Starting phenix.real_space_refine on Sat Feb 17 07:06:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4n_30079/02_2024/6m4n_30079_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4n_30079/02_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_30079/02_2024/6m4n_30079.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4n_30079/02_2024/6m4n_30079.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4n_30079/02_2024/6m4n_30079_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m4n_30079/02_2024/6m4n_30079_updated.pdb" } 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-5238/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: 9.73, per 1000 atoms: 0.55 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: 7.45 Conformation dependent library (CDL) restraints added in 3.5 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... running ksdssp... Secondary structure from input PDB file: 78 helices and 12 sheets defined 40.9% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 Creating SS restraints... Processing helix chain 'A' and resid 24 through 39 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) Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.927A pdb=" N GLU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 195 through 201 removed outlier: 3.921A pdb=" N GLN A 200 " --> pdb=" O GLN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 258 through 267 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 289 through 293 Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.554A pdb=" N SER A 331 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 360 through 373 removed outlier: 3.572A pdb=" N PHE A 363 " --> pdb=" O PRO A 360 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 366 " --> pdb=" O PHE A 363 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 368 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 373 " --> pdb=" O CYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 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 454 through 471 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 68 through 91 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 121 through 125 Processing helix chain 'B' and resid 186 through 198 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 214 through 227 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 238 through 248 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) Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 285 through 297 removed outlier: 3.838A pdb=" N ILE B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 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 358 through 362 Processing helix chain 'B' and resid 392 through 398 Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.553A pdb=" N GLU B 417 " --> pdb=" O PRO B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 455 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 476 through 488 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 518 through 534 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 22 through 38 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 45 through 62 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 79 through 82 removed outlier: 4.434A pdb=" N LEU C 82 " --> pdb=" O LYS C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 79 through 82' Processing helix chain 'C' and resid 89 through 92 Processing helix chain 'C' and resid 99 through 119 Proline residue: C 106 - end of helix removed outlier: 3.669A pdb=" N THR C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR C 117 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYS C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR C 119 " --> pdb=" O PHE C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 135 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 9 through 25 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) removed outlier: 5.034A pdb=" N THR D 24 " --> pdb=" O TYR D 20 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 52 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 24 through 39 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) Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.927A pdb=" N GLU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 115 through 128 Processing helix chain 'E' and resid 143 through 156 Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' Processing helix chain 'E' and resid 195 through 201 removed outlier: 3.921A pdb=" N GLN E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 228 Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 258 through 267 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 289 through 293 Processing helix chain 'E' and resid 297 through 299 No H-bonds generated for 'chain 'E' and resid 297 through 299' Processing helix chain 'E' and resid 327 through 331 removed outlier: 3.553A pdb=" N SER E 331 " --> pdb=" O GLN E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 358 Processing helix chain 'E' and resid 360 through 373 removed outlier: 3.572A pdb=" N PHE E 363 " --> pdb=" O PRO E 360 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU E 366 " --> pdb=" O PHE E 363 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU E 368 " --> pdb=" O VAL E 365 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN E 372 " --> pdb=" O LYS E 369 