Starting phenix.real_space_refine on Sat Feb 17 12:42:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpx_22426/02_2024/7jpx_22426_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpx_22426/02_2024/7jpx_22426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpx_22426/02_2024/7jpx_22426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpx_22426/02_2024/7jpx_22426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpx_22426/02_2024/7jpx_22426_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jpx_22426/02_2024/7jpx_22426_neut_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 11 5.49 5 S 110 5.16 5 Cl 1 4.86 5 C 12168 2.51 5 N 2984 2.21 5 O 3365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 342": "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 PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ASP 589": "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 GLU 666": "OE1" <-> "OE2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ASP 836": "OD1" <-> "OD2" Residue "A ASP 872": "OD1" <-> "OD2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A PHE 940": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "A TYR 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 984": "OE1" <-> "OE2" Residue "A PHE 997": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1022": "NH1" <-> "NH2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1082": "OD1" <-> "OD2" Residue "A TYR 1091": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1099": "NH1" <-> "NH2" Residue "A TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "A ASP 1151": "OD1" <-> "OD2" Residue "A PHE 1172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1201": "OE1" <-> "OE2" Residue "A PHE 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1236": "NH1" <-> "NH2" Residue "A PHE 1238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1242": "NH1" <-> "NH2" Residue "A GLU 1251": "OE1" <-> "OE2" Residue "A PHE 1260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1327": "OE1" <-> "OE2" Residue "A TYR 1334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1341": "OE1" <-> "OE2" Residue "A TYR 1344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1348": "OE1" <-> "OE2" Residue "A TYR 1360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1389": "NH1" <-> "NH2" Residue "A GLU 1401": "OE1" <-> "OE2" Residue "A ASP 1410": "OD1" <-> "OD2" Residue "A ARG 1427": "NH1" <-> "NH2" Residue "A ARG 1428": "NH1" <-> "NH2" Residue "E PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 30": "OD1" <-> "OD2" Residue "E GLU 47": "OE1" <-> "OE2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 213": "OE1" <-> "OE2" Residue "E GLU 219": "OE1" <-> "OE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F ASP 66": "OD1" <-> "OD2" Residue "F TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ASP 132": "OD1" <-> "OD2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F ASP 202": "OD1" <-> "OD2" Residue "F ARG 230": "NH1" <-> "NH2" Residue "F ARG 241": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F ARG 315": "NH1" <-> "NH2" Residue "F TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 368": "OE1" <-> "OE2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 441": "OD1" <-> "OD2" Residue "F GLU 457": "OE1" <-> "OE2" Residue "F GLU 497": "OE1" <-> "OE2" Residue "F ASP 498": "OD1" <-> "OD2" Residue "F ARG 544": "NH1" <-> "NH2" Residue "F ARG 546": "NH1" <-> "NH2" Residue "F GLU 567": "OE1" <-> "OE2" Residue "F ASP 571": "OD1" <-> "OD2" Residue "F ASP 582": "OD1" <-> "OD2" Residue "F GLU 587": "OE1" <-> "OE2" Residue "F ARG 591": "NH1" <-> "NH2" Residue "F ARG 607": "NH1" <-> "NH2" Residue "F GLU 658": "OE1" <-> "OE2" Residue "F PHE 663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 668": "OD1" <-> "OD2" Residue "F TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 691": "OD1" <-> "OD2" Residue "F ARG 692": "NH1" <-> "NH2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 745": "NH1" <-> "NH2" Residue "F TYR 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 774": "OD1" <-> "OD2" Residue "F TYR 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 826": "OE1" <-> "OE2" Residue "F ARG 846": "NH1" <-> "NH2" Residue "F ASP 868": "OD1" <-> "OD2" Residue "F GLU 880": "OE1" <-> "OE2" Residue "F ASP 882": "OD1" <-> "OD2" Residue "F PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 989": "OD1" <-> "OD2" Residue "F PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 998": "OD1" <-> "OD2" Residue "F ARG 1004": "NH1" <-> "NH2" Residue "F ASP 1045": "OD1" <-> "OD2" Residue "F GLU 1069": "OE1" <-> "OE2" Residue "F ASP 1070": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18640 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 9016 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 35, 'TRANS': 1080} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1326 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 7, 'TRANS': 161} Chain breaks: 4 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: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 494 Unusual residues: {' CA': 1, '3PE': 9, '6UB': 1, 'PC1': 1, 'POV': 1} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'3PE:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 13.41, per 1000 atoms: 0.72 Number of scatterers: 18640 At special positions: 0 Unit cell: (142.592, 138.136, 155.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 Cl 1 17.00 S 110 16.00 P 11 15.00 O 3365 8.00 N 2984 7.00 C 12168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 254 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1338 " - pdb=" SG CYS A1352 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 80 " distance=2.04 Simple disulfide: pdb=" SG CYS F 305 " - pdb=" SG CYS F1047 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.06 Conformation dependent library (CDL) restraints added in 4.1 seconds 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4274 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 13 sheets defined 47.1% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.27 Creating SS restraints... Processing helix chain 'A' and resid 46 through 49 No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.603A pdb=" N PHE A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.866A pdb=" N LYS A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 142 removed outlier: 3.585A pdb=" N PHE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 128 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN A 141 " --> pdb=" O ALA A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 176 removed outlier: 3.617A pdb=" N PHE A 167 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL A 169 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 171 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 195 through 217 removed outlier: 4.185A pdb=" N HIS A 198 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 199 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA A 200 " --> pdb=" O PHE A 197 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 201 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 204 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 208 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 217 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 289 Processing helix chain 'A' and resid 294 through 305 Processing helix chain 'A' and resid 310 through 320 removed outlier: 4.299A pdb=" N VAL A 315 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR A 316 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 318 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 320 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 346 removed outlier: 3.991A pdb=" N SER A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 450 removed outlier: 3.815A pdb=" N ILE A 439 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 484 Processing helix chain 'A' and resid 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 500 through 515 removed outlier: 3.764A pdb=" N ILE A 508 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 515 " --> pdb=" O LEU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 541 removed outlier: 4.093A pdb=" N LEU A 532 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 