Starting phenix.real_space_refine on Tue Aug 6 23:24:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4n_30079/08_2024/6m4n_30079.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4n_30079/08_2024/6m4n_30079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4n_30079/08_2024/6m4n_30079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4n_30079/08_2024/6m4n_30079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4n_30079/08_2024/6m4n_30079.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4n_30079/08_2024/6m4n_30079.cif" } resolution = 3.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 30 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 100 5.16 5 C 11492 2.51 5 N 3014 2.21 5 O 3228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A ARG 181": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 116": "NH1" <-> "NH2" Residue "E ARG 151": "NH1" <-> "NH2" Residue "E ARG 181": "NH1" <-> "NH2" Residue "E ARG 189": "NH1" <-> "NH2" Residue "E ARG 236": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E ARG 270": "NH1" <-> "NH2" Residue "E ARG 287": "NH1" <-> "NH2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ARG 329": "NH1" <-> "NH2" Residue "E ARG 405": "NH1" <-> "NH2" Residue "E ARG 422": "NH1" <-> "NH2" Residue "E ARG 459": "NH1" <-> "NH2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F ARG 129": "NH1" <-> "NH2" Residue "F ARG 151": "NH1" <-> "NH2" Residue "F ARG 207": "NH1" <-> "NH2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F ARG 271": "NH1" <-> "NH2" Residue "F ARG 278": "NH1" <-> "NH2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "F ARG 326": "NH1" <-> "NH2" Residue "F TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 447": "NH1" <-> "NH2" Residue "F ARG 450": "NH1" <-> "NH2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F ARG 489": "NH1" <-> "NH2" Residue "F ARG 507": "NH1" <-> "NH2" Residue "F ARG 509": "NH1" <-> "NH2" Residue "G ARG 15": "NH1" <-> "NH2" Residue "G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17836 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3498 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3887 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "D" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 390 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3498 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3887 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 473} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1128 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 7, 'TRANS': 131} Chain: "H" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 390 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 47} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C2 PLP B 601 " occ=0.80 ... (13 atoms not shown) pdb=" P PLP B 601 " occ=0.80 residue: pdb=" C2 PLP F 601 " occ=0.80 ... (13 atoms not shown) pdb=" P PLP F 601 " occ=0.80 Time building chain proxies: 9.68, per 1000 atoms: 0.54 Number of scatterers: 17836 At special positions: 0 Unit cell: (125.882, 157.074, 118.084, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 2 15.00 O 3228 8.00 N 3014 7.00 C 11492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.60 Conformation dependent library (CDL) restraints added in 2.9 seconds 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4172 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 14 sheets defined 47.4% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 23 through 40 removed outlier: 3.683A pdb=" N LEU A 27 " --> pdb=" O TYR A 23 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ILE A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 62 removed outlier: 3.692A pdb=" N GLU A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 removed outlier: 3.563A pdb=" N ASP A 113 " --> pdb=" O GLY A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.547A pdb=" N GLY A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 157 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 194 through 202 removed outlier: 3.919A pdb=" N GLY A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 200 " --> pdb=" O GLN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 257 through 268 removed outlier: 4.279A pdb=" N LEU A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 361 through 374 removed outlier: 3.666A pdb=" N VAL A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A 367 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.962A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 472 removed outlier: 3.707A pdb=" N LEU A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN A 469 " --> pdb=" O LYS A 465 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 92 removed outlier: 3.740A pdb=" N LEU B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.751A pdb=" N ARG B 124 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 199 removed outlier: 4.546A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA B 192 " --> pdb=" O CYS B 188 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.516A pdb=" N GLU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 246 removed outlier: 4.096A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.717A pdb=" N VAL B 267 " --> pdb=" O HIS B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 removed outlier: 3.838A pdb=" N ILE