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE E 373 " --> pdb=" O CYS E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 421 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 454 through 471 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 68 through 91 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 121 through 125 Processing helix chain 'F' and resid 186 through 198 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 214 through 227 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 238 through 248 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) Proline residue: F 247 - end of helix Processing helix chain 'F' and resid 264 through 272 Processing helix chain 'F' and resid 285 through 297 removed outlier: 3.839A pdb=" N ILE F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 337 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 358 through 362 Processing helix chain 'F' and resid 392 through 398 Processing helix chain 'F' and resid 413 through 427 removed outlier: 3.553A pdb=" N GLU F 417 " --> pdb=" O PRO F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 455 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 476 through 488 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 518 through 534 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 22 through 38 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 45 through 62 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 79 through 82 removed outlier: 4.434A pdb=" N LEU G 82 " --> pdb=" O LYS G 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 82' Processing helix chain 'G' and resid 89 through 92 Processing helix chain 'G' and resid 99 through 119 Proline residue: G 106 - end of helix removed outlier: 3.669A pdb=" N THR G 113 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR G 117 " --> pdb=" O THR G 113 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR G 119 " --> pdb=" O PHE G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 135 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 9 through 25 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) removed outlier: 5.033A pdb=" N THR H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA H 25 " --> pdb=" O LEU H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 52 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= A, first strand: chain 'A' and resid 92 through 95 Processing sheet with id= B, first strand: chain 'A' and resid 160 through 164 Processing sheet with id= C, first strand: chain 'A' and resid 206 through 208 removed outlier: 6.032A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N PHE A 241 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing sheet with id= D, 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= E, 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: 6.393A pdb=" N LEU B 255 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU B 313 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 257 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLU B 315 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG B 278 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 468 through 471 Processing sheet with id= G, first strand: chain 'E' and resid 92 through 95 Processing sheet with id= H, first strand: chain 'E' and resid 160 through 164 Processing sheet with id= I, first strand: chain 'E' and resid 206 through 208 removed outlier: 6.032A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N PHE E 241 " --> pdb=" O PHE E 186 " (cutoff:3.500A) Processing sheet with id= J, 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= K, 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: 6.393A pdb=" N LEU F 255 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU F 313 " --> pdb=" O LEU F 255 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU F 257 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLU F 315 " --> pdb=" O LEU F 257 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR F 276 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER F 258 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG F 278 " --> pdb=" O SER F 258 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 468 through 471 540 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 7.96 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: 1075 2.71 - 3.26: 17885 3.26 - 3.81: 30112 3.81 - 4.35: 36403 4.35 - 4.90: 60148 Nonbonded interactions: 145623 Sorted by model distance: nonbonded pdb=" OG1 THR A 427 " pdb=" OE1 GLU B 209 " model vdw 2.164 2.440 nonbonded pdb=" OG1 THR E 427 " pdb=" OE1 GLU F 209 " model vdw 2.250 2.440 nonbonded pdb=" OD2 ASP E 188 " pdb=" OH TYR E 248 " model vdw 2.276 2.440 nonbonded pdb=" OD2 ASP A 188 " pdb=" OH TYR A 248 " model vdw 2.276 2.440 nonbonded pdb=" OE1 GLN C 121 " pdb=" OH TYR E 23 " model vdw 2.294 2.440 ... (remaining 145618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 7.820 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 48.780 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.830 ------------------------------------------------------------------------------- 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= 0.613 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 : 2.236 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: 0.3187 time to fit residues: 175.5393 