533 " --> pdb=" O CYS A 529 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU A 535 " --> pdb=" O ARG A 531 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A 537 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE A 538 " --> pdb=" O ARG A 534 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR A 539 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 580 removed outlier: 3.712A pdb=" N VAL A 549 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA A 550 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N SER A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N SER A 561 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 Processing helix chain 'A' and resid 616 through 626 Processing helix chain 'A' and resid 634 through 657 removed outlier: 3.659A pdb=" N PHE A 641 " --> pdb=" O CYS A 638 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 643 " --> pdb=" O TYR A 640 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 644 " --> pdb=" O PHE A 641 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 645 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 646 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N CYS A 647 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 648 " --> pdb=" O PHE A 645 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 656 " --> pdb=" O LEU A 653 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 657 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 672 Processing helix chain 'A' and resid 799 through 817 removed outlier: 3.585A pdb=" N LEU A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 816 " --> pdb=" O SER A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 845 removed outlier: 3.749A pdb=" N TYR A 834 " --> pdb=" O GLN A 830 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 835 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.858A pdb=" N ASP A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL A 878 " --> pdb=" O LEU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 898 Processing helix chain 'A' and resid 904 through 906 No H-bonds generated for 'chain 'A' and resid 904 through 906' Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 930 through 950 removed outlier: 3.694A pdb=" N VAL A 934 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 942 " --> pdb=" O LEU A 938 " (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 1024 Processing helix chain 'A' and resid 1039 through 1052 removed outlier: 3.515A pdb=" N ILE A1043 " --> pdb=" O GLU A1040 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A1044 " --> pdb=" O MET A1041 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A1047 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A1049 " --> pdb=" O ILE A1046 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A1052 " --> pdb=" O ILE A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1060 No H-bonds generated for 'chain 'A' and resid 1057 through 1060' Processing helix chain 'A' and resid 1062 through 1067 removed outlier: 4.281A pdb=" N THR A1067 " --> pdb=" O PHE A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1094 removed outlier: 3.663A pdb=" N GLN A1087 " --> pdb=" O LYS A1083 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A1091 " --> pdb=" O GLN A1087 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A1092 " --> pdb=" O CYS A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1115 removed outlier: 3.531A pdb=" N VAL A1114 " --> pdb=" O GLN A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1136 removed outlier: 3.755A pdb=" N PHE A1125 " --> pdb=" O GLU A1121 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE A1128 " --> pdb=" O MET A1124 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A1133 " --> pdb=" O MET A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1172 removed outlier: 3.680A pdb=" N ILE A1152 " --> pdb=" O HIS A1148 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1204 removed outlier: 3.590A pdb=" N VAL A1197 " --> pdb=" O SER A1193 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A1203 " --> pdb=" O LEU A1199 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N THR A1204 " --> pdb=" O SER A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1238 Processing helix chain 'A' and resid 1241 through 1248 removed outlier: 3.725A pdb=" N LYS A1245 " --> pdb=" O ARG A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1265 removed outlier: 3.902A pdb=" N SER A1263 " --> pdb=" O THR A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1288 removed outlier: 3.847A pdb=" N ILE A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN A1287 " --> pdb=" O VAL A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1321 Processing helix chain 'A' and resid 1325 through 1331 Processing helix chain 'A' and resid 1355 through 1387 removed outlier: 4.137A pdb=" N PHE A1361 " --> pdb=" O TYR A1358 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR A1365 " --> pdb=" O ILE A1362 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET A1366 " --> pdb=" O SER A1363 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A1371 " --> pdb=" O CYS A1368 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A1372 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A1373 " --> pdb=" O PHE A1370 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A1377 " --> pdb=" O ASN A1374 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A1378 " --> pdb=" O LEU A1375 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP A1382 " --> pdb=" O VAL A1379 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A1383 " --> pdb=" O ILE A1380 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASP A1385 " --> pdb=" O ASP A1382 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A1387 " --> pdb=" O PHE A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1409 removed outlier: 3.649A pdb=" N TYR A1409 " --> pdb=" O ILE A1405 " (cutoff:3.500A) Processing helix chain 'A' and resid 1419 through 1427 removed outlier: 3.508A pdb=" N LEU A1426 " --> pdb=" O VAL A1422 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG A1427 " --> pdb=" O VAL A1423 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 26 removed outlier: 3.992A pdb=" N THR E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY E 19 " --> pdb=" O CYS E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 127 removed outlier: 3.822A pdb=" N CYS E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 164 Proline residue: E 139 - end of helix Processing helix chain 'E' and resid 181 through 203 removed outlier: 4.145A pdb=" N VAL E 190 " --> pdb=" O CYS E 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 52 Processing helix chain 'F' and resid 54 through 62 Processing helix chain 'F' and resid 75 through 109 removed outlier: 3.616A pdb=" N ALA F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 201 removed outlier: 3.789A pdb=" N TRP F 187 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER F 189 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N ALA F 190 " --> pdb=" O ASN F 186 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU F 191 " --> pdb=" O TRP F 187 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASP F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) 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 250 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: 3.739A pdb=" N THR F 284 " --> pdb=" O GLU F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 326 removed outlier: 3.910A pdb=" N ASN F 326 " --> pdb=" O ASP F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 347 removed outlier: 3.637A pdb=" N LEU F 347 " --> pdb=" O PHE F 343 " (cutoff:3.500A) 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 424 removed outlier: 4.968A pdb=" N ARG F 422 " --> pdb=" O GLY F 419 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE F 423 " --> pdb=" O ALA F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 437 No H-bonds generated for 'chain 'F' and resid 434 through 437' Processing helix chain 'F' and resid 440 through 443 Processing helix chain 'F' and resid 496 through 499 No H-bonds generated for 'chain 'F' and resid 496 through 499' 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 572 through 581 Processing helix chain 