B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 338 removed outlier: 3.517A pdb=" N LEU B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 335 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 336 " --> pdb=" O ALA B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 removed outlier: 4.087A pdb=" N GLU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 399 Processing helix chain 'B' and resid 412 through 428 removed outlier: 3.536A pdb=" N VAL B 416 " --> pdb=" O SER B 412 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 456 removed outlier: 4.261A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG B 451 " --> pdb=" O ARG B 447 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.666A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 535 removed outlier: 3.720A pdb=" N GLU B 530 " --> pdb=" O LYS B 526 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 533 " --> pdb=" O ASP B 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 39 removed outlier: 3.577A pdb=" N LEU C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 30 " --> pdb=" O TYR C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 63 removed outlier: 4.152A pdb=" N TRP C 49 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 removed outlier: 3.500A pdb=" N ARG C 81 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU C 82 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.681A pdb=" N TYR C 91 " --> pdb=" O GLN C 88 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 93 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 Proline residue: C 106 - end of helix removed outlier: 3.669A pdb=" N THR C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 120 removed outlier: 3.647A pdb=" N ASP C 120 " --> pdb=" O THR C 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 117 through 120' Processing helix chain 'C' and resid 121 through 136 removed outlier: 3.640A pdb=" N ASN C 127 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 129 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 131 " --> pdb=" O ASN C 127 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 removed outlier: 3.698A pdb=" N SER D 14 " --> pdb=" O TRP D 10 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP D 15 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE D 16 " --> pdb=" O GLN D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 30 through 53 removed outlier: 3.695A pdb=" N THR D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL D 36 " --> pdb=" O TRP D 32 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE D 44 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 45 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 40 removed outlier: 3.683A pdb=" N LEU E 27 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 62 removed outlier: 3.693A pdb=" N GLU E 58 " --> pdb=" O VAL E 54 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 113 removed outlier: 3.562A pdb=" N ASP E 113 " --> pdb=" O GLY E 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 110 through 113' Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.547A pdb=" N GLY E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 157 Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 194 through 202 removed outlier: 3.918A pdb=" N GLY E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 229 Processing helix chain 'E' and resid 233 through 237 Processing helix chain 'E' and resid 257 through 268 removed outlier: 4.278A pdb=" N LEU E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR E 265 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 294 Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 342 through 359 Processing helix chain 'E' and resid 361 through 374 removed outlier: 3.665A pdb=" N VAL E 365 " --> pdb=" O GLY E 361 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS E 367 " --> pdb=" O PHE E 363 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU E 368 " --> pdb=" O ALA E 364 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 373 " --> pdb=" O LYS E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 422 removed outlier: 3.962A pdb=" N ILE E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL E 416 " --> pdb=" O LEU E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 472 removed outlier: 3.706A pdb=" N LEU E 457 " --> pdb=" O THR E 453 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG E 459 " --> pdb=" O GLU E 455 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 467 " --> pdb=" O THR E 463 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN E 469 " --> pdb=" O LYS E 465 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA E 470 " --> pdb=" O GLU E 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 92 removed outlier: 3.740A pdb=" N LEU F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 126 removed outlier: 3.751A pdb=" N ARG F 124 " --> pdb=" O ASN F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 199 removed outlier: 4.546A pdb=" N GLN F 189 " --> pdb=" O THR F 185 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU F 190 " --> pdb=" O GLY F 186 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA F 191 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA F 192 " --> pdb=" O CYS F 188 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA F 193 " --> pdb=" O GLN F 189 