Evaluate side-chains 192 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 2.428 ------------------------------------------------------------------------------- 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: 1.9990 chunk 166 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 199 optimal weight: 0.3980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 212 ASN B 242 ASN B 245 ASN B 263 HIS B 282 HIS ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 490 ASN C 57 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 242 ASN F 245 ASN F 263 HIS F 282 HIS ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 HIS F 490 ASN G 57 ASN G 94 GLN G 127 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18224 Z= 0.190 Angle : 0.729 11.109 24656 Z= 0.365 Chirality : 0.045 0.152 2760 Planarity : 0.005 0.074 3124 Dihedral : 7.954 150.895 2470 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 3.87 % Allowed : 11.41 % Favored : 84.71 % 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: -2.92 (0.16), residues: 2226 helix: -1.30 (0.15), residues: 938 sheet: -1.80 (0.32), residues: 240 loop : -2.56 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 15 HIS 0.004 0.001 HIS A 211 PHE 0.020 0.002 PHE F 59 TYR 0.011 0.001 TYR G 116 ARG 0.003 0.000 ARG B 447 *********************** 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 327 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 253 time to evaluate : 2.183 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: A 143 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: A 183 ASP cc_start: 0.7135 (m-30) cc_final: 0.6511 (m-30) REVERT: A 214 MET cc_start: 0.7932 (mmp) cc_final: 0.7377 (mmm) REVERT: A 274 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7148 (tm-30) REVERT: A 275 GLU cc_start: 0.8307 (pt0) cc_final: 0.7799 (pp20) REVERT: A 307 MET cc_start: 0.8483 (mpp) cc_final: 0.8209 (mpp) REVERT: B 126 LEU cc_start: 0.9023 (mp) cc_final: 0.8807 (tt) REVERT: B 149 MET cc_start: 0.7558 (mtt) cc_final: 0.7300 (mtt) REVERT: B 456 MET cc_start: 0.8005 (ttm) cc_final: 0.7728 (ttm) REVERT: B 472 MET cc_start: 0.8586 (tpp) cc_final: 0.8318 (tpp) REVERT: B 475 MET cc_start: 0.8450 (mpt) cc_final: 0.8242 (mpp) REVERT: C 34 HIS cc_start: 0.8594 (t-90) cc_final: 0.8158 (t70) REVERT: C 118 LYS cc_start: 0.8080 (mptt) cc_final: 0.7532 (mmtm) REVERT: D 13 MET cc_start: 0.8610 (tpt) cc_final: 0.7994 (tmm) REVERT: D 40 MET cc_start: 0.8296 (mmp) cc_final: 0.7906 (mtm) REVERT: E 183 ASP cc_start: 0.7327 (m-30) cc_final: 0.6622 (m-30) REVERT: E 214 MET cc_start: 0.7705 (mmm) cc_final: 0.7400 (mmt) REVERT: E 275 GLU cc_start: 0.8323 (pt0) cc_final: 0.7759 (pp20) REVERT: E 307 MET cc_start: 0.8454 (mpp) cc_final: 0.8150 (mpp) REVERT: F 126 LEU cc_start: 0.8991 (mp) cc_final: 0.8741 (tt) REVERT: F 131 ARG cc_start: 0.9135 (ptm-80) cc_final: 0.8884 (ptt90) REVERT: F 456 MET cc_start: 0.7966 (ttm) cc_final: 0.7707 (ttm) REVERT: F 504 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9094 (mp) REVERT: G 34 HIS cc_start: 0.8633 (t-90) cc_final: 0.8169 (t70) REVERT: G 58 MET cc_start: 0.8416 (tpt) cc_final: 0.8185 (tpp) REVERT: G 89 MET cc_start: 0.8585 (mtt) cc_final: 0.8341 (mtt) REVERT: H 13 MET cc_start: 0.8464 (tpt) cc_final: 0.8061 (tmm) REVERT: H 40 MET cc_start: 0.8400 (mmp) cc_final: 0.8127 (mmp) outliers start: 74 outliers final: 30 residues processed: 307 average time/residue: 0.2690 time to fit residues: 130.7351 Evaluate side-chains 217 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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 171 ILE Chi-restraints excluded: chain A residue 249 MET 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 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 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 249 MET 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 487 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 133 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 292 HIS ** A 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 GLN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN C 94 GLN E 83 ASN E 328 GLN ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 154 HIS F 245 ASN ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN G 94 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 18224 Z= 0.328 Angle : 0.747 10.013 24656 Z= 0.374 Chirality : 0.047 0.263 2760 Planarity : 0.005 0.073 3124 Dihedral : 7.524 143.004 2469 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 4.08 % Allowed : 13.82 % Favored : 82.09 % 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: -2.18 (0.17), residues: 2226 helix: -0.52 (0.16), residues: 950 sheet: -1.51 (0.35), residues: 234 loop : -2.32 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 134 HIS 0.005 0.001 HIS A 211 PHE 0.013 0.002 PHE A 168 TYR 0.016 0.002 TYR A 248 ARG 0.003 0.001 ARG B 447 *********************** 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 267 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 189 time to evaluate : 1.882 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: A 274 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7385 (tm-30) REVERT: A 307 MET cc_start: 0.8686 (mpp) cc_final: 0.8152 (mpp) REVERT: B 126 LEU cc_start: 0.9088 (mp) cc_final: 0.8844 (tt) REVERT: B 472 MET cc_start: 0.8608 (tpp) cc_final: 0.8356 (tpp) REVERT: C 34 HIS cc_start: 0.8586 (t-90) cc_final: 0.8107 (t70) REVERT: C 118 LYS cc_start: 0.8094 (mptt) cc_final: 0.7702 (mmtm) REVERT: D 13 MET cc_start: 0.8607 (tpt) cc_final: 0.8060 (tmm) REVERT: D 19 GLN cc_start: 0.9147 (tp40) cc_final: 0.8344 (tm-30) REVERT: D 37 PHE cc_start: 0.9271 (t80) cc_final: 0.9037 (t80) REVERT: E 275 GLU cc_start: 0.8397 (pt0) cc_final: 0.7703 (pp20) REVERT: E 307 MET cc_start: 0.8782 (mpp) cc_final: 0.8228 (mpp) REVERT: F 126 LEU cc_start: 0.9047 (mp) cc_final: 0.8833 (tt) REVERT: F 173 MET cc_start: 0.8395 (mmm) cc_final: 0.8157 (mmm) REVERT: G 34 HIS cc_start: 0.8574 (t-90) cc_final: 0.8100 (t70) REVERT: H 13 MET cc_start: 0.8539 (tpt) cc_final: 0.8032 (tmm) REVERT: H 19 GLN cc_start: 0.8942 (tp40) cc_final: 0.8274 (tm-30) outliers start: 78 outliers final: 46 residues processed: 249 average time/residue: 0.2603 time to fit residues: 104.4013 Evaluate side-chains 210 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 164 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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 255 CYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 331 SER 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 394 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 105 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain D residue 49 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 249 MET Chi-restraints excluded: chain E residue 255 CYS 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 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 394 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 G residue 32 LEU Chi-restraints excluded: chain G residue 94 GLN Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 133 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 22 optimal weight: 0.0770 chunk 95 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 190 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- 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 B 154 HIS B 245 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18224 Z= 0.255 Angle : 0.698 10.093 24656 Z= 0.346 Chirality : 0.046 0.229 2760 Planarity : 0.005 0.065 3124 Dihedral : 7.204 138.280 2469 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.70 % Favored : 90.25 % Rotamer: Outliers : 4.66 % Allowed : 14.71 % Favored : 80.63 % 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: -1.75 (0.17), residues: 2226 helix: -0.03 (0.17), residues: 954 sheet: -1.35 (0.35), residues: 234 loop : -2.24 (0.18), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 134 HIS 0.005 0.001 HIS G 143 PHE 0.011 0.001 PHE A 209 TYR 0.010 0.001 TYR A 248 ARG 0.005 0.000 ARG F 105 *********************** 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 269 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 180 time to evaluate : 2.128 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: A 275 GLU cc_start: 0.8317 (pt0) cc_final: 0.7933 (pp20) REVERT: A 307 MET cc_start: 0.8752 (mpp) cc_final: 0.8151 (mpp) REVERT: A 419 CYS cc_start: 0.8948 (t) cc_final: 0.8722 (t) REVERT: A 426 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7741 (mm) REVERT: B 126 LEU cc_start: 0.9088 (mp) cc_final: 0.8846 (tt) REVERT: B 244 MET cc_start: 0.8111 (mtt) cc_final: 0.7472 (mtt) REVERT: B 472 MET cc_start: 0.8599 (tpp) cc_final: 0.8313 (tpp) REVERT: C 34 HIS cc_start: 0.8602 (t-90) cc_final: 0.8091 (t70) REVERT: C 118 LYS cc_start: 0.8061 (mptt) cc_final: 0.7660 (mmtm) REVERT: D 13 MET cc_start: 0.8634 (tpt) cc_final: 0.8111 (tmm) REVERT: D 19 GLN cc_start: 0.9094 (tp40) cc_final: 0.8309 (tm-30) REVERT: D 37 PHE cc_start: 0.9242 (t80) cc_final: 0.9022 (t80) REVERT: E 275 GLU cc_start: 0.8528 (pt0) cc_final: 0.7903 (pp20) REVERT: E 307 MET cc_start: 0.8726 (mpp) cc_final: 0.8225 (mpp) REVERT: F 126 LEU cc_start: 0.9065 (mp) cc_final: 0.8837 (tt) REVERT: F 173 MET cc_start: 0.8435 (mmm) cc_final: 0.8201 (mmm) REVERT: F 456 MET cc_start: 0.8228 (ttm) cc_final: 0.8021 (ttm) REVERT: G 34 HIS cc_start: 0.8575 (t-90) cc_final: 0.8116 (t70) REVERT: H 13 MET cc_start: 0.8535 (tpt) cc_final: 0.8020 (tmm) REVERT: H 19 GLN cc_start: 0.8873 (tp40) cc_final: 0.8061 (tm-30) outliers start: 89 outliers final: 56 residues processed: 251 average time/residue: 0.2623 time to fit residues: 105.7233 Evaluate side-chains 224 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 167 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 331 SER 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 426 LEU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 99 CYS Chi-restraints excluded: chain B residue 161 LYS 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 320 MET 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 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 133 SER 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 102 ASN 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 188 ASP 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 133 ASN 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 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 133 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 181 optimal weight: 0.2980 chunk 146 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN F 154 HIS ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18224 