYR 0.012 0.001 TYR F 163 ARG 0.004 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 274 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 182 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7973 (tt) REVERT: A 302 ASN cc_start: 0.7769 (t0) cc_final: 0.7228 (t0) REVERT: A 828 ARG cc_start: 0.4595 (ttp-170) cc_final: 0.4265 (tpp-160) REVERT: A 938 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8018 (mp) REVERT: A 1059 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8100 (mt) REVERT: A 1060 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.6571 (t80) REVERT: A 1069 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.4674 (mp10) REVERT: A 1186 ASP cc_start: 0.8052 (t0) cc_final: 0.7564 (t0) REVERT: A 1286 MET cc_start: 0.8282 (mtp) cc_final: 0.7900 (mtm) REVERT: F 281 MET cc_start: 0.8777 (tpp) cc_final: 0.8111 (ttm) REVERT: F 348 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8138 (t0) REVERT: F 368 GLU cc_start: 0.7324 (pt0) cc_final: 0.7110 (pt0) REVERT: F 380 LYS cc_start: 0.8354 (ttpp) cc_final: 0.7872 (ttpt) REVERT: F 413 TYR cc_start: 0.9290 (m-80) cc_final: 0.8949 (m-80) REVERT: F 442 LYS cc_start: 0.8712 (ttpp) cc_final: 0.8381 (ttpt) REVERT: F 593 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8438 (pp) REVERT: F 727 LYS cc_start: 0.8674 (tppt) cc_final: 0.8336 (mmtp) REVERT: F 729 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.7962 (mm) REVERT: F 858 ASP cc_start: 0.7951 (p0) cc_final: 0.7579 (p0) outliers start: 121 outliers final: 79 residues processed: 375 average time/residue: 0.2803 time to fit residues: 164.2142 Evaluate side-chains 339 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 252 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 792 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1036 ASN Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1069 GLN Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 212 SER Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 348 ASN Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 478 LYS Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 729 ILE Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 167 optimal weight: 0.4980 chunk 136 optimal weight: 0.0060 chunk 55 optimal weight: 9.9990 chunk 201 optimal weight: 7.9990 chunk 217 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 453 HIS A1108 GLN F 74 ASN ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 888 HIS ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18688 Z= 0.248 Angle : 0.545 7.106 25260 Z= 0.281 Chirality : 0.041 0.236 2817 Planarity : 0.004 0.057 3153 Dihedral : 13.881 82.110 2913 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.48 % Favored : 93.48 % Rotamer: Outliers : 6.26 % Allowed : 23.47 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.18), residues: 2194 helix: -0.02 (0.16), residues: 1074 sheet: -1.88 (0.34), residues: 210 loop : -2.82 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 187 HIS 0.010 0.001 HIS A 453 PHE 0.019 0.001 PHE F 993 TYR 0.016 0.001 TYR E 135 ARG 0.003 0.000 ARG F 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 250 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8263 (mtm) REVERT: A 183 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: A 444 LEU cc_start: 0.8816 (tt) cc_final: 0.8308 (mt) REVERT: A 828 ARG cc_start: 0.4535 (ttp-170) cc_final: 0.4207 (tpp-160) REVERT: A 938 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8083 (mp) REVERT: A 1018 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7691 (mt0) REVERT: A 1060 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.6530 (t80) REVERT: A 1068 PHE cc_start: 0.7148 (m-10) cc_final: 0.6795 (m-80) REVERT: A 1186 ASP cc_start: 0.8118 (t0) cc_final: 0.7744 (t0) REVERT: F 281 MET cc_start: 0.8884 (tpp) cc_final: 0.8470 (ttm) REVERT: F 368 GLU cc_start: 0.7368 (pt0) cc_final: 0.7123 (pt0) REVERT: F 380 LYS cc_start: 0.8395 (ttpp) cc_final: 0.7907 (ttpt) REVERT: F 593 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8539 (pp) REVERT: F 730 LYS cc_start: 0.5549 (mttt) cc_final: 0.5316 (mttt) REVERT: F 858 ASP cc_start: 0.8004 (p0) cc_final: 0.7646 (p0) outliers start: 123 outliers final: 98 residues processed: 352 average time/residue: 0.2793 time to fit residues: 153.7149 Evaluate side-chains 346 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 242 