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.517A pdb=" N GLU F 221 " --> pdb=" O GLU F 217 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA F 224 " --> pdb=" O GLU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 246 removed outlier: 4.097A pdb=" N ASN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE F 246 " --> pdb=" O ASN F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 263 through 273 removed outlier: 3.717A pdb=" N VAL F 267 " --> pdb=" O HIS F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.839A pdb=" N ILE F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 338 removed outlier: 3.517A pdb=" N LEU F 333 " --> pdb=" O GLU F 329 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS F 335 " --> pdb=" O ILE F 331 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 336 " --> pdb=" O ALA F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 363 removed outlier: 4.087A pdb=" N GLU F 361 " --> pdb=" O ARG F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 399 Processing helix chain 'F' and resid 412 through 428 removed outlier: 3.537A pdb=" N VAL F 416 " --> pdb=" O SER F 412 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU F 417 " --> pdb=" O PRO F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 436 through 456 removed outlier: 4.261A pdb=" N GLN F 440 " --> pdb=" O LYS F 436 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG F 451 " --> pdb=" O ARG F 447 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS F 454 " --> pdb=" O ARG F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 3.666A pdb=" N GLY F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG F 484 " --> pdb=" O GLY F 480 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 535 removed outlier: 3.720A pdb=" N GLU F 530 " --> pdb=" O LYS F 526 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 533 " --> pdb=" O ASP F 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 39 removed outlier: 3.577A pdb=" N LEU G 28 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 63 removed outlier: 4.152A pdb=" N TRP G 49 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN G 57 " --> pdb=" O ASN G 53 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR G 61 " --> pdb=" O ASN G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.500A pdb=" N ARG G 81 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU G 82 " --> pdb=" O LYS G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 93 removed outlier: 3.682A pdb=" N TYR G 91 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL G 93 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 116 Proline residue: G 106 - end of helix removed outlier: 3.669A pdb=" N THR G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 120 removed outlier: 3.647A pdb=" N ASP G 120 " --> pdb=" O THR G 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 117 through 120' Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.641A pdb=" N ASN G 127 " --> pdb=" O HIS G 123 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL G 129 " --> pdb=" O VAL G 125 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER G 130 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU G 131 " --> pdb=" O ASN G 127 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU G 135 " --> pdb=" O LEU G 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 23 removed outlier: 3.697A pdb=" N SER H 14 " --> pdb=" O TRP H 10 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP H 15 " --> pdb=" O LYS H 11 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE H 16 " --> pdb=" O GLN H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 26 No H-bonds generated for 'chain 'H' and resid 24 through 26' Processing helix chain 'H' and resid 30 through 53 removed outlier: 3.695A pdb=" N THR H 35 " --> pdb=" O PRO H 31 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL H 36 " --> pdb=" O TRP H 32 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE H 44 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL H 45 " --> pdb=" O LEU H 41 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR H 50 " --> pdb=" O GLY H 46 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 95 removed outlier: 6.943A pdb=" N ALA A 425 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 101 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.581A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE A 186 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.530A pdb=" N VAL A 446 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 152 removed outlier: 5.321A pdb=" N VAL B 146 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY B 169 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN B 165 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N GLN B 152 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR B 163 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N GLY B 492 " --> pdb=" O GLY B 169 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.847A pdb=" N GLY B 375 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR B 376 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.762A pdb=" N SER B 323 " --> pdb=" O TYR B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 471 removed outlier: 3.794A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 92 through 95 removed outlier: 6.942A pdb=" N ALA E 425 