Z= 0.258 Angle : 0.721 13.029 24656 Z= 0.351 Chirality : 0.047 0.369 2760 Planarity : 0.004 0.064 3124 Dihedral : 6.888 130.176 2469 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 4.61 % Allowed : 15.71 % Favored : 79.69 % 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: -1.44 (0.18), residues: 2226 helix: 0.35 (0.17), residues: 940 sheet: -1.19 (0.36), residues: 230 loop : -2.16 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 134 HIS 0.004 0.001 HIS E 395 PHE 0.010 0.001 PHE G 111 TYR 0.012 0.001 TYR A 248 ARG 0.002 0.000 ARG B 489 *********************** 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 273 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 185 time to evaluate : 2.080 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 275 GLU cc_start: 0.8296 (pt0) cc_final: 0.7765 (pp20) REVERT: A 307 MET cc_start: 0.8700 (mpp) cc_final: 0.8151 (mpp) REVERT: A 426 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.7797 (mm) REVERT: B 126 LEU cc_start: 0.9155 (mp) cc_final: 0.8886 (tt) REVERT: B 128 MET cc_start: 0.8958 (mmm) cc_final: 0.8535 (tpt) REVERT: B 227 LEU cc_start: 0.8925 (mm) cc_final: 0.8724 (mp) REVERT: B 244 MET cc_start: 0.8087 (mtt) cc_final: 0.7477 (mtt) REVERT: B 472 MET cc_start: 0.8608 (tpp) cc_final: 0.8262 (tpp) REVERT: C 34 HIS cc_start: 0.8641 (t-90) cc_final: 0.8088 (t70) REVERT: C 118 LYS cc_start: 0.8021 (mptt) cc_final: 0.7626 (mmtm) REVERT: D 13 MET cc_start: 0.8655 (tpt) cc_final: 0.8074 (tmm) REVERT: D 19 GLN cc_start: 0.9068 (tp40) cc_final: 0.8355 (tm-30) REVERT: D 40 MET cc_start: 0.8772 (tmm) cc_final: 0.8488 (tmm) REVERT: E 275 GLU cc_start: 0.8498 (pt0) cc_final: 0.7763 (pp20) REVERT: E 307 MET cc_start: 0.8680 (mpp) cc_final: 0.8147 (mpp) REVERT: E 395 HIS cc_start: 0.6739 (m-70) cc_final: 0.6425 (m-70) REVERT: F 173 MET cc_start: 0.8489 (mmm) cc_final: 0.8244 (mmm) REVERT: G 17 MET cc_start: 0.8486 (mpp) cc_final: 0.8148 (mpp) REVERT: G 34 HIS cc_start: 0.8607 (t-90) cc_final: 0.8120 (t70) REVERT: H 13 MET cc_start: 0.8560 (tpt) cc_final: 0.8024 (tmm) REVERT: H 19 GLN cc_start: 0.8830 (tp40) cc_final: 0.8125 (tm-30) outliers start: 88 outliers final: 55 residues processed: 254 average time/residue: 0.2642 time to fit residues: 106.1046 Evaluate side-chains 226 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 170 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 434 LYS 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 292 LEU Chi-restraints excluded: chain B residue 320 MET 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 C residue 133 SER 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 102 ASN 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 284 GLU Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 331 SER 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 133 ASN Chi-restraints excluded: chain F residue 161 LYS 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 320 MET 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 32 LEU Chi-restraints excluded: chain G residue 119 TYR Chi-restraints excluded: chain G residue 133 SER 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: 2.9990 chunk 42 optimal weight: 8.9990 chunk 124 optimal weight: 0.0050 chunk 52 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18224 Z= 0.165 Angle : 0.701 10.652 24656 Z= 0.332 Chirality : 0.045 0.202 2760 Planarity : 0.004 0.065 3124 Dihedral : 6.488 121.143 2469 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.07 % Favored : 90.84 % Rotamer: Outliers : 3.04 % Allowed : 18.01 % Favored : 78.95 % 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: -1.14 (0.18), residues: 2226 helix: 0.69 (0.18), residues: 936 sheet: -1.13 (0.35), residues: 230 loop : -2.07 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 32 HIS 0.004 0.001 HIS A 211 PHE 0.017 0.001 PHE G 111 TYR 0.013 0.001 TYR A 248 ARG 0.002 0.000 ARG A 151 *********************** 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 261 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 203 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.6851 (m-30) cc_final: 0.6474 (m-30) REVERT: A 275 GLU cc_start: 0.8399 (pt0) cc_final: 0.7873 (pp20) REVERT: A 307 MET cc_start: 0.8599 (mpp) cc_final: 0.8329 (mpp) REVERT: A 420 MET cc_start: 0.8920 (tpp) cc_final: 0.8480 (tmm) REVERT: B 126 LEU cc_start: 0.9118 (mp) cc_final: 0.8850 (tt) REVERT: B 128 MET cc_start: 0.8953 (mmm) cc_final: 0.8561 (tpt) REVERT: B 374 MET cc_start: 0.7740 (tmm) cc_final: 0.7382 (tmm) REVERT: B 472 MET cc_start: 0.8533 (tpp) cc_final: 0.8164 (tpp) REVERT: C 34 HIS cc_start: 0.8621 (t-90) cc_final: 0.8041 (t70) REVERT: C 55 ILE cc_start: 0.9485 (mm) cc_final: 0.9160 (tt) REVERT: C 118 LYS cc_start: 0.7976 (mptt) cc_final: 0.7579 (mmtm) REVERT: D 13 MET cc_start: 0.8580 (tpt) cc_final: 0.7998 (tmm) REVERT: D 19 GLN cc_start: 0.9030 (tp40) cc_final: 0.8247 (tm-30) REVERT: D 40 MET cc_start: 0.8874 (tmm) cc_final: 0.8472 (tmm) REVERT: E 183 ASP cc_start: 0.7010 (m-30) cc_final: 0.6632 (m-30) REVERT: E 275 GLU cc_start: 0.8472 (pt0) cc_final: 0.8245 (pt0) REVERT: E 307 MET cc_start: 0.8585 (mpp) cc_final: 0.8053 (mpp) REVERT: F 128 MET cc_start: 0.8996 (tpp) cc_final: 0.8698 (tmm) REVERT: F 173 MET cc_start: 0.8489 (mmm) cc_final: 0.8258 (mmm) REVERT: F 227 LEU cc_start: 0.8925 (mm) cc_final: 