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 792 CYS Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1069 GLN Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1382 ASP Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 212 SER Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 774 ASP Chi-restraints excluded: chain F residue 806 GLN Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 201 optimal weight: 0.7980 chunk 213 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A1108 GLN F 74 ASN ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18688 Z= 0.146 Angle : 0.498 7.242 25260 Z= 0.255 Chirality : 0.040 0.153 2817 Planarity : 0.004 0.055 3153 Dihedral : 13.039 79.475 2900 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 6.21 % Allowed : 23.93 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.18), residues: 2194 helix: 0.44 (0.16), residues: 1066 sheet: -1.54 (0.34), residues: 207 loop : -2.55 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 187 HIS 0.002 0.000 HIS F 888 PHE 0.022 0.001 PHE F1018 TYR 0.014 0.001 TYR E 176 ARG 0.003 0.000 ARG F 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 257 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LEU cc_start: 0.8829 (tt) cc_final: 0.8303 (mt) REVERT: A 483 MET cc_start: 0.2206 (tpt) cc_final: 0.1794 (tpt) REVERT: A 828 ARG cc_start: 0.4589 (ttp-170) cc_final: 0.4247 (tpp-160) REVERT: A 916 HIS cc_start: 0.4424 (t-90) cc_final: 0.2739 (m90) REVERT: A 1029 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6559 (tp30) REVERT: A 1060 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6544 (t80) REVERT: A 1068 PHE cc_start: 0.7143 (m-10) cc_final: 0.6911 (m-80) REVERT: A 1186 ASP cc_start: 0.7952 (t0) cc_final: 0.7484 (t0) REVERT: A 1286 MET cc_start: 0.8305 (mtp) cc_final: 0.8046 (mtm) REVERT: F 281 MET cc_start: 0.8722 (tpp) cc_final: 0.8449 (ttm) REVERT: F 368 GLU cc_start: 0.7327 (pt0) cc_final: 0.7066 (pt0) REVERT: F 380 LYS cc_start: 0.8459 (ttpp) cc_final: 0.7956 (ttpt) REVERT: F 413 TYR cc_start: 0.9255 (m-80) cc_final: 0.8908 (m-80) REVERT: F 593 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8457 (pp) REVERT: F 735 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7880 (ptt-90) REVERT: F 858 ASP cc_start: 0.7954 (p0) cc_final: 0.7599 (p0) outliers start: 122 outliers final: 88 residues processed: 355 average time/residue: 0.2956 time to fit residues: 165.0803 Evaluate side-chains 337 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 245 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 792 CYS Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1069 GLN Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1381 MET Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 160 GLN Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 212 SER Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 182 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 53 optimal weight: 40.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 663 ASN A1058 ASN A1108 GLN ** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18688 Z= 0.217 Angle : 0.523 7.331 25260 Z= 0.267 Chirality : 0.041 0.190 2817 Planarity : 0.004 0.055 3153 Dihedral : 12.662 80.628 2888 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.06 % Favored : 93.89 % Rotamer: Outliers : 6.26 % Allowed : 24.85 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.18), residues: 2194 helix: 0.49 (0.16), residues: 1074 sheet: -1.54 (0.34), residues: 214 loop : -2.47 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 187 HIS 0.002 0.001 HIS A1398 PHE 0.022 0.001 PHE F1018 TYR 0.014 0.001 TYR A1109 ARG 0.002 0.000 ARG A 897 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 253 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7527 (mt0) REVERT: A 483 MET cc_start: 0.2091 (tpt) cc_final: 0.1680 (tpt) REVERT: A 652 LEU cc_start: 0.9138 (tt) cc_final: 0.8934 (tt) REVERT: A 828 ARG cc_start: 0.4613 (ttp-170) cc_final: 0.4254 (tpp-160) REVERT: A 1018 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7611 (mt0) REVERT: A 1029 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6645 (tp30) REVERT: A 1060 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6636 (t80) REVERT: A 1186 ASP cc_start: 0.7963 (t0) cc_final: 0.7568 (t0) REVERT: F 281 MET cc_start: 0.8847 (tpp) cc_final: 0.8484 (ttm) REVERT: F 368 GLU cc_start: 0.7329 (pt0) cc_final: 0.7073 (pt0) REVERT: F 380 LYS cc_start: 0.8308 (ttpp) cc_final: 0.7857 (ttpt) REVERT: F 413 TYR cc_start: 0.9268 (m-80) cc_final: 0.8913 (m-80) REVERT: F 735 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7937 (ptt-90) REVERT: F 858 ASP cc_start: 0.7983 (p0) cc_final: 0.7627 (p0) outliers start: 123 outliers final: 100 residues processed: 351 average time/residue: 0.2734 time to fit residues: 150.7381 Evaluate side-chains 347 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 242 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 925 ILE Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 160 GLN Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 212 SER Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 806 GLN Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 213 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A1058 ASN A1108 GLN ** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18688 Z= 0.193 Angle : 0.515 7.047 25260 Z= 0.263 Chirality : 0.041 0.157 2817 Planarity : 0.004 0.054 3153 Dihedral : 12.330 80.984 2882 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.88 % Favored : 94.07 % Rotamer: Outliers : 6.31 % Allowed : 24.85 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 2194 helix: 0.58 (0.16), residues: 1078 sheet: -1.44 (0.34), residues: 216 loop : -2.42 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 187 HIS 0.003 0.001 HIS A1398 PHE 0.028 0.001 PHE A 92 TYR 0.010 0.001 TYR F 514 ARG 0.001 0.000 ARG F 876 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 250 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7547 (mt0) REVERT: A 326 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8228 (mp) REVERT: A 464 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7526 (mt0) REVERT: A 480 LEU cc_start: 0.4027 (OUTLIER) cc_final: 0.3644 (mp) REVERT: A 483 MET cc_start: 0.1876 (tpt) cc_final: 0.1446 (tpt) REVERT: A 652 LEU cc_start: 0.9160 (tt) cc_final: 0.8953 (tt) REVERT: A 828 ARG cc_start: 0.4608 (ttp-170) cc_final: 0.4259 (tpp-160) REVERT: A 916 HIS cc_start: 0.4511 (t-90) cc_final: 0.2789 (m90) REVERT: A 1018 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7593 (mt0) REVERT: A 1029 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6616 (tp30) REVERT: A 1060 PHE cc_start: 0.7637 (OUTLIER) cc_final: 0.6709 (t80) REVERT: A 1101 TYR cc_start: 0.6549 (m-80) cc_final: 0.5959 (m-80) REVERT: A 1186 ASP cc_start: 0.7912 (t0) cc_final: 0.7527 (t0) REVERT: E 206 ARG cc_start: 0.5638 (OUTLIER) cc_final: 0.4944 (mmp-170) REVERT: F 281 MET cc_start: 0.8823 (tpp) cc_final: 0.8431 (ttm) REVERT: F 368 GLU cc_start: 0.7327 (pt0) cc_final: 0.7065 (pt0) REVERT: F 380 LYS cc_start: 0.8304 (ttpp) cc_final: 0.7807 (ttpt) REVERT: F 413 TYR cc_start: 0.9252 (m-80) cc_final: 0.8896 (m-80) REVERT: F 735 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7972 (ptt-90) REVERT: F 858 ASP cc_start: 0.7974 (p0) cc_final: 0.7622 (p0) outliers start: 124 outliers final: 98 residues processed: 349 average time/residue: 0.2690 time to fit residues: 148.4164 Evaluate side-chains 351 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 244 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 160 GLN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 212 SER Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 735 ARG Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1012 MET Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1062 CYS Chi-restraints excluded: chain F residue 1068 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 179 optimal weight: 0.0570 chunk 119 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 133 optimal weight: 0.0270 chunk 129 optimal weight: 0.4980 chunk 98 optimal weight: 5.9990 overall best weight: 1.