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE E 101 " --> pdb=" O ALA E 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 160 through 164 removed outlier: 6.581A pdb=" N ILE E 242 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N PHE E 186 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 393 through 395 removed outlier: 3.529A pdb=" N VAL E 446 " --> pdb=" O PHE E 394 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 145 through 152 removed outlier: 5.320A pdb=" N VAL F 146 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY F 169 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN F 165 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLN F 152 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR F 163 " --> pdb=" O GLN F 152 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N GLY F 492 " --> pdb=" O GLY F 169 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE F 171 " --> pdb=" O GLY F 492 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.847A pdb=" N GLY F 375 " --> pdb=" O TYR F 387 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR F 376 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N TYR F 342 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE F 312 " --> pdb=" O TYR F 342 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASP F 344 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL F 314 " --> pdb=" O ASP F 344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 317 through 318 removed outlier: 3.762A pdb=" N SER F 323 " --> pdb=" O TYR F 318 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 468 through 471 removed outlier: 3.795A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5613 1.34 - 1.45: 3574 1.45 - 1.57: 8871 1.57 - 1.69: 2 1.69 - 1.81: 164 Bond restraints: 18224 Sorted by residual: bond pdb=" CA ILE E 175 " pdb=" CB ILE E 175 " ideal model delta sigma weight residual 1.539 1.524 0.015 5.40e-03 3.43e+04 7.78e+00 bond pdb=" CA ILE A 175 " pdb=" CB ILE A 175 " ideal model delta sigma weight residual 1.539 1.524 0.015 5.40e-03 3.43e+04 7.49e+00 bond pdb=" CA TYR F 342 " pdb=" CB TYR F 342 " ideal model delta sigma weight residual 1.531 1.497 0.034 1.52e-02 4.33e+03 4.94e+00 bond pdb=" CA TYR B 342 " pdb=" CB TYR B 342 " ideal model delta sigma weight residual 1.531 1.498 0.033 1.52e-02 4.33e+03 4.69e+00 bond pdb=" C HIS G 65 " pdb=" N THR G 66 " ideal model delta sigma weight residual 1.331 1.303 0.029 1.40e-02 5.10e+03 4.21e+00 ... (remaining 18219 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.33: 390 105.33 - 112.64: 9359 112.64 - 119.95: 6938 119.95 - 127.27: 7787 127.27 - 134.58: 182 Bond angle restraints: 24656 Sorted by residual: angle pdb=" C PRO E 72 " pdb=" N VAL E 73 " pdb=" CA VAL E 73 " ideal model delta sigma weight residual 120.43 127.18 -6.75 9.60e-01 1.09e+00 4.95e+01 angle pdb=" C PRO A 72 " pdb=" N VAL A 73 " pdb=" CA VAL A 73 " ideal model delta sigma weight residual 120.43 127.15 -6.72 9.60e-01 1.09e+00 4.90e+01 angle pdb=" N VAL F 406 " pdb=" CA VAL F 406 " pdb=" C VAL F 406 " ideal model delta sigma weight residual 113.53 107.70 5.83 9.80e-01 1.04e+00 3.54e+01 angle pdb=" N VAL B 406 " pdb=" CA VAL B 406 " pdb=" C VAL B 406 " ideal model delta sigma weight residual 113.53 107.73 5.80 9.80e-01 1.04e+00 3.50e+01 angle pdb=" C LYS F 538 " pdb=" N TYR F 539 " pdb=" CA TYR F 539 " ideal model delta sigma weight residual 120.28 127.24 -6.96 1.44e+00 4.82e-01 2.33e+01 ... (remaining 24651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.03: 10684 30.03 - 60.06: 190 60.06 - 90.09: 18 90.09 - 120.12: 0 120.12 - 150.15: 2 Dihedral angle restraints: 10894 sinusoidal: 4378 harmonic: 6516 Sorted by residual: dihedral pdb=" CA ALA A 20 " pdb=" C ALA A 20 " pdb=" N PRO A 21 " pdb=" CA PRO A 21 " ideal model delta harmonic sigma weight residual 180.00 143.16 36.84 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CA ALA E 20 " pdb=" C ALA E 20 " pdb=" N PRO E 21 " pdb=" CA PRO E 21 " ideal model delta harmonic sigma weight residual 180.00 143.16 36.84 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" C5A PLP F 601 " pdb=" O4P PLP F 601 " pdb=" P PLP F 601 " pdb=" O1P PLP F 601 " ideal model delta sinusoidal sigma weight residual 76.43 -133.43 -150.15 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 10891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1873 0.059 - 0.117: 718 0.117 - 0.176: 147 0.176 - 0.234: 12 0.234 - 0.293: 10 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CB ILE B 459 " pdb=" CA ILE B 459 " pdb=" CG1 ILE B 459 " pdb=" CG2 ILE B 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE F 459 " pdb=" CA ILE F 459 " pdb=" CG1 ILE F 459 " pdb=" CG2 ILE F 459 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB VAL E 237 " pdb=" CA VAL E 237 " pdb=" CG1 VAL E 237 " pdb=" CG2 VAL E 237 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2757 not shown) Planarity restraints: 3124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 501 " 0.056 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO F 502 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO F 502 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 502 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.055 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO B 502 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 