Starting phenix.real_space_refine on Thu Mar 14 16:49:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/03_2024/7yiy_33866_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/03_2024/7yiy_33866.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/03_2024/7yiy_33866_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/03_2024/7yiy_33866_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/03_2024/7yiy_33866_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/03_2024/7yiy_33866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/03_2024/7yiy_33866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/03_2024/7yiy_33866_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiy_33866/03_2024/7yiy_33866_updated.pdb" } resolution = 2.7 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 52 5.16 5 C 5971 2.51 5 N 1559 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ASP 294": "OD1" <-> "OD2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 345": "OE1" <-> "OE2" Residue "B ASP 369": "OD1" <-> "OD2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B ASP 465": "OD1" <-> "OD2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 530": "OE1" <-> "OE2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A GLU 159": "OE1" <-> "OE2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9257 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3940 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 481} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 324 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1236 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 411 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "A" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3285 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 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: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'Z1T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.12, per 1000 atoms: 0.55 Number of scatterers: 9257 At special positions: 0 Unit cell: (91.8, 85.32, 122.04, 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 52 16.00 P 1 15.00 O 1674 8.00 N 1559 7.00 C 5971 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.8 seconds 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 6 sheets defined 46.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'B' and resid 68 through 91 removed outlier: 3.855A pdb=" N TYR B 75 " --> pdb=" O ALA B 71 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 76 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 127 through 129 No H-bonds generated for 'chain 'B' and resid 127 through 129' Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.681A pdb=" N GLU B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.660A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.781A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 285 through 298 removed outlier: 3.692A pdb=" N ILE B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 336 removed outlier: 3.803A 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 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.749A pdb=" N THR B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 427 removed outlier: 3.522A pdb=" N GLN B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 454 removed outlier: 3.783A pdb=" N CYS B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 removed outlier: 3.942A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 535 Processing helix chain 'E' and resid 11 through 19 Processing helix chain 'E' and resid 22 through 40 removed outlier: 3.919A pdb=" N LEU E 27 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 37 " --> pdb=" O LEU E 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 14 No H-bonds generated for 'chain 'D' and resid 12 through 14' Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 22 through 39 removed outlier: 3.599A pdb=" N ILE D 30 " --> pdb=" O TYR D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 65 Processing helix chain 'D' and resid 85 through 92 removed outlier: 6.247A pdb=" N ASP D 90 " --> pdb=" O TRP D 86 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TYR D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 117 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 121 through 138 removed outlier: 3.789A pdb=" N VAL D 125 " --> pdb=" O GLN D 121 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) Proline residue: D 137 - end of helix Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 31 through 54 removed outlier: 3.614A pdb=" N VAL C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 51 " --> pdb=" O MET C 47 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 removed outlier: 3.844A pdb=" N GLU A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.676A pdb=" N LYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 Processing helix chain 'A' and resid 167 through 178 removed outlier: 4.780A pdb=" N ILE A 171 " --> pdb=" O GLY A 167 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 214 through 230 removed outlier: 3.592A