0.8705 (mp) REVERT: F 374 MET cc_start: 0.7804 (tmm) cc_final: 0.7571 (tmm) REVERT: G 34 HIS cc_start: 0.8672 (t-90) cc_final: 0.8074 (t70) REVERT: H 13 MET cc_start: 0.8569 (tpt) cc_final: 0.8075 (tmm) REVERT: H 19 GLN cc_start: 0.8808 (tp40) cc_final: 0.8131 (tm-30) outliers start: 58 outliers final: 33 residues processed: 247 average time/residue: 0.2622 time to fit residues: 102.4269 Evaluate side-chains 210 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 177 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 255 CYS Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 320 MET 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 C residue 105 THR 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 331 SER Chi-restraints excluded: chain E residue 341 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 320 MET Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain F residue 521 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 129 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 120 ASN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 GLN ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18224 Z= 0.225 Angle : 0.711 11.917 24656 Z= 0.341 Chirality : 0.045 0.250 2760 Planarity : 0.004 0.063 3124 Dihedral : 6.264 110.116 2469 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.34 % Favored : 90.61 % Rotamer: Outliers : 3.56 % Allowed : 18.53 % Favored : 77.91 % 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: -1.07 (0.18), residues: 2226 helix: 0.78 (0.18), residues: 932 sheet: -1.22 (0.35), residues: 232 loop : -2.02 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 134 HIS 0.005 0.001 HIS A 211 PHE 0.009 0.001 PHE G 111 TYR 0.025 0.001 TYR F 461 ARG 0.005 0.000 ARG E 151 *********************** 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 245 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 177 time to evaluate : 2.514 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: A 274 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7400 (tm-30) REVERT: A 275 GLU cc_start: 0.8459 (pt0) cc_final: 0.7936 (pp20) REVERT: A 307 MET cc_start: 0.8807 (mpp) cc_final: 0.8240 (mpp) REVERT: B 126 LEU cc_start: 0.9173 (mp) cc_final: 0.8933 (tt) REVERT: B 128 MET cc_start: 0.8976 (mmm) cc_final: 0.8598 (tpt) REVERT: B 244 MET cc_start: 0.8031 (mtt) cc_final: 0.7306 (mtt) REVERT: B 374 MET cc_start: 0.7857 (tmm) cc_final: 0.7197 (tmm) REVERT: B 472 MET cc_start: 0.8564 (tpp) cc_final: 0.8178 (tpp) REVERT: C 34 HIS cc_start: 0.8658 (t-90) cc_final: 0.8084 (t70) REVERT: C 118 LYS cc_start: 0.7946 (mptt) cc_final: 0.7519 (mmtm) REVERT: D 13 MET cc_start: 0.8597 (tpt) cc_final: 0.8015 (tmm) REVERT: D 19 GLN cc_start: 0.9043 (tp40) cc_final: 0.8270 (tm-30) REVERT: D 40 MET cc_start: 0.8708 (tmm) cc_final: 0.8317 (tmm) REVERT: E 275 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8248 (pt0) REVERT: E 307 MET cc_start: 0.8599 (mpp) cc_final: 0.8364 (mpp) REVERT: F 128 MET cc_start: 0.9035 (tpp) cc_final: 0.8717 (tmm) REVERT: F 227 LEU cc_start: 0.8941 (mm) cc_final: 0.8721 (mp) REVERT: F 374 MET cc_start: 0.7815 (tmm) cc_final: 0.7486 (tmm) REVERT: F 486 MET cc_start: 0.9058 (tpp) cc_final: 0.8610 (mmm) REVERT: G 34 HIS cc_start: 0.8705 (t-90) cc_final: 0.8085 (t70) REVERT: H 13 MET cc_start: 0.8590 (tpt) cc_final: 0.8089 (tmm) REVERT: H 19 GLN cc_start: 0.8838 (tp40) cc_final: 0.8161 (tm-30) outliers start: 68 outliers final: 46 residues processed: 231 average time/residue: 0.2667 time to fit residues: 98.3965 Evaluate side-chains 221 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 174 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 255 CYS Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 331 SER 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 133 ASN 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 394 LEU 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 C residue 32 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 112 LEU 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 117 VAL Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain F residue 161 LYS 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 320 MET 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 32 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 63 optimal weight: 0.0770 chunk 41 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 104 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 192 optimal weight: 0.2980 overall best weight: 0.8742 ------------------------------------------------------------------------------- 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 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18224 Z= 0.168 Angle : 0.711 12.102 24656 Z= 0.333 Chirality : 0.045 0.279 2760 Planarity : 0.004 0.062 3124 Dihedral : 5.946 98.525 2469 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.85 % Favored : 91.06 % Rotamer: Outliers : 2.51 % Allowed : 19.42 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.18), residues: 2226 helix: 0.86 (0.18), residues: 930 sheet: -1.24 (0.35), residues: 232 loop : -1.90 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 49 HIS 0.005 0.001 HIS A 211 PHE 0.009 0.001 PHE A 209 TYR 0.014 0.001 TYR F 461 ARG 0.005 0.000 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 8 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 