20 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO E 21 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 21 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 21 " 0.039 5.00e-02 4.00e+02 ... (remaining 3121 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1063 2.71 - 3.26: 17785 3.26 - 3.81: 29960 3.81 - 4.35: 36183 4.35 - 4.90: 60112 Nonbonded interactions: 145103 Sorted by model distance: nonbonded pdb=" OG1 THR A 427 " pdb=" OE1 GLU B 209 " model vdw 2.164 3.040 nonbonded pdb=" OG1 THR E 427 " pdb=" OE1 GLU F 209 " model vdw 2.250 3.040 nonbonded pdb=" OD2 ASP E 188 " pdb=" OH TYR E 248 " model vdw 2.276 3.040 nonbonded pdb=" OD2 ASP A 188 " pdb=" OH TYR A 248 " model vdw 2.276 3.040 nonbonded pdb=" OE1 GLN C 121 " pdb=" OH TYR E 23 " model vdw 2.294 3.040 ... (remaining 145098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 44.600 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 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 : 0.009 0.084 18224 Z= 0.603 Angle : 1.175 10.267 24656 Z= 0.647 Chirality : 0.062 0.293 2760 Planarity : 0.008 0.084 3124 Dihedral : 11.939 150.149 6722 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.87 % Favored : 88.95 % Rotamer: Outliers : 0.73 % Allowed : 8.06 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.09 % 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: -4.50 (0.14), residues: 2226 helix: -3.26 (0.11), residues: 932 sheet: -1.78 (0.35), residues: 230 loop : -2.96 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 64 HIS 0.016 0.003 HIS A 211 PHE 0.027 0.003 PHE A 209 TYR 0.028 0.003 TYR B 176 ARG 0.013 0.002 ARG F 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 362 time to evaluate : 1.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 126 LEU cc_start: 0.9194 (mp) cc_final: 0.8801 (tt) REVERT: C 34 HIS cc_start: 0.8253 (t-90) cc_final: 0.7985 (t70) REVERT: C 89 MET cc_start: 0.8611 (mtt) cc_final: 0.8319 (mtt) REVERT: C 118 LYS cc_start: 0.8009 (mptt) cc_final: 0.7606 (mmtm) REVERT: D 13 MET cc_start: 0.8742 (tpt) cc_final: 0.8026 (tmm) REVERT: D 19 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8479 (tm-30) REVERT: D 44 ILE cc_start: 0.9247 (mm) cc_final: 0.8972 (pt) REVERT: F 126 LEU cc_start: 0.9130 (mp) cc_final: 0.8733 (tt) REVERT: F 128 MET cc_start: 0.8575 (tpt) cc_final: 0.8356 (tpp) REVERT: F 131 ARG cc_start: 0.9192 (ptm-80) cc_final: 0.8719 (ptt180) REVERT: G 34 HIS cc_start: 0.8457 (t-90) cc_final: 0.8131 (t70) REVERT: G 58 MET cc_start: 0.8430 (tpt) cc_final: 0.8222 (tpp) REVERT: H 13 MET cc_start: 0.8642 (tpt) cc_final: 0.8202 (tmm) REVERT: H 19 GLN cc_start: 0.9101 (tp-100) cc_final: 0.8427 (tm-30) REVERT: H 44 ILE cc_start: 0.9232 (mm) cc_final: 0.8982 (pt) outliers start: 14 outliers final: 4 residues processed: 374 average time/residue: 0.3068 time to fit residues: 168.3178 Evaluate side-chains 192 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain F residue 372 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 114 ASN A 224 GLN A 231 ASN A 309 ASN ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 242 ASN B 263 HIS B 282 HIS B 284 ASN B 403 HIS B 490 ASN E 114 ASN E 224 GLN E 231 ASN E 309 ASN ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 407 GLN F 50 GLN F 242 ASN F 245 ASN F 263 HIS F 282 HIS F 284 ASN F 403 HIS F 490 ASN G 94 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18224 Z= 0.199 Angle : 0.762 10.956 24656 Z= 0.388 Chirality : 0.046 0.152 2760 Planarity : 0.006 0.074 3124 Dihedral : 8.224 168.194 2470 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 3.82 % Allowed : 11.05 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.17), residues: 2226 helix: -1.18 (0.15), residues: 966 sheet: -1.73 (0.33), residues: 240 loop : -2.52 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 15 HIS 0.004 0.001 HIS A 211 PHE 0.029 0.002 PHE F 59 TYR 0.013 0.001 TYR G 116 ARG 0.004 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 258 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7027 (m-30) cc_final: 0.6401 (m-30) REVERT: A 214 MET cc_start: 0.7895 (mmp) cc_final: 0.7331 (mmm) REVERT: A 274 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7116 (tm-30) REVERT: A 275 GLU cc_start: 0.8317 (pt0) cc_final: 0.7773 (pp20) REVERT: A 307 MET cc_start: 0.8525 (mpp) cc_final: 0.8254 (mpp) REVERT: B 126 LEU cc_start: 0.9055 (mp) cc_final: 0.8815 (tt) REVERT: B 128 MET cc_start: 0.8920 (mmm) cc_final: 0.8516 (tpt) REVERT: B 472 MET cc_start: 0.8586 (tpp) cc_final: 0.8323 (tpp) REVERT: C 34 HIS cc_start: 0.8478 (t-90) cc_final: 0.8072 (t70) REVERT: C 118 LYS cc_start: 0.8121 (mptt) cc_final: 0.7566 (mmtm) REVERT: D 13 MET cc_start: 0.8536 (tpt) cc_final: 0.7938 (tmm) REVERT: D 28 MET cc_start: 0.8447 (pmt) cc_final: 0.8119 (pmt) REVERT: E 183 ASP cc_start: 0.7245 (m-30) cc_final: 0.6504 (m-30) REVERT: E 228 ASP cc_start: 0.7865 (m-30) cc_final: 0.7393 (m-30) REVERT: E 307 MET cc_start: 0.8494 (mpp) cc_final: 0.8203 (mpp) REVERT: F 126 LEU cc_start: 0.9037 (mp) cc_final: 0.8755 (tt) REVERT: F 131 ARG cc_start: 0.9134 (ptm-80) cc_final: 0.8856 (ptt90) REVERT: F 173 MET cc_start: 0.8969 (mmm) cc_final: 0.8744 (mmm) REVERT: F 503 ILE cc_start: 0.8824 (tp) cc_final: 0.8621 (tp) REVERT: F 504 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9064 (mp) REVERT: G 34 HIS cc_start: 0.8534 (t-90) cc_final: 0.8008 (t70) REVERT: G 58 MET cc_start: 0.8383 (tpt) cc_final: 0.8156 (tpp) REVERT: H 13 MET cc_start: 0.8359 (tpt) cc_final: 0.7984 (tmm) REVERT: H 19 GLN cc_start: 0.8840 (tp-100) cc_final: 0.8068 (tm-30) REVERT: H 40 MET cc_start: 0.8426 (mmp) cc_final: 0.8118 (mmp) REVERT: H 44 ILE cc_start: 0.9091 (mm) cc_final: 0.8872 (pt) outliers start: 73 outliers final: 32 residues processed: 310 average time/residue: 0.2620 time to fit residues: 127.4289 Evaluate side-chains 220 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 94 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 216 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN G 123 HIS G 127 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18224 Z= 0.250 Angle : 0.728 10.503 24656 Z= 0.365 Chirality : 0.046 0.299 2760 Planarity : 0.005 0.074 3124 Dihedral : 7.879 167.756 2470 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.56 % Allowed : 13.56 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.17), residues: 2226 helix: -0.39 (0.16), residues: 962 sheet: -1.56 (0.34), residues: 234 loop : -2.30 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 15 HIS 0.005 0.001 HIS E 211 PHE 0.016 0.001 PHE B 59 TYR 0.014 0.001 TYR A 248 ARG 0.006 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 202 time to evaluate : 2.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.7122 (m-30) cc_final: 0.6552 (m-30) REVERT: A 274 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 307 MET cc_start: 0.8683 (mpp) cc_final: 0.8148 (mpp) REVERT: B 126 LEU cc_start: 0.9087 (mp) cc_final: 0.8845 (tt) REVERT: B 472 MET cc_start: 0.8598 (tpp) cc_final: 0.8366 (tpp) REVERT: C 34 HIS cc_start: 0.8527 (t-90) cc_final: 0.8007 (t70) REVERT: C 57 ASN cc_start: 0.8177 (m-40) cc_final: 0.7743 (m-40) REVERT: C 118 LYS cc_start: 0.8106 (mptt) cc_final: 0.7703 (mmtm) REVERT: D 13 MET cc_start: 0.8618 (tpt) cc_final: 0.8045 (tmm) REVERT: D 19 GLN cc_start: 0.9104 (tp40) cc_final: 0.8386 (tm-30) REVERT: D 28 MET cc_start: 0.8457 (pmt) cc_final: 0.8216 (pmt) REVERT: D 44 ILE cc_start: 0.8825 (pt) cc_final: 0.8226 (mm) REVERT: E 183 ASP cc_start: 0.7434 (m-30) cc_final: 0.6790 (m-30) REVERT: E 275 GLU cc_start: 0.8189 (pt0) cc_final: 0.7514 (pp20) REVERT: E 307 MET cc_start: 0.8730 (mpp) cc_final: 0.8165 (mpp) REVERT: F 126 LEU cc_start: 0.9069 (mp) cc_final: 0.8819 (tt) REVERT: F 128 MET cc_start: 0.9037 (tpp) cc_final: 0.8625 (tmm) REVERT: F 173 MET cc_start: 0.9020 (mmm) cc_final: 0.8682 (mmm) REVERT: G 34 HIS cc_start: 0.8502 (t-90) cc_final: 0.8028 (t70) REVERT: G 57 ASN cc_start: 0.8369 (m-40) cc_final: 0.7995 (m-40) REVERT: G 58 MET cc_start: 0.8372 (tpt) cc_final: 0.8092 (tpp) REVERT: H 13 MET cc_start: 0.8458 (tpt) cc_final: 0.8038 (tmm) REVERT: H 44 ILE cc_start: 0.9062 (mm) cc_final: 0.8846 (pt) outliers start: 68 outliers final: 41 residues processed: 252 average time/residue: 0.2511 time to fit residues: 102.2340 Evaluate side-chains 226 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 185 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 255 CYS Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 319 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 423 MET Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 119 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 134 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 100 HIS B 120 ASN B 154 HIS B 157 ASN C 94 GLN E 292 HIS ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN F 120 ASN F 154 HIS F 157 ASN ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 516 HIS G 77 GLN G 94 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 18224 Z= 0.495 Angle : 0.855 11.367 24656 Z= 0.435 Chirality : 0.050 0.208 2760 Planarity : 0.006 0.065 3124 Dihedral : 7.969 164.959 2470 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.37 % Favored : 88.63 % Rotamer: Outliers : 4.66 % Allowed : 14.87 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.06 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.17), residues: 2226 helix: -0.37 (0.16), residues: 984 sheet: -1.56 (0.34), residues: 234 loop : -2.32 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP F 134 HIS 0.009 0.002 HIS E 211 PHE 0.020 0.002 PHE B 160 TYR 0.020 0.002 TYR A 248 ARG 0.006 0.001 ARG F 484 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 179 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8352 (pt0) cc_final: 0.7896 (pp20) REVERT: A 307 MET cc_start: 0.8830 (mpp) cc_final: 0.8234 (mpp) REVERT: B 126 LEU cc_start: 0.9252 (mp) cc_final: 0.8987 (tt) REVERT: B 472 MET cc_start: 0.8629 (tpp) cc_final: 0.8363 (tpp) REVERT: C 34 HIS cc_start: 0.8644 (t-90) cc_final: 0.8046 (t70) REVERT: C 57 ASN cc_start: 0.8357 (m-40) cc_final: 0.8108 (m-40) REVERT: C 118 LYS cc_start: 0.8136 (mptt) cc_final: 0.7738 (mmtm) REVERT: D 13 MET cc_start: 0.8664 (tpt) cc_final: 0.8096 (tmm) REVERT: D 19 GLN cc_start: 0.9051 (tp40) cc_final: 0.8391 (tm-30) REVERT: D 37 PHE cc_start: 0.9244 (t80) cc_final: 0.9023 (t80) REVERT: D 40 MET cc_start: 0.8800 (tpp) cc_final: 0.8128 (mmp) REVERT: E 275 GLU cc_start: 0.8356 (pt0) cc_final: 0.7799 (pp20) REVERT: E 307 MET cc_start: 0.8829 (mpp) cc_final: 0.8298 (mpp) REVERT: F 173 MET cc_start: 0.9145 (mmm) cc_final: 0.8769 (mmm) REVERT: G 34 HIS cc_start: 