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A1108 GLN ** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1039 GLN F1065 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18688 Z= 0.212 Angle : 0.522 6.957 25260 Z= 0.267 Chirality : 0.041 0.159 2817 Planarity : 0.004 0.054 3153 Dihedral : 12.108 81.817 2880 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.84 % Favored : 94.12 % Rotamer: Outliers : 6.36 % Allowed : 25.10 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.18), residues: 2194 helix: 0.62 (0.16), residues: 1078 sheet: -1.35 (0.34), residues: 214 loop : -2.36 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 187 HIS 0.003 0.001 HIS A1398 PHE 0.026 0.001 PHE A 92 TYR 0.011 0.001 TYR F 514 ARG 0.005 0.000 ARG A1099 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 248 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7555 (mt0) REVERT: A 326 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8228 (mp) REVERT: A 464 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7534 (mt0) REVERT: A 480 LEU cc_start: 0.3957 (OUTLIER) cc_final: 0.3579 (mp) REVERT: A 483 MET cc_start: 0.1911 (tpt) cc_final: 0.1444 (tpt) REVERT: A 652 LEU cc_start: 0.9194 (tt) cc_final: 0.8967 (tt) REVERT: A 828 ARG cc_start: 0.4613 (ttp-170) cc_final: 0.4263 (tpp-160) REVERT: A 916 HIS cc_start: 0.4522 (t-90) cc_final: 0.2792 (m90) REVERT: A 1018 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7594 (mt0) REVERT: A 1060 PHE cc_start: 0.7557 (OUTLIER) cc_final: 0.6696 (t80) REVERT: A 1186 ASP cc_start: 0.7907 (t0) cc_final: 0.7521 (t0) REVERT: E 206 ARG cc_start: 0.5654 (OUTLIER) cc_final: 0.4980 (mmp-170) REVERT: F 281 MET cc_start: 0.8835 (tpp) cc_final: 0.8201 (ttm) REVERT: F 361 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7228 (mtm) REVERT: F 368 GLU cc_start: 0.7351 (pt0) cc_final: 0.7118 (pt0) REVERT: F 380 LYS cc_start: 0.8308 (ttpp) cc_final: 0.7811 (ttpt) REVERT: F 413 TYR cc_start: 0.9265 (m-80) cc_final: 0.8897 (m-80) REVERT: F 858 ASP cc_start: 0.8002 (p0) cc_final: 0.7629 (p0) REVERT: F 1020 MET cc_start: 0.7278 (ttp) cc_final: 0.6931 (ttm) outliers start: 125 outliers final: 105 residues processed: 348 average time/residue: 0.2829 time to fit residues: 156.5070 Evaluate side-chains 358 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 245 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 160 GLN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 212 SER Chi-restraints excluded: chain F residue 228 ASN Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 421 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 806 GLN Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1012 MET Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 127 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 193 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A1058 ASN A1108 GLN ** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1065 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18688 Z= 0.154 Angle : 0.500 7.091 25260 Z= 0.255 Chirality : 0.040 0.154 2817 Planarity : 0.004 0.054 3153 Dihedral : 11.678 81.184 2876 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 6.16 % Allowed : 25.61 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.97 (0.18), residues: 2194 helix: 0.75 (0.16), residues: 1074 sheet: -1.30 (0.34), residues: 216 loop : -2.25 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 187 HIS 0.003 0.001 HIS A1398 PHE 0.025 0.001 PHE F1018 TYR 0.011 0.001 TYR A1107 ARG 0.002 0.000 ARG A1099 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 251 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7522 (mt0) REVERT: A 194 LEU cc_start: 0.8517 (tp) cc_final: 0.8136 (mp) REVERT: A 326 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8203 (mp) REVERT: A 464 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: A 480 LEU cc_start: 0.3870 (OUTLIER) cc_final: 0.3559 (mp) REVERT: A 483 MET cc_start: 0.1709 (tpt) cc_final: 0.1245 (tpt) REVERT: A 828 ARG cc_start: 0.4772 (ttp-170) cc_final: 0.4267 (tpp-160) REVERT: A 916 HIS cc_start: 0.4434 (t-90) cc_final: 0.2783 (m90) REVERT: A 1018 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7569 (mt0) REVERT: A 1060 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.6694 (t80) REVERT: A 1108 GLN cc_start: 0.6491 (OUTLIER) cc_final: 0.6043 (pp30) REVERT: A 1186 ASP cc_start: 0.7770 (t0) cc_final: 0.7477 (t0) REVERT: E 206 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.5038 (mmp-170) REVERT: F 281 MET cc_start: 0.8785 (tpp) cc_final: 0.7623 (tpp) REVERT: F 361 MET cc_start: 0.7919 (OUTLIER) cc_final: 0.7326 (mtm) REVERT: F 368 GLU cc_start: 0.7322 (pt0) cc_final: 0.7080 (pt0) REVERT: F 380 LYS cc_start: 0.8299 (ttpp) cc_final: 0.7808 (ttpt) REVERT: F 858 ASP cc_start: 0.7983 (p0) cc_final: 0.7579 (p0) REVERT: F 1020 MET cc_start: 0.7223 (ttp) cc_final: 0.6826 (ttm) outliers start: 121 outliers final: 95 residues processed: 350 average time/residue: 0.2748 time to fit residues: 