232 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.6793 (m-30) cc_final: 0.6446 (m-30) REVERT: A 274 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7344 (tm-30) REVERT: A 275 GLU cc_start: 0.8560 (pt0) cc_final: 0.8166 (pp20) REVERT: A 307 MET cc_start: 0.8718 (mpp) cc_final: 0.8191 (mpp) REVERT: A 420 MET cc_start: 0.8822 (tpp) cc_final: 0.8429 (tmm) REVERT: B 126 LEU cc_start: 0.9169 (mp) cc_final: 0.8921 (tt) REVERT: B 128 MET cc_start: 0.8959 (mmm) cc_final: 0.8602 (tpt) REVERT: B 244 MET cc_start: 0.8001 (mtt) cc_final: 0.7314 (mtt) REVERT: B 472 MET cc_start: 0.8556 (tpp) cc_final: 0.8179 (tpp) REVERT: B 486 MET cc_start: 0.8926 (tpp) cc_final: 0.8687 (tpp) REVERT: C 34 HIS cc_start: 0.8664 (t-90) cc_final: 0.8090 (t70) REVERT: C 118 LYS cc_start: 0.7870 (mptt) cc_final: 0.7461 (mmtm) REVERT: D 13 MET cc_start: 0.8535 (tpt) cc_final: 0.7996 (tmm) REVERT: D 19 GLN cc_start: 0.9051 (tp40) cc_final: 0.8267 (tm-30) REVERT: D 40 MET cc_start: 0.8690 (tmm) cc_final: 0.8167 (tmm) REVERT: E 183 ASP cc_start: 0.6913 (m-30) cc_final: 0.6573 (m-30) REVERT: E 307 MET cc_start: 0.8804 (mpp) cc_final: 0.8314 (mpp) REVERT: F 128 MET cc_start: 0.9012 (tpp) cc_final: 0.8698 (tmm) REVERT: F 227 LEU cc_start: 0.8913 (mm) cc_final: 0.8658 (mp) REVERT: F 374 MET cc_start: 0.7783 (tmm) cc_final: 0.7329 (tmm) REVERT: G 34 HIS cc_start: 0.8695 (t-90) cc_final: 0.8170 (t70) REVERT: H 13 MET cc_start: 0.8588 (tpt) cc_final: 0.8087 (tmm) REVERT: H 40 MET cc_start: 0.8569 (tmm) cc_final: 0.8097 (mtm) outliers start: 48 outliers final: 36 residues processed: 221 average time/residue: 0.2591 time to fit residues: 92.7328 Evaluate side-chains 211 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 175 time to evaluate : 2.108 ------------------------------------------------------------------------------- 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 255 CYS Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU 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 491 ILE Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 LEU 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 320 MET 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 491 ILE Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Chi-restraints excluded: chain G residue 32 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.2980 chunk 185 optimal weight: 40.0000 chunk 197 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 178 optimal weight: 0.0770 chunk 186 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- 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** A 452 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 ASN ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18224 Z= 0.163 Angle : 0.720 14.275 24656 Z= 0.336 Chirality : 0.045 0.263 2760 Planarity : 0.004 0.062 3124 Dihedral : 5.631 83.381 2469 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.98 % Favored : 90.93 % Rotamer: Outliers : 2.15 % Allowed : 20.05 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.18), residues: 2226 helix: 0.79 (0.18), residues: 930 sheet: -1.28 (0.35), residues: 232 loop : -1.83 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 49 HIS 0.004 0.001 HIS A 211 PHE 0.018 0.001 PHE D 37 TYR 0.015 0.001 TYR F 461 ARG 0.005 0.000 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 9 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 231 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 ASP cc_start: 0.6739 (m-30) cc_final: 0.6416 (m-30) REVERT: A 274 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7293 (tm-30) REVERT: A 275 GLU cc_start: 0.8564 (pt0) cc_final: 0.8138 (pp20) REVERT: A 307 MET cc_start: 0.8687 (mpp) cc_final: 0.8176 (mpp) REVERT: B 126 LEU cc_start: 0.9186 (mp) cc_final: 0.8932 (tt) REVERT: B 128 MET cc_start: 0.8957 (mmm) cc_final: 0.8606 (tpt) REVERT: B 173 MET cc_start: 0.8663 (mmm) cc_final: 0.8347 (mmm) REVERT: B 244 MET cc_start: 0.8065 (mtt) cc_final: 0.7380 (mtt) REVERT: B 472 MET cc_start: 0.8566 (tpp) cc_final: 0.8184 (tpp) REVERT: B 486 MET cc_start: 0.8961 (tpp) cc_final: 0.8743 (tpp) REVERT: C 34 HIS cc_start: 0.8635 (t-90) cc_final: 0.8098 (t70) REVERT: C 118 LYS cc_start: 0.7733 (mptt) cc_final: 0.7317 (mmtm) REVERT: D 13 MET cc_start: 0.8560 (tpt) cc_final: 0.8020 (tmm) REVERT: D 19 GLN cc_start: 0.9041 (tp40) cc_final: 0.8243 (tm-30) REVERT: D 40 MET cc_start: 0.8761 (tmm) cc_final: 0.8232 (tmm) REVERT: E 183 ASP cc_start: 0.6942 (m-30) cc_final: 0.6627 (m-30) REVERT: E 275 GLU cc_start: 0.8229 (pt0) cc_final: 0.7836 (pp20) REVERT: F 128 MET cc_start: 0.9031 (tpp) cc_final: 0.8700 (tmm) REVERT: F 173 MET cc_start: 0.8773 (mmm) cc_final: 0.8506 (mmm) REVERT: F 209 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7901 (mm-30) REVERT: F 227 LEU cc_start: 0.8897 (mm) cc_final: 0.8640 (mp) REVERT: F 374 MET cc_start: 0.7806 (tmm) cc_final: 0.7320 (tmm) REVERT: F 486 MET cc_start: 0.8875 (tpp) cc_final: 0.8644 (tpp) REVERT: G 34 HIS cc_start: 0.8671 (t-90) cc_final: 0.8148 (t70) REVERT: H 13 MET cc_start: 0.8593 (tpt) cc_final: 0.8094 (tmm) outliers start: 41 outliers final: 35 residues processed: 222 average time/residue: 0.2497 time to fit residues: 89.6427 Evaluate side-chains 208 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 1.937 ------------------------------------------------------------------------------- 