0.8580 (t-90) cc_final: 0.8043 (t70) REVERT: G 57 ASN cc_start: 0.8553 (m-40) cc_final: 0.8243 (m-40) REVERT: G 118 LYS cc_start: 0.7744 (mmtp) cc_final: 0.7230 (mmtm) REVERT: H 13 MET cc_start: 0.8704 (tpt) cc_final: 0.8085 (tmm) REVERT: H 37 PHE cc_start: 0.9240 (t80) cc_final: 0.9021 (t80) outliers start: 89 outliers final: 61 residues processed: 248 average time/residue: 0.2681 time to fit residues: 106.7756 Evaluate side-chains 230 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 169 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 255 CYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 76 VAL Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 243 SER Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 423 MET Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 119 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 181 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN C 85 HIS C 94 GLN C 123 HIS ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18224 Z= 0.257 Angle : 0.740 12.362 24656 Z= 0.365 Chirality : 0.047 0.347 2760 Planarity : 0.005 0.064 3124 Dihedral : 7.729 166.883 2470 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 4.24 % Allowed : 16.49 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.18), residues: 2226 helix: 0.13 (0.17), residues: 972 sheet: -1.44 (0.34), residues: 234 loop : -2.24 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 32 HIS 0.005 0.001 HIS A 211 PHE 0.012 0.001 PHE A 209 TYR 0.013 0.001 TYR F 342 ARG 0.004 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 187 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8414 (pt0) cc_final: 0.7842 (pp20) REVERT: A 307 MET cc_start: 0.8719 (mpp) cc_final: 0.8183 (mpp) REVERT: B 126 LEU cc_start: 0.9232 (mp) cc_final: 0.8941 (tt) REVERT: B 244 MET cc_start: 0.8055 (mtt) cc_final: 0.7502 (mtt) REVERT: B 374 MET cc_start: 0.7905 (tmm) cc_final: 0.7667 (tmm) REVERT: B 472 MET cc_start: 0.8665 (tpp) cc_final: 0.8395 (tpp) REVERT: C 34 HIS cc_start: 0.8662 (t-90) cc_final: 0.8024 (t70) REVERT: C 57 ASN cc_start: 0.8332 (m-40) cc_final: 0.8051 (m-40) REVERT: C 118 LYS cc_start: 0.8063 (mptt) cc_final: 0.7667 (mmtm) REVERT: D 13 MET cc_start: 0.8679 (tpt) cc_final: 0.8050 (tmm) REVERT: D 19 GLN cc_start: 0.9080 (tp40) cc_final: 0.8309 (tm-30) REVERT: D 37 PHE cc_start: 0.9253 (t80) cc_final: 0.9036 (t80) REVERT: D 49 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7193 (pp) REVERT: E 307 MET cc_start: 0.8732 (mpp) cc_final: 0.8212 (mpp) REVERT: F 128 MET cc_start: 0.8961 (tpp) cc_final: 0.8700 (tmm) REVERT: F 173 MET cc_start: 0.9089 (mmm) cc_final: 0.8715 (mmm) REVERT: G 34 HIS cc_start: 0.8602 (t-90) cc_final: 0.7996 (t70) REVERT: G 57 ASN cc_start: 0.8408 (m-40) cc_final: 0.8117 (m-40) REVERT: H 13 MET cc_start: 0.8581 (tpt) cc_final: 0.7945 (tmm) REVERT: H 37 PHE cc_start: 0.9241 (t80) cc_final: 0.9006 (t80) REVERT: H 44 ILE cc_start: 0.9033 (mm) cc_final: 0.8801 (pt) outliers start: 81 outliers final: 53 residues processed: 247 average time/residue: 0.2472 time to fit residues: 98.2468 Evaluate side-chains 225 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 171 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 255 CYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 423 MET Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 119 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18224 Z= 0.204 Angle : 0.734 12.459 24656 Z= 0.354 Chirality : 0.048 0.297 2760 Planarity : 0.004 0.063 3124 Dihedral : 7.498 166.083 2470 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 3.56 % Allowed : 18.06 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.18), residues: 2226 helix: 0.41 (0.17), residues: 974 sheet: -1.41 (0.34), residues: 234 loop : -2.07 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 32 HIS 0.007 0.001 HIS G 123 PHE 0.011 0.001 PHE A 209 TYR 0.012 0.001 TYR F 342 ARG 0.004 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 188 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 VAL cc_start: 0.9045 (t) cc_final: 0.8811 (p) REVERT: A 275 GLU cc_start: 0.8436 (pt0) cc_final: 0.7951 (pp20) REVERT: A 307 MET cc_start: 0.8640 (mpp) cc_final: 0.8089 (mpp) REVERT: B 126 LEU cc_start: 0.9224 (mp) cc_final: 0.8934 (tt) REVERT: B 374 MET cc_start: 0.7854 (tmm) cc_final: 0.7624 (tmm) REVERT: B 472 MET cc_start: 0.8520 (tpp) cc_final: 0.8203 (tpp) REVERT: C 34 HIS cc_start: 0.8670 (t-90) cc_final: 0.8014 (t70) REVERT: C 57 ASN cc_start: 0.8362 (m-40) cc_final: 0.8051 (m-40) REVERT: C 118 LYS cc_start: 0.8004 (mptt) cc_final: 0.7603 (mmtm) REVERT: D 13 MET cc_start: 0.8659 (tpt) cc_final: 0.8017 (tmm) REVERT: D 19 GLN cc_start: 0.9033 (tp40) cc_final: 0.8292 (tm-30) REVERT: D 37 PHE cc_start: 0.9221 (t80) cc_final: 0.9000 (t80) REVERT: D 49 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7261 (pp) REVERT: E 275 GLU cc_start: 0.8332 (pt0) cc_final: 0.7801 (pp20) REVERT: E 307 MET cc_start: 0.8680 (mpp) cc_final: 0.8156 (mpp) REVERT: F 128 MET cc_start: 0.8956 (tpp) cc_final: 0.8655 (tmm) REVERT: F 472 MET cc_start: 0.8728 (tpp) cc_final: 0.8478 (tpp) REVERT: G 34 HIS cc_start: 0.8647 (t-90) cc_final: 0.7999 (t70) REVERT: G 57 ASN cc_start: 0.8514 (m-40) cc_final: 0.8233 (m-40) REVERT: H 13 MET cc_start: 0.8601 (tpt) cc_final: 0.7961 (tmm) REVERT: H 37 PHE cc_start: 