pdb=" N ILE A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 258 through 267 removed outlier: 3.641A pdb=" N LYS A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 263 " --> pdb=" O GLU A 259 " (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 322 through 327 removed outlier: 4.916A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.537A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.942A pdb=" N GLN A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS A 374 " --> pdb=" O CYS A 370 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 422 removed outlier: 3.538A pdb=" N ILE A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG A 422 " --> pdb=" O GLN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 454 through 468 Processing sheet with id= A, first strand: chain 'B' and resid 231 through 234 removed outlier: 8.201A pdb=" N GLU B 315 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG B 278 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.833A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 92 through 94 Processing sheet with id= D, first strand: chain 'A' and resid 160 through 164 Processing sheet with id= E, first strand: chain 'A' and resid 205 through 209 removed outlier: 7.955A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG A 270 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL A 244 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE A 272 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 383 through 386 339 hydrogen bonds defined for protein. 993 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: 2.53 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2604 1.33 - 1.45: 1510 1.45 - 1.57: 5255 1.57 - 1.69: 1 1.69 - 1.81: 87 Bond restraints: 9457 Sorted by residual: bond pdb=" C14 Z1T D 201 " pdb=" C15 Z1T D 201 " ideal model delta sigma weight residual 1.343 1.523 -0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" C19 Z1T D 201 " pdb=" N1 Z1T D 201 " ideal model delta sigma weight residual 1.481 1.335 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.485 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.483 -0.093 2.00e-02 2.50e+03 2.14e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.04e+01 ... (remaining 9452 not shown) Histogram of bond angle deviations from ideal: 98.19 - 105.37: 174 105.37 - 112.55: 4682 112.55 - 119.72: 3441 119.72 - 126.90: 4388 126.90 - 134.07: 102 Bond angle restraints: 12787 Sorted by residual: angle pdb=" C14 Z1T D 201 " pdb=" C15 Z1T D 201 " pdb=" C16 Z1T D 201 " ideal model delta sigma weight residual 152.64 115.74 36.90 3.00e+00 1.11e-01 1.51e+02 angle pdb=" N ILE B 503 " pdb=" CA ILE B 503 " pdb=" C ILE B 503 " ideal model delta sigma weight residual 110.62 118.43 -7.81 1.02e+00 9.61e-01 5.86e+01 angle pdb=" N GLN B 116 " pdb=" CA GLN B 116 " pdb=" C GLN B 116 " ideal model delta sigma weight residual 109.76 99.56 10.20 1.59e+00 3.96e-01 4.12e+01 angle pdb=" N PRO A 78 " pdb=" CA PRO A 78 " pdb=" CB PRO A 78 " ideal model delta sigma weight residual 103.44 109.98 -6.54 1.12e+00 7.97e-01 3.41e+01 angle pdb=" N GLY B 497 " pdb=" CA GLY B 497 " pdb=" C GLY B 497 " ideal model delta sigma weight residual 112.81 120.13 -7.32 1.38e+00 5.25e-01 2.82e+01 ... (remaining 12782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 4934 16.31 - 32.63: 475 32.63 - 48.94: 174 48.94 - 65.26: 65 65.26 - 81.57: 12 Dihedral angle restraints: 5660 sinusoidal: 2291 harmonic: 3369 Sorted by residual: dihedral pdb=" CA ASN B 120 " pdb=" C ASN B 120 " pdb=" N PHE B 121 " pdb=" CA PHE B 121 " ideal model delta harmonic sigma weight residual 180.00 155.33 24.67 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA ILE B 96 " pdb=" C ILE B 96 " pdb=" N GLU B 97 " pdb=" CA GLU B 97 " ideal model delta harmonic sigma weight residual -180.00 -158.19 -21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" C TYR E 44 " pdb=" N TYR E 44 " pdb=" CA TYR E 44 " pdb=" CB TYR E 44 " ideal model delta harmonic sigma weight residual -122.60 -132.97 10.37 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 5657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1249 0.087 - 0.174: 156 0.174 - 0.261: 18 0.261 - 0.347: 2 0.347 - 0.434: 3 Chirality restraints: 1428 Sorted by residual: chirality pdb=" CA LYS B 168 " pdb=" N LYS B 168 " pdb=" C LYS B 168 " pdb=" CB LYS B 168 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CA TYR E 44 " pdb=" N TYR E 44 " pdb=" C TYR E 44 " pdb=" CB TYR E 44 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.59e+00 chirality pdb=" CA PHE B 498 " pdb=" N PHE B 498 " pdb=" C PHE B 498 " pdb=" CB PHE B 498 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.41 2.00e-01 2.50e+01 4.10e+00 ... (remaining 1425 not shown) Planarity restraints: 1619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO B 502 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 166 " 0.022 2.00e-02 2.50e+03 1.68e-02 5.62e+00 pdb=" CG TYR A 166 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 166 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 