'F' and resid 641 through 650 Processing helix chain 'F' and resid 653 through 659 removed outlier: 4.370A pdb=" N GLU F 657 " --> pdb=" O ASP F 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 692 Processing helix chain 'F' and resid 702 through 721 Processing helix chain 'F' and resid 765 through 772 Processing helix chain 'F' and resid 821 through 828 Processing helix chain 'F' and resid 878 through 880 No H-bonds generated for 'chain 'F' and resid 878 through 880' Processing helix chain 'F' and resid 883 through 892 Processing helix chain 'F' and resid 1046 through 1049 No H-bonds generated for 'chain 'F' and resid 1046 through 1049' Processing sheet with id= A, first strand: chain 'A' and resid 225 through 228 Processing sheet with id= B, first strand: chain 'A' and resid 955 through 957 Processing sheet with id= C, first strand: chain 'A' and resid 971 through 975 Processing sheet with id= D, first strand: chain 'E' and resid 34 through 36 removed outlier: 3.802A pdb=" N TYR E 177 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 68 through 72 Processing sheet with id= F, first strand: chain 'F' and resid 124 through 126 Processing sheet with id= G, first strand: chain 'F' and resid 167 through 169 removed outlier: 6.724A pdb=" N VAL F 468 " --> pdb=" O LEU F 487 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL F 489 " --> pdb=" O LEU F 466 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU F 466 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY F 491 " --> pdb=" O GLY F 464 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLY F 464 " --> pdb=" O GLY F 491 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASP F 493 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE F 462 " --> pdb=" O ASP F 493 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 411 through 415 removed outlier: 6.231A pdb=" N ASP F 255 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N MET F 361 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU F 257 " --> pdb=" O MET F 361 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N PHE F 363 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU F 259 " --> pdb=" O PHE F 363 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N PHE F 290 " --> pdb=" O MET F 256 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE F 258 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN F 292 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL F 260 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALA F 294 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 513 through 517 Processing sheet with id= J, first strand: chain 'F' and resid 661 through 664 removed outlier: 3.924A pdb=" N ILE F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS F 818 " --> pdb=" O LYS F 733 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ARG F 735 " --> pdb=" O GLY F 816 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY F 816 " --> pdb=" O ARG F 735 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL F 737 " --> pdb=" O VAL F 814 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL F 814 " --> pdb=" O VAL F 737 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA F 813 " --> pdb=" O VAL F 801 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET F 796 " --> pdb=" O THR F 779 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 992 through 998 removed outlier: 6.056A pdb=" N ILE F1005 " --> pdb=" O GLU F1022 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP F 857 " --> pdb=" O LEU F 862 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU F 862 " --> pdb=" O ASP F 857 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 896 through 902 Processing sheet with id= M, first strand: chain 'F' and resid 905 through 907 744 hydrogen bonds defined for protein. 1901 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: 6.28 Time building geometry restraints manager: 7.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2986 1.31 - 1.44: 5189 1.44 - 1.57: 10684 1.57 - 1.70: 23 1.70 - 1.83: 171 Bond restraints: 19053 Sorted by residual: bond pdb=" CAW 6UB A1913 " pdb=" CAY 6UB A1913 " ideal model delta sigma weight residual 1.357 1.526 -0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" CAT 6UB A1913 " pdb=" CAX 6UB A1913 " ideal model delta sigma weight residual 1.357 1.525 -0.168 2.00e-02 2.50e+03 7.02e+01 bond pdb=" C21 3PE A1902 " pdb=" O21 3PE A1902 " 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 A1904 " pdb=" O21 3PE A1904 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C21 3PE A1903 " pdb=" O21 3PE A1903 " ideal model delta sigma weight residual 1.316 1.453 -0.137 2.00e-02 2.50e+03 4.70e+01 ... (remaining 19048 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.95: 371 105.95 - 113.01: 10322 113.01 - 120.06: 7008 120.06 - 127.12: 7863 127.12 - 134.17: 180 Bond angle restraints: 25744 Sorted by residual: angle pdb=" C THR A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.84 129.92 -10.08 1.25e+00 6.40e-01 6.51e+01 angle pdb=" N THR A 520 " pdb=" CA THR A 520 " pdb=" C THR A 520 " ideal model delta sigma weight residual 109.81 125.38 -15.57 2.21e+00 2.05e-01 4.97e+01 angle pdb=" N GLY F 177 " pdb=" CA GLY F 177 " pdb=" C GLY F 177 " ideal model delta sigma weight residual 114.48 107.34 7.14 1.19e+00 7.06e-01 3.60e+01 angle pdb=" N VAL F 894 " pdb=" CA VAL F 894 " pdb=" C VAL F 894 " ideal model delta sigma weight residual 113.39 105.55 7.84 1.47e+00 4.63e-01 2.85e+01 angle pdb=" N THR E 58 " pdb=" CA THR E 58 " pdb=" C THR E 58 " ideal model delta sigma weight residual 110.17 118.20 -8.03 1.51e+00 4.39e-01 2.83e+01 ... (remaining 25739 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.84: 10495 29.84 - 59.68: 924 59.68 - 89.52: 71 89.52 - 119.36: 4 119.36 - 149.20: 1 Dihedral angle restraints: 11495 sinusoidal: 4874 harmonic: 6621 Sorted by residual: dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 80 " pdb=" CB CYS E 80 " ideal model delta sinusoidal sigma weight residual 93.00 13.67 79.33 1 1.00e+01 1.00e-02 7.82e+01 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 39.88 53.12 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CA SER E 214 " pdb=" C SER E 214 " pdb=" N CYS E 215 " pdb=" CA CYS E 215 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 11492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2463 0.084 - 0.168: 362 0.168 - 0.252: 23 0.252 - 0.336: 1 0.336 - 0.420: 1 Chirality restraints: 2850 Sorted by residual: chirality pdb=" CA THR A 520 " pdb=" N THR A 520 " pdb=" C THR A 520 " pdb=" CB THR A 520 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CG LEU F 257 " pdb=" CB LEU F 257 " pdb=" CD1 LEU F 257 " pdb=" CD2 LEU F 257 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA PRO A 268 " pdb=" N PRO A 268 " pdb=" C PRO A 268 " pdb=" CB PRO A 268 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 2847 not shown) Planarity restraints: 3210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN F 530 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO F 531 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO F 531 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 531 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 267 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO A 268 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 155 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C LEU E 155 " 0.042 2.00e-02 2.50e+03 pdb=" O LEU E 155 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU E 156 " -0.014 2.00e-02 2.50e+03 ... (remaining 3207 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 388 2.64 - 3.21: 16951 3.21 - 3.77: 27999 3.77 - 4.34: 40718 4.34 - 4.90: 66270 Nonbonded interactions: 152326 Sorted by model distance: nonbonded pdb=" N 3PE A1906 " pdb=" O11 3PE A1906 " model vdw 2.078 2.520 nonbonded pdb=" O ASN F 233 " pdb=" ND2 ASN F 233 " model vdw 2.078 2.520 nonbonded pdb=" N 3PE A1908 " pdb=" O14 3PE A1908 " model vdw 2.078 2.520 nonbonded pdb=" CG ARG E 55 " pdb=" O SER E 81 " model vdw 2.086 3.440 nonbonded pdb=" OH TYR F 452 " pdb=" OG1 THR F 463 " model vdw 2.096 2.440 ... (remaining 152321 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.870 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 