151.1551 Evaluate side-chains 348 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 244 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1397 HIS Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 212 SER Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 7.9990 chunk 186 optimal weight: 0.0270 chunk 198 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 179 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A1058 ASN A1108 GLN A1397 HIS ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18688 Z= 0.242 Angle : 0.539 8.469 25260 Z= 0.274 Chirality : 0.042 0.161 2817 Planarity : 0.004 0.054 3153 Dihedral : 11.672 82.624 2873 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.97 % Favored : 93.98 % Rotamer: Outliers : 6.01 % Allowed : 25.71 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.98 (0.18), residues: 2194 helix: 0.71 (0.16), residues: 1077 sheet: -1.27 (0.34), residues: 214 loop : -2.23 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.004 0.001 HIS A1398 PHE 0.026 0.001 PHE F1018 TYR 0.011 0.001 TYR F1071 ARG 0.002 0.000 ARG A1099 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 242 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: A 464 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: A 480 LEU cc_start: 0.3906 (OUTLIER) cc_final: 0.3536 (mp) REVERT: A 483 MET cc_start: 0.1782 (tpt) cc_final: 0.1308 (tpt) REVERT: A 828 ARG cc_start: 0.4780 (ttp-170) cc_final: 0.4262 (tpp-160) REVERT: A 916 HIS cc_start: 0.4586 (t-90) cc_final: 0.2853 (m90) REVERT: A 1018 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: A 1054 PHE cc_start: 0.6359 (OUTLIER) cc_final: 0.5724 (m-80) REVERT: A 1060 PHE cc_start: 0.7645 (OUTLIER) cc_final: 0.6695 (t80) REVERT: A 1186 ASP cc_start: 0.7894 (t0) cc_final: 0.7508 (t0) REVERT: E 206 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.5123 (mmp-170) REVERT: F 281 MET cc_start: 0.8831 (tpp) cc_final: 0.8197 (ttm) REVERT: F 361 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7264 (mtm) REVERT: F 368 GLU cc_start: 0.7247 (pt0) cc_final: 0.7017 (pt0) REVERT: F 380 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7834 (ttpt) REVERT: F 858 ASP cc_start: 0.8023 (p0) cc_final: 0.7621 (p0) REVERT: F 864 MET cc_start: 0.6986 (tpp) cc_final: 0.6584 (tpp) outliers start: 118 outliers final: 100 residues processed: 339 average time/residue: 0.2676 time to fit residues: 143.7528 Evaluate side-chains 348 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 240 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 788 VAL Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1058 ASN Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1198 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 212 SER Chi-restraints excluded: chain F residue 228 ASN Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 821 VAL Chi-restraints excluded: chain F residue 849 ASP Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1026 THR Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 220 optimal weight: 0.0370 chunk 202 optimal weight: 4.9990 chunk 175 optimal weight: 0.0770 chunk 18 optimal weight: 0.8980 chunk 135 optimal weight: 0.0470 chunk 107 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A1108 GLN ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1065 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18688 Z= 0.124 Angle : 0.506 10.174 25260 Z= 0.256 Chirality : 0.040 0.153 2817 Planarity : 0.004 0.053 3153 Dihedral : 11.295 80.986 2873 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.34 % Favored : 94.62 % Rotamer: Outliers : 4.43 % Allowed : 27.14 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: -0.68 (0.18), residues: 2194 helix: 0.99 (0.16), residues: 1061 sheet: -1.11 (0.34), residues: 211 loop : -2.05 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 187 HIS 0.004 0.001 HIS A1398 PHE 0.028 0.001 PHE F1018 TYR 0.012 0.001 TYR A1107 ARG 0.002 0.000 ARG F 735 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4388 Ramachandran restraints generated. 