166 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 166 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 166 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 166 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 166 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 501 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.98e+00 pdb=" C THR B 501 " 0.039 2.00e-02 2.50e+03 pdb=" O THR B 501 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO B 502 " -0.013 2.00e-02 2.50e+03 ... (remaining 1616 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1024 2.74 - 3.28: 8416 3.28 - 3.82: 14380 3.82 - 4.36: 18317 4.36 - 4.90: 31311 Nonbonded interactions: 73448 Sorted by model distance: nonbonded pdb=" O ALA B 201 " pdb=" OG SER B 412 " model vdw 2.205 2.440 nonbonded pdb=" OH TYR B 407 " pdb=" OE2 GLU A 436 " model vdw 2.218 2.440 nonbonded pdb=" O THR B 66 " pdb=" NH1 ARG D 20 " model vdw 2.240 2.520 nonbonded pdb=" OG1 THR B 432 " pdb=" CD2 LEU B 434 " model vdw 2.261 3.460 nonbonded pdb=" NZ LYS B 338 " pdb=" O TRP A 64 " model vdw 2.296 2.520 ... (remaining 73443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.110 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.710 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 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 : 0.008 0.180 9457 Z= 0.531 Angle : 1.005 36.900 12787 Z= 0.591 Chirality : 0.063 0.434 1428 Planarity : 0.006 0.086 1619 Dihedral : 16.202 81.572 3504 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.20 % Favored : 94.19 % Rotamer: Outliers : 4.77 % Allowed : 2.44 % Favored : 92.79 % 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: -1.48 (0.24), residues: 1154 helix: -0.40 (0.22), residues: 505 sheet: -0.01 (0.50), residues: 118 loop : -1.77 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 134 HIS 0.005 0.001 HIS A 91 PHE 0.032 0.003 PHE A 138 TYR 0.039 0.003 TYR A 166 ARG 0.007 0.001 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 125 time to evaluate : 1.046 Fit side-chains REVERT: B 93 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6711 (m-10) REVERT: B 152 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8163 (pm20) REVERT: B 183 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.8112 (ptm160) REVERT: B 281 LYS cc_start: 0.8394 (mttp) cc_final: 0.8153 (mttt) REVERT: B 344 ASP cc_start: 0.8647 (t0) cc_final: 0.8445 (t70) REVERT: B 427 MET cc_start: 0.9006 (mtm) cc_final: 0.8589 (mtm) REVERT: B 434 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6958 (tp) REVERT: B 436 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7592 (mtpp) REVERT: B 518 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8162 (tppt) REVERT: E 42 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6616 (mmtm) REVERT: C 11 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7289 (tmtt) REVERT: C 13 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7928 (mmp) REVERT: A 56 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 375 LYS cc_start: 0.8657 (tttm) cc_final: 0.8448 (tttp) REVERT: A 434 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8239 (mmpt) REVERT: A 435 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: A 459 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7018 (tmm-80) outliers start: 47 outliers final: 22 residues processed: 149 average time/residue: 1.6307 time to fit residues: 255.1852 Evaluate side-chains 145 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 168 LYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 518 LYS Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 541 ARG Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 45 LYS Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 13 MET Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 459 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN B 463 ASN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9457 Z= 0.243 Angle : 0.616 7.578 12787 Z= 0.329 Chirality : 0.047 0.196 1428 Planarity : 0.005 0.052 1619 Dihedral : 11.125 69.394 1416 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.05 % Allowed : 9.54 % Favored : 87.41 % 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: -0.73 (0.24), residues: 1154 helix: 0.59 (0.23), residues: 515 sheet: 0.20 (0.49), residues: 119 loop : -1.79 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 134 HIS 0.003 0.001 HIS A 91 PHE 0.018 0.002 PHE A 138 TYR 0.020 0.002 TYR A 166 ARG 0.003 0.000 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 1.022 Fit side-chains REVERT: B 93 TYR cc_start: 0.7148 (OUTLIER) cc_final: 0.6771 (m-10) REVERT: B 150 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: B 152 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8101 (pm20) REVERT: B 427 MET cc_start: 0.8742 (mtm) cc_final: 0.8343 (mtm) REVERT: B 434 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7004 (tp) REVERT: B 490 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8165 (t0) REVERT: B 526 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7992 (ttpp) REVERT: D 