54.960 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 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 : 0.013 0.169 19053 Z= 0.864 Angle : 1.104 15.574 25744 Z= 0.579 Chirality : 0.059 0.420 2850 Planarity : 0.006 0.075 3210 Dihedral : 20.318 149.203 7182 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.22 % Favored : 91.51 % Rotamer: Outliers : 11.89 % Allowed : 22.52 % Favored : 65.60 % 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: -4.18 (0.14), residues: 2227 helix: -2.70 (0.12), residues: 1120 sheet: -1.51 (0.32), residues: 208 loop : -3.03 (0.18), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP F 245 HIS 0.007 0.002 HIS F 394 PHE 0.035 0.003 PHE F 157 TYR 0.029 0.003 TYR A1334 ARG 0.011 0.001 ARG F 735 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 266 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.4759 (OUTLIER) cc_final: 0.4494 (pt) REVERT: A 62 PHE cc_start: 0.8472 (t80) cc_final: 0.8244 (t80) REVERT: A 80 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8681 (p0) REVERT: A 114 GLN cc_start: 0.5789 (tt0) cc_final: 0.5018 (tm-30) REVERT: A 190 PHE cc_start: 0.7311 (t80) cc_final: 0.6569 (m-80) REVERT: A 247 ARG cc_start: 0.7252 (OUTLIER) cc_final: 0.6915 (ptp-170) REVERT: A 452 GLU cc_start: 0.7833 (tt0) cc_final: 0.7607 (tt0) REVERT: A 494 SER cc_start: 0.1341 (OUTLIER) cc_final: 0.1013 (m) REVERT: A 519 MET cc_start: 0.4256 (ttp) cc_final: 0.4009 (ttp) REVERT: A 540 LYS cc_start: 0.3659 (OUTLIER) cc_final: 0.2106 (ttpp) REVERT: A 554 ASN cc_start: 0.6322 (OUTLIER) cc_final: 0.6053 (m-40) REVERT: A 871 LEU cc_start: 0.4977 (OUTLIER) cc_final: 0.4609 (tp) REVERT: A 933 LEU cc_start: 0.7909 (mt) cc_final: 0.7698 (mm) REVERT: A 1041 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8727 (tpp) REVERT: A 1105 ASN cc_start: 0.5037 (t160) cc_final: 0.4450 (t0) REVERT: A 1147 ASN cc_start: 0.5119 (OUTLIER) cc_final: 0.4692 (m110) REVERT: A 1151 ASP cc_start: 0.8065 (t0) cc_final: 0.7607 (p0) REVERT: A 1196 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7357 (t0) REVERT: A 1272 LEU cc_start: 0.8608 (tp) cc_final: 0.8264 (mm) REVERT: A 1286 MET cc_start: 0.8883 (mtp) cc_final: 0.8671 (mtm) REVERT: A 1337 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8828 (tt) REVERT: A 1339 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.8008 (p0) REVERT: A 1384 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.5970 (t80) REVERT: E 79 ASN cc_start: 0.4992 (OUTLIER) cc_final: 0.4701 (p0) REVERT: E 81 SER cc_start: 0.4180 (OUTLIER) cc_final: 0.3930 (p) REVERT: E 127 MET cc_start: 0.7649 (ttp) cc_final: 0.6766 (tmt) REVERT: E 158 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6235 (mtm) REVERT: F 234 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6713 (mttt) REVERT: F 307 GLN cc_start: 0.8136 (mt0) cc_final: 0.7784 (mm110) REVERT: F 326 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8310 (m-40) REVERT: F 430 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7941 (m-30) REVERT: F 545 LYS cc_start: 0.8312 (mttm) cc_final: 0.8073 (mmtt) REVERT: F 674 LYS cc_start: 0.8107 (ptpp) cc_final: 0.7804 (ttmm) REVERT: F 804 TYR cc_start: 0.8264 (m-80) cc_final: 0.7848 (m-80) outliers start: 237 outliers final: 135 residues processed: 467 average time/residue: 0.9640 time to fit residues: 525.7862 Evaluate side-chains 386 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 232 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 506 SER Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 536 PHE Chi-restraints excluded: chain A residue 540 LYS Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 551 SER Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 618 SER Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 669 SER Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 826 SER Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 932 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 956 SER Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1041 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1114 VAL Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1147 ASN Chi-restraints excluded: chain A residue 1148 HIS Chi-restraints excluded: chain A residue 1196 ASP Chi-restraints excluded: chain A residue 1200 SER Chi-restraints excluded: chain A residue 1204 THR Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1371 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 79 ASN Chi-restraints excluded: chain E residue 81 SER Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 178 TYR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 326 ASN Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 430 ASP Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 594 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 655 ASN Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 694 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 814 VAL Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 881 ILE Chi-restraints excluded: chain F residue 900 SER Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 994 SER Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1008 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1050 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 2.9990 chunk 169 optimal weight: 0.0870 chunk 94 optimal weight: 0.2980 chunk 57 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 239 ASN A 277 ASN A 307 ASN A 455 ASN A 599 ASN A 803 ASN A 939 GLN A 948 GLN A 999 ASN A1037 ASN A1105 ASN A1131 ASN A1138 GLN A1383 ASN A1419 HIS F 165 HIS F 169 HIS F 233 ASN F 450 ASN F 470 ASN F 483 ASN F 511 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN F 655 ASN F 679 ASN F 685 ASN F 696 ASN F 806 GLN F 847 ASN F 866 ASN F1039 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19053 Z= 0.177 Angle : 0.609 9.334 25744 Z= 0.317 Chirality : 0.042 0.156 2850 Planarity : 0.005 0.063 3210 Dihedral : 15.842 122.142 3160 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.70 % Rotamer: Outliers : 7.47 % Allowed : 26.78 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.40 (0.16), residues: 2227 helix: -1.05 (0.14), residues: 1118 sheet: -1.05 (0.33), residues: 209 loop : -2.33 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 113 HIS 0.003 0.001 HIS F 394 PHE 0.018 0.001 PHE F 993 TYR 0.024 0.001 TYR F 629 ARG 0.004 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 264 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: A 114 GLN cc_start: 0.5691 (tt0) cc_final: 0.5055 (tm-30) REVERT: A 190 PHE cc_start: 0.7096 (t80) cc_final: 0.6413 (m-10) REVERT: A 247 ARG cc_start: 0.7315 (ttp80) cc_final: 0.6917 (ptm160) REVERT: A 494 SER cc_start: 0.1057 (OUTLIER) cc_final: 0.0791 (m) REVERT: A 548 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6280 (tt) REVERT: A 670 LEU cc_start: 0.4274 (OUTLIER) cc_final: 0.3978 (tt) REVERT: A 983 MET cc_start: 0.8330 (ptm) cc_final: 0.8104 (ptp) REVERT: A 1105 ASN cc_start: 0.4925 (t0) cc_final: 0.4316 (t0) REVERT: A 1145 GLU cc_start: 0.1688 (OUTLIER) cc_final: 0.0827 (mm-30) REVERT: A 1151 ASP cc_start: 0.8095 (t0) cc_final: 0.7487 (p0) REVERT: A 1196 ASP cc_start: 0.7612 (t70) cc_final: 0.7205 (t0) REVERT: A 1272 LEU cc_start: 0.8454 (tp) cc_final: 0.8137 (mm) REVERT: A 1276 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7663 (ttm) REVERT: A 1286 MET cc_start: 0.8821 (mtp) cc_final: 0.8515 (mtm) REVERT: A 1384 PHE cc_start: 0.6600 (OUTLIER) cc_final: 0.6326 (t80) REVERT: E 22 LEU cc_start: 0.6742 (mt) cc_final: 0.6469 (tp) REVERT: E 113 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: E 127 MET cc_start: 0.7600 (ttp) cc_final: 0.6661 (tmt) REVERT: E 138 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7320 (mtt90) REVERT: F 205 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8273 (tt) REVERT: F 233 ASN cc_start: 0.3786 (OUTLIER) cc_final: 0.3144 (p0) REVERT: F 234 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6566 (mmtt) REVERT: F 297 ASN cc_start: 0.7877 (p0) cc_final: 0.7632 (p0) REVERT: F 505 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7625 (ppt-90) REVERT: F 674 LYS cc_start: 0.7964 (ptpp) cc_final: 0.7605 (ttmm) REVERT: F 804 TYR cc_start: 0.8112 (m-80) cc_final: 0.7707 (m-80) REVERT: F 851 MET