0.9224 (t80) cc_final: 0.9010 (t80) REVERT: H 44 ILE cc_start: 0.9075 (mm) cc_final: 0.8785 (pt) outliers start: 68 outliers final: 47 residues processed: 237 average time/residue: 0.2823 time to fit residues: 107.2223 Evaluate side-chains 225 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 177 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain H residue 28 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18224 Z= 0.206 Angle : 0.732 12.003 24656 Z= 0.354 Chirality : 0.047 0.268 2760 Planarity : 0.004 0.061 3124 Dihedral : 7.358 165.643 2470 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.66 % Allowed : 18.90 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 2226 helix: 0.54 (0.17), residues: 962 sheet: -1.41 (0.34), residues: 234 loop : -2.01 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 32 HIS 0.005 0.001 HIS C 123 PHE 0.012 0.001 PHE H 37 TYR 0.013 0.001 TYR B 342 ARG 0.003 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4452 Ramachandran restraints generated. 2226 Oldfield, 0 Emsley, 2226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 187 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 VAL cc_start: 0.9050 (t) cc_final: 0.8813 (p) REVERT: A 275 GLU cc_start: 0.8421 (pt0) cc_final: 0.7986 (pp20) REVERT: A 307 MET cc_start: 0.8611 (mpp) cc_final: 0.8056 (mpp) REVERT: B 126 LEU cc_start: 0.9221 (mp) cc_final: 0.8921 (tt) REVERT: B 374 MET cc_start: 0.7828 (tmm) cc_final: 0.7476 (tmm) REVERT: B 472 MET cc_start: 0.8519 (tpp) cc_final: 0.8192 (tpp) REVERT: C 34 HIS cc_start: 0.8682 (t-90) cc_final: 0.7996 (t70) REVERT: C 57 ASN cc_start: 0.8435 (m-40) cc_final: 0.8110 (m-40) REVERT: C 118 LYS cc_start: 0.7987 (mptt) cc_final: 0.7557 (mmtm) REVERT: D 13 MET cc_start: 0.8668 (tpt) cc_final: 0.8018 (tmm) REVERT: D 19 GLN cc_start: 0.9035 (tp40) cc_final: 0.8318 (tm-30) REVERT: D 37 PHE cc_start: 0.9221 (t80) cc_final: 0.8982 (t80) REVERT: E 275 GLU cc_start: 0.8323 (pt0) cc_final: 0.7819 (pp20) REVERT: E 307 MET cc_start: 0.8645 (mpp) cc_final: 0.8144 (mpp) REVERT: E 420 MET cc_start: 0.8607 (tpp) cc_final: 0.8376 (tmm) REVERT: F 128 MET cc_start: 0.8965 (tpp) cc_final: 0.8636 (tmm) REVERT: F 227 LEU cc_start: 0.8861 (mm) cc_final: 0.8619 (mp) REVERT: F 472 MET cc_start: 0.8775 (tpp) cc_final: 0.8520 (tpp) REVERT: G 34 HIS cc_start: 0.8615 (t-90) cc_final: 0.7939 (t70) REVERT: G 57 ASN cc_start: 0.8492 (m-40) cc_final: 0.8216 (m-40) REVERT: G 89 MET cc_start: 0.8430 (tpp) cc_final: 0.8068 (mpp) REVERT: H 13 MET cc_start: 0.8613 (tpt) cc_final: 0.7965 (tmm) REVERT: H 40 MET cc_start: 0.8639 (tmm) cc_final: 0.8105 (mtm) outliers start: 70 outliers final: 49 residues processed: 239 average time/residue: 0.2623 time to fit residues: 99.6145 Evaluate side-chains 226 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 177 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 116 GLN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 111 PHE Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 310 ILE Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 394 LEU Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain F residue 521 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain H residue 28 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.7537 > 50: distance: 47 - 49: 13.233 distance: 49 - 50: 16.371 distance: 50 - 51: 12.444 distance: 50 - 53: 7.341 distance: 51 - 52: 5.143 distance: 51 - 57: 17.907 distance: 52 - 77: 21.917 distance: 54 - 55: 11.143 distance: 55 - 56: 7.731 distance: 57 - 58: 17.119 distance: 58 - 59: 19.130 distance: 59 - 60: 30.231 distance: 59 - 61: 21.335 distance: 61 - 62: 9.949 distance: 62 - 63: 13.754 distance: 62 - 65: 9.950 distance: 63 - 64: 11.180 distance: 63 - 72: 4.449 distance: 64 - 92: 11.271 distance: 65 - 66: 9.159 distance: 66 - 67: 7.901 distance: 66 - 68: 6.340 distance: 67 - 69: 9.507 distance: 68 - 70: 10.760 distance: 69 - 71: 6.996 distance: 70 - 71: 6.104 distance: 72 - 73: 11.943 distance: 73 - 74: 11.342 distance: 73 - 76: 19.871 distance: 74 - 75: 11.324 distance: 74 - 77: 9.037 distance: 75 - 98: 24.359 distance: 77 - 78: 14.242 distance: 78 - 79: 6.593 distance: 78 - 81: 17.361 distance: 79 - 80: 21.191 distance: 79 - 84: 18.562 distance: 80 - 106: 42.891 distance: 81 - 82: 4.840 distance: 81 - 83: 16.928 distance: 84 - 85: 13.551 distance: 85 - 86: 12.933 distance: 85 - 88: 8.575 distance: 86 - 87: 20.739 distance: 86 - 92: 21.148 distance: 88 - 89: 17.657 distance: 89 - 90: 11.360 distance: 89 - 91: 14.583 distance: 92 - 93: 26.495 distance: 93 - 94: 9.408 distance: 93 - 96: 25.793 distance: 94 - 95: 20.794 distance: 94 - 98: 6.299 distance: 96 - 97: 18.887 distance: 98 - 99: 13.439 distance: 99 - 100: 26.135 distance: 99 - 102: 9.426 distance: 100 - 101: 35.849 distance: 100 - 106: 17.148 distance: 102 - 103: 7.212 distance: 103 - 104: 19.907 distance: 104 - 105: 35.019 distance: 106 - 107: 12.406 distance: 107 - 108: 16.171 distance: 107 - 110: 13.301 distance: 108 - 109: 17.921 distance: 108 - 114: 3.730 distance: 110 - 111: 13.260 distance: 111 - 112: 17.276 distance: 111 - 113: 25.233 distance: 114 - 115: 14.269 distance: 115 - 116: 8.299 distance: 115 - 118: 8.201 distance: 116 - 117: 10.425 distance: 116 - 122: 9.125 distance: 118 - 119: 17.287 distance: 118 - 120: 8.948 distance: 119 - 121: 14.777