2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 249 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 PHE cc_start: 0.8726 (m-80) cc_final: 0.8398 (m-80) REVERT: A 183 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: A 194 LEU cc_start: 0.8532 (tp) cc_final: 0.8151 (mp) REVERT: A 464 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7514 (mt0) REVERT: A 480 LEU cc_start: 0.3782 (OUTLIER) cc_final: 0.3509 (mp) REVERT: A 483 MET cc_start: 0.1744 (tpt) cc_final: 0.1226 (tpt) REVERT: A 500 ASP cc_start: 0.6551 (p0) cc_final: 0.6156 (p0) REVERT: A 828 ARG cc_start: 0.4675 (ttp-170) cc_final: 0.4213 (tpp-160) REVERT: A 916 HIS cc_start: 0.4363 (t-90) cc_final: 0.2784 (m90) REVERT: A 1018 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7541 (mt0) REVERT: A 1054 PHE cc_start: 0.6232 (OUTLIER) cc_final: 0.5676 (m-80) REVERT: A 1060 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.6603 (t80) REVERT: E 206 ARG cc_start: 0.5762 (OUTLIER) cc_final: 0.4981 (mmp-170) REVERT: F 281 MET cc_start: 0.8694 (tpp) cc_final: 0.7652 (tpp) REVERT: F 361 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7304 (mtm) REVERT: F 368 GLU cc_start: 0.7256 (pt0) cc_final: 0.6999 (pt0) REVERT: F 380 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7807 (ttpt) REVERT: F 604 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7940 (mttm) REVERT: F 858 ASP cc_start: 0.7980 (p0) cc_final: 0.7493 (p0) outliers start: 87 outliers final: 70 residues processed: 320 average time/residue: 0.2706 time to fit residues: 135.5354 Evaluate side-chains 328 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 250 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 183 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 464 GLN Chi-restraints excluded: chain A residue 468 ASN Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 876 VAL Chi-restraints excluded: chain A residue 977 ASP Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1018 GLN Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1054 PHE Chi-restraints excluded: chain A residue 1060 PHE Chi-restraints excluded: chain A residue 1082 ASP Chi-restraints excluded: chain A residue 1108 GLN Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1149 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1272 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1289 PHE Chi-restraints excluded: chain A residue 1295 VAL Chi-restraints excluded: chain A residue 1343 ASP Chi-restraints excluded: chain A residue 1400 ASP Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 206 ARG Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 61 TYR Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 212 SER Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 361 MET Chi-restraints excluded: chain F residue 401 ILE Chi-restraints excluded: chain F residue 608 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 652 LYS Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 732 VAL Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 744 THR Chi-restraints excluded: chain F residue 815 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 853 CYS Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 1002 CYS Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1019 ILE Chi-restraints excluded: chain F residue 1027 CYS Chi-restraints excluded: chain F residue 1062 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.0050 chunk 53 optimal weight: 30.0000 chunk 161 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 180 optimal weight: 0.0970 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A1058 ASN A1108 GLN ** F 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1065 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.150699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114420 restraints weight = 26766.562| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.32 r_work: 0.3101 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18688 Z= 0.143 Angle : 0.501 9.614 25260 Z= 0.253 Chirality : 0.040 0.152 2817 Planarity : 0.004 0.053 3153 Dihedral : 11.077 81.942 2867 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.38 % Favored : 94.57 % Rotamer: Outliers : 4.28 % Allowed : 27.34 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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 (0.19), residues: 2194 helix: 1.02 (0.16), residues: 1074 sheet: -1.02 (0.35), residues: 209 loop : -2.01 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 187 HIS 0.004 0.000 HIS A1398 PHE 0.028 0.001 PHE F1018 TYR 0.017 0.001 TYR E 176 ARG 0.007 0.000 ARG E 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4463.95 seconds wall clock time: 81 minutes 12.36 seconds (4872.36 seconds total)