cc_start: 0.6807 (ptp) cc_final: 0.6473 (ptm) REVERT: F 1040 THR cc_start: 0.8964 (t) cc_final: 0.8567 (m) outliers start: 149 outliers final: 59 residues processed: 376 average time/residue: 0.9872 time to fit residues: 431.8203 Evaluate side-chains 309 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 237 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1145 GLU Chi-restraints excluded: chain A residue 1276 MET Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1417 ILE Chi-restraints excluded: chain A residue 1426 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 233 ASN Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 202 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 143 ASN A 599 ASN A 939 GLN A 948 GLN A1265 GLN E 79 ASN F 233 ASN F 307 GLN F 483 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 556 GLN F 644 GLN F 806 GLN F 888 HIS F 975 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19053 Z= 0.320 Angle : 0.646 9.372 25744 Z= 0.335 Chirality : 0.044 0.171 2850 Planarity : 0.005 0.058 3210 Dihedral : 14.518 118.122 3004 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 7.77 % Allowed : 26.18 % Favored : 66.05 % 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: -1.89 (0.17), residues: 2227 helix: -0.65 (0.15), residues: 1128 sheet: -0.74 (0.33), residues: 206 loop : -2.09 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 245 HIS 0.004 0.001 HIS F 394 PHE 0.026 0.002 PHE F 157 TYR 0.020 0.002 TYR F 629 ARG 0.005 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 240 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: A 100 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: A 114 GLN cc_start: 0.5657 (tt0) cc_final: 0.5027 (tm-30) REVERT: A 190 PHE cc_start: 0.7067 (t80) cc_final: 0.6613 (m-10) REVERT: A 247 ARG cc_start: 0.7336 (ttp80) cc_final: 0.6949 (ptm160) REVERT: A 460 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8013 (tt) REVERT: A 494 SER cc_start: 0.0881 (OUTLIER) cc_final: 0.0653 (m) REVERT: A 670 LEU cc_start: 0.4304 (OUTLIER) cc_final: 0.4074 (mt) REVERT: A 805 ILE cc_start: 0.4466 (OUTLIER) cc_final: 0.4230 (tt) REVERT: A 983 MET cc_start: 0.8300 (ptm) cc_final: 0.8098 (ptp) REVERT: A 1063 PHE cc_start: 0.7850 (m-80) cc_final: 0.7177 (t80) REVERT: A 1105 ASN cc_start: 0.4923 (t0) cc_final: 0.4313 (t0) REVERT: A 1151 ASP cc_start: 0.8074 (t0) cc_final: 0.7468 (p0) REVERT: A 1272 LEU cc_start: 0.8482 (tp) cc_final: 0.8167 (mm) REVERT: A 1286 MET cc_start: 0.8839 (mtp) cc_final: 0.8567 (mtm) REVERT: A 1384 PHE cc_start: 0.6577 (OUTLIER) cc_final: 0.5932 (t80) REVERT: E 127 MET cc_start: 0.7671 (ttp) cc_final: 0.6672 (tmt) REVERT: E 138 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7395 (mtt90) REVERT: E 158 MET cc_start: 0.7121 (mmm) cc_final: 0.6470 (mmm) REVERT: F 205 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8401 (tt) REVERT: F 234 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6675 (mmtt) REVERT: F 505 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7657 (ppt-90) REVERT: F 674 LYS cc_start: 0.7916 (ptpp) cc_final: 0.7637 (ttmm) REVERT: F 804 TYR cc_start: 0.8184 (m-80) cc_final: 0.7826 (m-80) REVERT: F 975 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6664 (mt0) REVERT: F 1040 THR cc_start: 0.9004 (t) cc_final: 0.8611 (m) outliers start: 155 outliers final: 85 residues processed: 352 average time/residue: 1.0853 time to fit residues: 442.2145 Evaluate side-chains 327 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 230 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 143 ASN Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 499 PHE 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 639 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 666 GLU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 869 ASN Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1070 GLU Chi-restraints excluded: chain A residue 1102 ILE Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1267 LEU Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 442 LYS Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 518 ASP Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 975 GLN Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Chi-restraints excluded: chain F residue 1060 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 136 optimal weight: 0.0570 chunk 204 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 106 optimal weight: 0.7980 chunk 193 optimal weight: 0.0980 chunk 58 optimal weight: 0.9980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 939 GLN A 948 GLN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN F 56 GLN F 233 ASN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 HIS F 484 GLN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN F 806 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 19053 Z= 0.153 Angle : 0.555 8.839 25744 Z= 0.289 Chirality : 0.041 0.196 2850 Planarity : 0.004 0.056 3210 Dihedral : 13.578 112.888 2994 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 6.42 % Allowed : 27.38 % Favored : 66.20 % 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: -1.30 (0.17), residues: 2227 helix: -0.15 (0.15), residues: 1126 sheet: -0.65 (0.33), residues: 211 loop : -1.78 (0.20), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 245 HIS 0.003 0.001 HIS F 169 PHE 0.025 0.001 PHE F 993 TYR 0.022 0.001 TYR F 629 ARG 0.004 0.000 ARG F1032 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 252 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: A 114 GLN cc_start: 0.5632 (tt0) cc_final: 0.5063 (tm-30) REVERT: A 190 PHE cc_start: 0.6940 (t80) cc_final: 0.6416 (m-10) REVERT: A 224 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8398 (mtmm) REVERT: A 247 ARG cc_start: 0.7291 (ttp80) cc_final: 0.6967 (ptm160) REVERT: A 509 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8070 (tt) REVERT: A 553 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6881 (mp) REVERT: A 670 LEU cc_start: 0.4272 (OUTLIER) cc_final: 0.4064 (mt) REVERT: A 805 ILE cc_start: 0.4455 (OUTLIER) cc_final: 0.4218 (tt) REVERT: A 912 LYS cc_start: 0.6097 (OUTLIER) cc_final: 0.5804 (mmmm) REVERT: A 927 THR cc_start: 0.6836 (OUTLIER) cc_final: 0.6556 (p) REVERT: A 983 MET cc_start: 0.8275 (ptm) cc_final: 0.8035 (ptp) REVERT: A 1063 PHE cc_start: 0.7769 (m-80) cc_final: 0.6997 (t80) REVERT: A 1105 ASN cc_start: 0.4913 (t0) cc_final: 0.4309 (t0) REVERT: A 1151 ASP cc_start: 0.7947 (t0) cc_final: 0.7448 (p0) REVERT: A 1286 MET cc_start: 0.8808 (mtp) cc_final: 0.8556 (mtm) REVERT: A 1337 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 1384 PHE cc_start: 0.6579 (OUTLIER) cc_final: 0.5952 (t80) REVERT: E 31 HIS cc_start: 0.6246 (m90) cc_final: 0.5766 (m170) REVERT: E 113 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: E 127 MET cc_start: 0.7632 (ttp) cc_final: 0.6683 (tmt) REVERT: E 138 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7402 (mtt90) REVERT: E 158 MET cc_start: 0.7165 (mmm) cc_final: 0.6549 (mmm) REVERT: F 120 ASN cc_start: 0.7762 (OUTLIER) cc_final: 0.7292 (m-40) REVERT: F 205 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8268 (tt) REVERT: F 234 LYS cc_start: 0.6536 (OUTLIER) cc_final: 0.6330 (mttt) REVERT: F 269 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8639 (tp) REVERT: F 297 ASN cc_start: 0.8161 (p0) cc_final: 0.7896 (p0) REVERT: F 381 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7633 (p0) REVERT: F 508 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8416 (mt) REVERT: F 545 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7657 (mmtt) REVERT: F 674 LYS cc_start: 0.7912 (ptpp) cc_final: 0.7643 (ttmm) REVERT: F 804 TYR cc_start: 0.8093 (m-80) cc_final: 0.7693 (m-80) REVERT: F 1020 MET cc_start: 0.7558 (ttp) cc_final: 0.7310 (ttp) outliers start: 128 outliers final: 58 residues processed: 350 average time/residue: 0.9546 time to fit residues: 390.2805 Evaluate side-chains 304 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 229 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 509 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 638 CYS Chi-restraints excluded: chain A residue 639 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 927 THR Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 