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 255 CYS Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 310 ILE 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 C residue 105 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 LEU 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 320 MET Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain F residue 491 ILE Chi-restraints excluded: chain F residue 504 ILE Chi-restraints excluded: chain F residue 511 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 145 optimal weight: 9.9990 chunk 219 optimal weight: 0.0170 chunk 201 optimal weight: 3.9990 chunk 174 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 overall best weight: 1.9222 ------------------------------------------------------------------------------- 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 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 GLN ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4702 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= 0.213 Angle : 0.736 13.353 24656 Z= 0.348 Chirality : 0.046 0.333 2760 Planarity : 0.004 0.060 3124 Dihedral : 5.478 69.968 2469 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.21 % Favored : 90.75 % Rotamer: Outliers : 2.15 % Allowed : 20.68 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2226 helix: 0.90 (0.18), residues: 930 sheet: -1.33 (0.35), residues: 232 loop : -1.81 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 134 HIS 0.005 0.001 HIS A 211 PHE 0.022 0.001 PHE G 111 TYR 0.015 0.001 TYR F 342 ARG 0.005 0.000 ARG E 151 ********************** REFINEMENT MACRO_CYCLE 10 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 216 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 175 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7357 (tm-30) REVERT: A 275 GLU cc_start: 0.8561 (pt0) cc_final: 0.8105 (pp20) REVERT: A 307 MET cc_start: 0.8722 (mpp) cc_final: 0.8188 (mpp) REVERT: B 126 LEU cc_start: 0.9209 (mp) cc_final: 0.8963 (tt) REVERT: B 128 MET cc_start: 0.8955 (mmm) cc_final: 0.8600 (tpt) REVERT: B 244 MET cc_start: 0.8041 (mtt) cc_final: 0.7349 (mtt) REVERT: B 472 MET cc_start: 0.8563 (tpp) cc_final: 0.8177 (tpp) REVERT: C 34 HIS cc_start: 0.8644 (t-90) cc_final: 0.8109 (t70) REVERT: C 118 LYS cc_start: 0.7765 (mptt) cc_final: 0.7359 (mmtm) REVERT: D 13 MET cc_start: 0.8612 (tpt) cc_final: 0.8014 (tmm) REVERT: D 19 GLN cc_start: 0.9064 (tp40) cc_final: 0.8294 (tm-30) REVERT: D 40 MET cc_start: 0.8669 (tmm) cc_final: 0.8378 (tmm) REVERT: E 275 GLU cc_start: 0.8200 (pt0) cc_final: 0.7739 (pp20) REVERT: F 128 MET cc_start: 0.9044 (tpp) cc_final: 0.8740 (tmm) REVERT: F 173 MET cc_start: 0.8783 (mmm) cc_final: 0.8499 (mmm) REVERT: F 374 MET cc_start: 0.7890 (tmm) cc_final: 0.7262 (tmm) REVERT: F 486 MET cc_start: 0.8919 (tpp) cc_final: 0.8709 (tpp) REVERT: G 34 HIS cc_start: 0.8696 (t-90) cc_final: 0.8178 (t70) REVERT: H 13 MET cc_start: 0.8606 (tpt) cc_final: 0.8160 (tmm) outliers start: 41 outliers final: 37 residues processed: 207 average time/residue: 0.2650 time to fit residues: 88.0013 Evaluate side-chains 208 residues out of total 1926 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 2.056 ------------------------------------------------------------------------------- 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 255 CYS Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 331 SER 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 171 ILE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 310 ILE 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 C residue 17 MET Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain D residue 28 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 331 SER Chi-restraints excluded: chain E residue 341 LEU 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 398 LEU 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 G residue 32 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 30.0000 chunk 53 optimal weight: 0.0030 chunk 160 optimal weight: 3.9990 chunk 25 optimal weight: 0.2980 chunk 48 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- 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 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.060149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.049282 restraints weight = 94668.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.050683 restraints weight = 52483.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.051621 restraints weight = 35409.049| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3159 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18224 Z= 0.163 Angle : 0.742 19.455 24656 Z= 0.345 Chirality : 0.045 0.298 2760 Planarity : 0.004 0.061 3124 Dihedral : 5.222 56.575 2469 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.72 % Favored : 91.19 % Rotamer: Outliers : 2.09 % Allowed : 20.73 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2226 helix: 0.91 (0.18), residues: 928 sheet: -1.33 (0.34), residues: 232 loop : -1.78 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 32 HIS 0.004 0.001 HIS A 211 PHE 0.020 0.001 PHE G 111 TYR 0.014 0.001 TYR F 342 ARG 0.007 0.000 ARG B 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3253.14 seconds wall clock time: 60 minutes 53.47 seconds (3653.47 seconds total)