999 ASN Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1332 CYS Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 381 ASP Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 550 VAL Chi-restraints excluded: chain F residue 602 ILE Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 699 SER Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 906 VAL Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Chi-restraints excluded: chain F residue 1060 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 161 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 184 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 194 optimal weight: 0.7980 chunk 54 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 649 ASN A 939 GLN A 948 GLN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 HIS F 483 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19053 Z= 0.167 Angle : 0.544 8.678 25744 Z= 0.283 Chirality : 0.041 0.200 2850 Planarity : 0.004 0.053 3210 Dihedral : 12.628 105.062 2977 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 6.27 % Allowed : 27.63 % Favored : 66.10 % 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: -0.92 (0.18), residues: 2227 helix: 0.19 (0.16), residues: 1124 sheet: -0.57 (0.32), residues: 226 loop : -1.60 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1406 HIS 0.002 0.001 HIS A 274 PHE 0.023 0.001 PHE F 689 TYR 0.021 0.001 TYR F 629 ARG 0.004 0.000 ARG F1032 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 247 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7316 (tt0) REVERT: A 114 GLN cc_start: 0.5819 (tt0) cc_final: 0.5286 (tm-30) REVERT: A 190 PHE cc_start: 0.6705 (t80) cc_final: 0.6455 (m-10) REVERT: A 241 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8531 (ptpt) REVERT: A 247 ARG cc_start: 0.7384 (ttp80) cc_final: 0.6870 (ptm160) REVERT: A 483 MET cc_start: 0.3022 (OUTLIER) cc_final: 0.2707 (tmt) REVERT: A 548 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6366 (tt) REVERT: A 553 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6838 (mp) REVERT: A 805 ILE cc_start: 0.4427 (OUTLIER) cc_final: 0.4183 (tt) REVERT: A 912 LYS cc_start: 0.5980 (OUTLIER) cc_final: 0.5708 (mmmm) REVERT: A 983 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8103 (ptp) REVERT: A 1063 PHE cc_start: 0.7659 (m-80) cc_final: 0.6836 (t80) REVERT: A 1105 ASN cc_start: 0.4842 (t0) cc_final: 0.4267 (t0) REVERT: A 1123 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8070 (pp) REVERT: A 1151 ASP cc_start: 0.7884 (t0) cc_final: 0.7460 (p0) REVERT: A 1286 MET cc_start: 0.8789 (mtp) cc_final: 0.8501 (mtm) REVERT: A 1384 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.5974 (t80) REVERT: E 31 HIS cc_start: 0.6240 (m90) cc_final: 0.5747 (m170) REVERT: E 127 MET cc_start: 0.7608 (ttp) cc_final: 0.6689 (tmt) REVERT: E 138 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7132 (mtt90) REVERT: E 216 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.5449 (tpt) REVERT: E 219 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6040 (pp20) REVERT: F 205 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8319 (tt) REVERT: F 234 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.6237 (mttt) REVERT: F 490 MET cc_start: 0.8604 (tpp) cc_final: 0.8386 (mmt) REVERT: F 508 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8347 (mt) REVERT: F 674 LYS cc_start: 0.7985 (ptpp) cc_final: 0.7706 (ttmm) REVERT: F 804 TYR cc_start: 0.7991 (m-80) cc_final: 0.7638 (m-80) outliers start: 125 outliers final: 56 residues processed: 343 average time/residue: 0.9586 time to fit residues: 383.1177 Evaluate side-chains 309 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 238 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 912 LYS Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 983 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 138 ARG Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 216 MET Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 699 SER Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Chi-restraints excluded: chain F residue 1060 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.6980 chunk 194 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 216 optimal weight: 10.0000 chunk 179 optimal weight: 0.0170 chunk 100 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 948 GLN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 644 GLN F 806 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 19053 Z= 0.148 Angle : 0.532 11.537 25744 Z= 0.274 Chirality : 0.040 0.170 2850 Planarity : 0.004 0.053 3210 Dihedral : 11.874 97.644 2960 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.47 % Allowed : 28.84 % Favored : 65.70 % 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: -0.54 (0.18), residues: 2227 helix: 0.52 (0.16), residues: 1114 sheet: -0.48 (0.33), residues: 224 loop : -1.42 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1406 HIS 0.002 0.001 HIS A 274 PHE 0.019 0.001 PHE F1006 TYR 0.018 0.001 TYR F 629 ARG 0.004 0.000 ARG F1032 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 260 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.5914 (tt0) cc_final: 0.5538 (tm-30) REVERT: A 241 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8600 (ptpt) REVERT: A 247 ARG cc_start: 0.7145 (ttp80) cc_final: 0.6683 (ptm160) REVERT: A 483 MET cc_start: 0.3211 (OUTLIER) cc_final: 0.2971 (tmt) REVERT: A 548 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6350 (tt) REVERT: A 553 LEU cc_start: 0.7243 (tp) cc_final: 0.6817 (mp) REVERT: A 554 ASN cc_start: 0.6292 (t0) cc_final: 0.5448 (p0) REVERT: A 668 GLU cc_start: 0.3636 (OUTLIER) cc_final: 0.2884 (tm-30) REVERT: A 805 ILE cc_start: 0.4325 (OUTLIER) cc_final: 0.4092 (tt) REVERT: A 1063 PHE cc_start: 0.7617 (m-80) cc_final: 0.6798 (t80) REVERT: A 1096 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6380 (ttm-80) REVERT: A 1105 ASN cc_start: 0.5137 (t0) cc_final: 0.4595 (t0) REVERT: A 1123 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8026 (pp) REVERT: A 1147 ASN cc_start: 0.4761 (OUTLIER) cc_final: 0.4235 (m110) REVERT: A 1151 ASP cc_start: 0.7804 (t0) cc_final: 0.7416 (p0) REVERT: A 1175 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6860 (mpp-170) REVERT: A 1286 MET cc_start: 0.8693 (mtp) cc_final: 0.8471 (mtm) REVERT: A 1384 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.5838 (t80) REVERT: E 113 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: E 127 MET cc_start: 0.7571 (ttp) cc_final: 0.6704 (tmt) REVERT: E 207 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7825 (mmm) REVERT: E 219 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5674 (pp20) REVERT: F 205 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8237 (tt) REVERT: F 234 LYS cc_start: 0.6504 (OUTLIER) cc_final: 0.6211 (mttt) REVERT: F 240 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8380 (p) REVERT: F 490 MET cc_start: 0.8579 (tpp) cc_final: 0.8375 (mmt) REVERT: F 508 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8281 (mt) REVERT: F 545 LYS cc_start: 0.8021 (mmtt) cc_final: 0.7800 (mmtt) REVERT: F 674 LYS cc_start: 0.8000 (ptpp) cc_final: 0.7676 (ttmm) REVERT: F 804 TYR cc_start: 0.8067 (m-80) cc_final: 0.7622 (m-80) REVERT: F 845 LYS cc_start: 0.6897 (mmpt) cc_final: 0.6617 (mmpt) outliers start: 109 outliers final: 51 residues processed: 342 average time/residue: 1.0360 time to fit residues: 410.6279 Evaluate side-chains 307 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 239 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 668 GLU Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1096 ARG Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1147 ASN Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Chi-restraints excluded: chain F residue 1060 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 445 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN E 209 GLN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN F 644 GLN F 806 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19053 Z= 0.332 Angle : 0.633 10.091 25744 Z= 0.327 Chirality : 0.045 0.190 2850 Planarity : 0.005 0.067 3210 Dihedral : 12.349 104.483 2955 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 6.12 % Allowed : 28.18 % Favored : 65.70 % 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: -0.82 (0.18), residues: 2227 helix: 0.23 (0.16), residues: 1128 sheet: -0.38 (0.32), residues: 223 loop : -1.56 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1406 HIS 0.009 0.001 HIS E 31 PHE 0.028 0.002 PHE F 157 TYR 0.016 0.002 TYR A1360 ARG 0.007 0.000 ARG F1032 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 229 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7328 (tt0) REVERT: A 114 GLN cc_start: 0.5959 (tt0) cc_final: 0.5452 (tm-30) REVERT: A 241 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8705 (ptpt) REVERT: A 247 ARG cc_start: 0.7403 (ttp80) cc_final: 0.6973 (ptm160) REVERT: A 493 MET cc_start: 0.3764 (OUTLIER) cc_final: 0.3524 (ttp) REVERT: A 553 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6895 (mp) REVERT: A 805 ILE cc_start: 0.4426 (OUTLIER) cc_final: 0.4203 (tt) REVERT: A 851 MET cc_start: 0.2664 (mmm) cc_final: 0.1962 (mmm) REVERT: A 948 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: A 1063 PHE cc_start: 0.7716 (m-80) cc_final: 0.6811 (t80) REVERT: A 1096 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6422 (ttm-80) REVERT: A 1105 ASN cc_start: 0.5060 (t0) cc_final: 0.4470 (t0) REVERT: A 1147 ASN cc_start: 0.4876 (OUTLIER) cc_final: 0.4276 (m110) REVERT: A 1151 ASP cc_start: 0.7787 (t0) cc_final: 0.7393 (p0) REVERT: A 1201 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5980 (tp30) REVERT: A 1272 LEU cc_start: 0.8514 (tp) cc_final: 0.8154 (mm) REVERT: A 1286 MET cc_start: 0.8857 (mtp) cc_final: 0.8544 (mtm) REVERT: A 1384 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.6024 (t80) REVERT: E 113 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.6914 (m-80) REVERT: E 127 MET cc_start: 0.7611 (ttp) cc_final: 0.6697 (tmt) REVERT: E 209 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6834 (tp-100) REVERT: F 205 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8437 (tt) REVERT: F 234 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.6203 (mttt) REVERT: F 505 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7661 (ppt-90) REVERT: F 508 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8324 (mt) REVERT: F 545 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7724 (mmtt) REVERT: F 674 LYS cc_start: 0.7990 (ptpp) cc_final: 0.7680 (ttmm) REVERT: F 804 TYR cc_start: 0.8108 (m-80) cc_final: 0.7694 (m-80) REVERT: F 845 LYS cc_start: 0.7196 (mmpt) cc_final: 0.6907 (mmpt) outliers start: 122 outliers final: 71 residues processed: 323 average time/residue: 1.0043 time to fit residues: 376.5694 Evaluate side-chains 311 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 225 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 493 MET Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 532 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 638 CYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 948 GLN Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1096 ARG Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1147 ASN Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1201 GLU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS 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 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 505 ARG Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 592 THR Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 817 ILE Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Chi-restraints excluded: chain F residue 1060 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 0.0870 chunk 106 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 169 optimal weight: 0.4980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 948 GLN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 ASN E 209 GLN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN F 644 GLN F 806 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 19053 Z= 0.150 Angle : 0.538 11.904 25744 Z= 0.280 Chirality : 0.040 0.205 2850 Planarity : 0.004 0.056 3210 Dihedral : 11.740 97.826 2955 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.56 % Allowed : 29.84 % Favored : 65.60 % 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: -0.43 (0.18), residues: 2227 helix: 0.62 (0.16), residues: 1116 sheet: -0.45 (0.33), residues: 220 loop : -1.36 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.002 0.000 HIS F 169 PHE 0.016 0.001 PHE A 112 TYR 0.018 0.001 TYR F 629 ARG 0.008 0.000 ARG F1032 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 237 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 PHE cc_start: 0.2892 (OUTLIER) cc_final: 0.2292 (m-80) REVERT: A 114 GLN cc_start: 0.5860 (tt0) cc_final: 0.5458 (tm-30) REVERT: A 241 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8602 (ptpt) REVERT: A 247 ARG cc_start: 0.7373 (ttp80) cc_final: 0.6962 (ptm160) REVERT: A 553 LEU cc_start: 0.7276 (tp) cc_final: 0.6883 (mp) REVERT: A 805 ILE cc_start: 0.4333 (OUTLIER) cc_final: 0.4105 (tt) REVERT: A 851 MET cc_start: 0.2601 (mmm) cc_final: 0.1914 (mmm) REVERT: A 1020 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8816 (tt) REVERT: A 1063 PHE cc_start: 0.7644 (m-80) cc_final: 0.6728 (t80) REVERT: A 1096 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6439 (ttm-80) REVERT: A 1123 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7950 (pp) REVERT: A 1147 ASN cc_start: 0.4835 (OUTLIER) cc_final: 0.4345 (m110) REVERT: A 1151 ASP cc_start: 0.7596 (t0) cc_final: 0.7218 (p0) REVERT: A 1286 MET cc_start: 0.8747 (mtp) cc_final: 0.8489 (mtm) REVERT: A 1384 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.5985 (t80) REVERT: E 113 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.6960 (m-80) REVERT: E 127 MET cc_start: 0.7559 (ttp) cc_final: 0.6753 (tmt) REVERT: E 207 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7841 (mmm) REVERT: E 216 MET cc_start: 0.6007 (tpt) cc_final: 0.5502 (tpt) REVERT: E 219 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.5497 (pp20) REVERT: F 205 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8258 (tt) REVERT: F 234 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5981 (mttt) REVERT: F 240 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8441 (p) REVERT: F 508 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8283 (mt) REVERT: F 674 LYS cc_start: 0.8075 (ptpp) cc_final: 0.7753 (ttmm) outliers start: 91 outliers final: 48 residues processed: 311 average time/residue: 1.0415 time to fit residues: 376.7916 Evaluate side-chains 289 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 226 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1020 LEU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1052 ILE Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1096 ARG Chi-restraints excluded: chain A residue 1123 LEU Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1147 ASN Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS 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 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 508 LEU Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1057 LYS Chi-restraints excluded: chain F residue 1060 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 201 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 181 optimal weight: 0.1980 chunk 190 optimal weight: 0.8980 chunk 200 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 948 GLN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN E 79 ASN E 209 GLN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN F 644 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 19053 Z= 0.154 Angle : 0.541 10.754 25744 Z= 0.279 Chirality : 0.040 0.208 2850 Planarity : 0.004 0.057 3210 Dihedral : 11.321 97.744 2951 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.56 % Allowed : 30.29 % Favored : 65.15 % 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: -0.24 (0.18), residues: 2227 helix: 0.79 (0.16), residues: 1110 sheet: -0.39 (0.33), residues: 220 loop : -1.26 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1406 HIS 0.007 0.001 HIS E 31 PHE 0.027 0.001 PHE F 689 TYR 0.025 0.001 TYR E 135 ARG 0.006 0.000 ARG E 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 240 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.7665 (m-80) cc_final: 0.7431 (m-80) REVERT: A 114 GLN cc_start: 0.5692 (tt0) cc_final: 0.5312 (tm-30) REVERT: A 241 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8622 (ptpt) REVERT: A 247 ARG cc_start: 0.7322 (ttp80) cc_final: 0.6932 (ptm160) REVERT: A 483 MET cc_start: 0.2934 (OUTLIER) cc_final: 0.2701 (tmt) REVERT: A 548 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6289 (tt) REVERT: A 553 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6900 (mp) REVERT: A 554 ASN cc_start: 0.6128 (t0) cc_final: 0.5344 (p0) REVERT: A 851 MET cc_start: 0.2485 (mmm) cc_final: 0.1824 (mmm) REVERT: A 1063 PHE cc_start: 0.7661 (m-80) cc_final: 0.6747 (t80) REVERT: A 1096 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6327 (ttm-80) REVERT: A 1147 ASN cc_start: 0.4784 (OUTLIER) cc_final: 0.4298 (m110) REVERT: A 1151 ASP cc_start: 0.7617 (t0) cc_final: 0.7237 (p0) REVERT: A 1272 LEU cc_start: 0.8400 (tp) cc_final: 0.8041 (mm) REVERT: A 1286 MET cc_start: 0.8688 (mtp) cc_final: 0.8472 (mtm) REVERT: A 1384 PHE cc_start: 0.6612 (OUTLIER) cc_final: 0.6114 (t80) REVERT: E 113 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.6910 (m-80) REVERT: E 127 MET cc_start: 0.7551 (ttp) cc_final: 0.6754 (tmt) REVERT: E 179 SER cc_start: 0.5727 (OUTLIER) cc_final: 0.5256 (m) REVERT: E 207 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7889 (mmm) REVERT: E 216 MET cc_start: 0.5892 (tpt) cc_final: 0.5370 (tpt) REVERT: E 219 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.5505 (pp20) REVERT: F 205 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8263 (tt) REVERT: F 234 LYS cc_start: 0.6244 (OUTLIER) cc_final: 0.5928 (mttt) REVERT: F 240 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8415 (p) REVERT: F 674 LYS cc_start: 0.8081 (ptpp) cc_final: 0.7798 (ptmt) outliers start: 91 outliers final: 52 residues processed: 310 average time/residue: 0.9912 time to fit residues: 357.4258 Evaluate side-chains 297 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 231 time to evaluate : 2.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1096 ARG Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1147 ASN Chi-restraints excluded: chain A residue 1148 HIS Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 372 GLN Chi-restraints excluded: chain F residue 517 ILE Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1014 THR Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1060 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 chunk 147 optimal weight: 0.0170 chunk 223 optimal weight: 0.5980 chunk 205 optimal weight: 0.9980 chunk 177 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 948 GLN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN E 79 ASN E 209 GLN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN F 644 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 19053 Z= 0.155 Angle : 0.542 10.882 25744 Z= 0.278 Chirality : 0.040 0.223 2850 Planarity : 0.004 0.056 3210 Dihedral : 11.071 97.321 2943 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.51 % Allowed : 31.14 % Favored : 65.35 % 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: -0.08 (0.18), residues: 2227 helix: 0.91 (0.16), residues: 1099 sheet: -0.33 (0.33), residues: 220 loop : -1.13 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1406 HIS 0.005 0.001 HIS E 31 PHE 0.021 0.001 PHE F 993 TYR 0.018 0.001 TYR E 135 ARG 0.006 0.000 ARG E 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4454 Ramachandran restraints generated. 2227 Oldfield, 0 Emsley, 2227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 237 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.7631 (m-80) cc_final: 0.7405 (m-80) REVERT: A 241 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8588 (ptpt) REVERT: A 247 ARG cc_start: 0.7369 (ttp80) cc_final: 0.6953 (ptm160) REVERT: A 483 MET cc_start: 0.2806 (OUTLIER) cc_final: 0.2592 (tmt) REVERT: A 548 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6231 (tt) REVERT: A 553 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6995 (mp) REVERT: A 554 ASN cc_start: 0.5929 (t0) cc_final: 0.5396 (p0) REVERT: A 851 MET cc_start: 0.2487 (mmm) cc_final: 0.1840 (mmm) REVERT: A 1063 PHE cc_start: 0.7658 (m-80) cc_final: 0.6742 (t80) REVERT: A 1096 ARG cc_start: 0.6576 (OUTLIER) cc_final: 0.6292 (ttm-80) REVERT: A 1151 ASP cc_start: 0.7584 (t0) cc_final: 0.7231 (p0) REVERT: A 1272 LEU cc_start: 0.8380 (tp) cc_final: 0.8017 (mm) REVERT: A 1384 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6087 (t80) REVERT: E 113 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: E 127 MET cc_start: 0.7486 (ttp) cc_final: 0.6740 (tmt) REVERT: E 207 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7816 (mmm) REVERT: E 216 MET cc_start: 0.5911 (tpt) cc_final: 0.5545 (tpt) REVERT: E 219 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.5537 (pp20) REVERT: F 205 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8260 (tt) REVERT: F 234 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5924 (mttt) REVERT: F 240 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8408 (p) REVERT: F 580 MET cc_start: 0.8894 (ttp) cc_final: 0.8626 (ttp) REVERT: F 674 LYS cc_start: 0.8098 (ptpp) cc_final: 0.7811 (ptmt) outliers start: 70 outliers final: 47 residues processed: 292 average time/residue: 1.0548 time to fit residues: 359.6534 Evaluate side-chains 288 residues out of total 1992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 229 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 499 PHE Chi-restraints excluded: chain A residue 541 TYR Chi-restraints excluded: chain A residue 547 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 663 ASN Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 984 GLU Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1056 MET Chi-restraints excluded: chain A residue 1096 ARG Chi-restraints excluded: chain A residue 1141 HIS Chi-restraints excluded: chain A residue 1148 HIS Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1241 MET Chi-restraints excluded: chain A residue 1298 THR Chi-restraints excluded: chain A residue 1363 SER Chi-restraints excluded: chain A residue 1384 PHE Chi-restraints excluded: chain A residue 1388 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 113 PHE Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 219 GLU Chi-restraints excluded: chain F residue 116 ASP Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 257 LEU Chi-restraints excluded: chain F residue 270 THR Chi-restraints excluded: chain F residue 286 SER Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 523 VAL Chi-restraints excluded: chain F residue 617 THR Chi-restraints excluded: chain F residue 680 THR Chi-restraints excluded: chain F residue 996 VAL Chi-restraints excluded: chain F residue 1031 THR Chi-restraints excluded: chain F residue 1060 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 163 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 chunk 182 optimal weight: 0.8980 chunk 22 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 948 GLN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN E 209 GLN ** F 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 483 ASN ** F 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 570 ASN F 644 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.170751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120060 restraints weight = 47890.994| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.08 r_work: 0.3095 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 19053 Z= 0.147 Angle : 0.541 10.616 25744 Z= 0.277 Chirality : 0.040 0.220 2850 Planarity : 0.004 0.055 3210 Dihedral : 10.774 96.534 2940 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.41 % Allowed : 31.24 % Favored : 65.35 % 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: 0.09 (0.18), residues: 2227 helix: 1.06 (0.16), residues: 1093 sheet: -0.28 (0.34), residues: 220 loop : -1.04 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1406 HIS 0.002 0.000 HIS A 274 PHE 0.027 0.001 PHE A 131 TYR 0.012 0.001 TYR F 629 ARG 0.006 0.000 ARG E 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6916.86 seconds wall clock time: 123 minutes 35.16 seconds (7415.16 seconds total)