118 LYS cc_start: 0.8809 (mttp) cc_final: 0.8586 (mttt) REVERT: C 11 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7438 (mptt) REVERT: A 56 GLU cc_start: 0.7829 (mp0) cc_final: 0.7269 (mp0) REVERT: A 205 ASP cc_start: 0.8005 (m-30) cc_final: 0.7788 (m-30) REVERT: A 434 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8171 (mmpt) REVERT: A 435 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6696 (mm-30) outliers start: 30 outliers final: 11 residues processed: 137 average time/residue: 1.6465 time to fit residues: 237.3167 Evaluate side-chains 131 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 422 ARG Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 0.2980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9457 Z= 0.179 Angle : 0.537 6.430 12787 Z= 0.287 Chirality : 0.044 0.193 1428 Planarity : 0.004 0.050 1619 Dihedral : 9.225 69.130 1352 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.44 % Allowed : 11.88 % Favored : 85.69 % 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: -0.19 (0.25), residues: 1154 helix: 1.22 (0.24), residues: 512 sheet: 0.13 (0.48), residues: 121 loop : -1.62 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 134 HIS 0.002 0.001 HIS A 91 PHE 0.014 0.001 PHE A 209 TYR 0.015 0.001 TYR B 235 ARG 0.002 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 1.087 Fit side-chains REVERT: B 93 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6683 (m-10) REVERT: B 152 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8084 (pm20) REVERT: B 189 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.6894 (mm-40) REVERT: B 427 MET cc_start: 0.8752 (mtm) cc_final: 0.8339 (mtm) REVERT: B 486 MET cc_start: 0.8976 (mmm) cc_final: 0.8724 (mmt) REVERT: B 490 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8012 (t0) REVERT: D 19 SER cc_start: 0.9091 (m) cc_final: 0.8844 (m) REVERT: A 205 ASP cc_start: 0.7961 (m-30) cc_final: 0.7756 (m-30) REVERT: A 434 LYS cc_start: 0.8539 (mmtm) cc_final: 0.8158 (mmpt) REVERT: A 435 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6805 (mm-30) outliers start: 24 outliers final: 11 residues processed: 134 average time/residue: 1.5694 time to fit residues: 221.7268 Evaluate side-chains 125 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9457 Z= 0.207 Angle : 0.554 6.853 12787 Z= 0.295 Chirality : 0.045 0.197 1428 Planarity : 0.005 0.060 1619 Dihedral : 8.218 68.353 1331 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.44 % Allowed : 13.50 % Favored : 84.06 % 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: -0.02 (0.25), residues: 1154 helix: 1.35 (0.24), residues: 516 sheet: 0.14 (0.47), residues: 123 loop : -1.52 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 134 HIS 0.002 0.001 HIS A 292 PHE 0.015 0.001 PHE A 209 TYR 0.015 0.001 TYR B 235 ARG 0.005 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 1.122 Fit side-chains REVERT: B 93 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6765 (m-10) REVERT: B 109 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8327 (mtpt) REVERT: B 152 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: B 189 GLN cc_start: 0.7600 (OUTLIER) cc_final: 0.6916 (mm-40) REVERT: B 190 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7551 (mt-10) REVERT: B 427 MET cc_start: 0.8706 (mtm) cc_final: 0.8294 (mtm) REVERT: B 490 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8049 (t0) REVERT: E 9 VAL cc_start: 0.4772 (OUTLIER) cc_final: 0.4369 (t) REVERT: D 19 SER cc_start: 0.9106 (m) cc_final: 0.8859 (m) REVERT: A 423 SER cc_start: 0.8654 (m) cc_final: 0.8042 (p) REVERT: A 434 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8165 (mmpt) REVERT: A 435 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7049 (mm-30) outliers start: 24 outliers final: 11 residues processed: 134 average time/residue: 1.5810 time to fit residues: 223.5736 Evaluate side-chains 134 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.0060 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9457 Z= 0.135 Angle : 0.484 6.070 12787 Z= 0.259 Chirality : 0.042 0.185 1428 Planarity : 0.004 0.050 1619 Dihedral : 7.734 78.857 1331 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.54 % Allowed : 14.21 % Favored : 83.25 % 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: 0.37 (0.25), residues: 1154 helix: 1.71 (0.24), residues: 516 sheet: 0.22 (0.47), residues: 123 loop : -1.32 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 134 HIS 0.001 0.000 HIS A 292 PHE 0.013 0.001 PHE B 121 TYR 0.011 0.001 TYR B 235 ARG 0.006 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 119 time to evaluate : 1.168 Fit side-chains REVERT: B 93 TYR cc_start: 0.7056 (OUTLIER) cc_final: 0.6561 (m-10) REVERT: B 109 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8167 (mmtt) REVERT: B 152 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: B 189 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.6931 (mm-40) REVERT: B 281 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7926 (mtmt) REVERT: B 427 MET cc_start: 0.8630 (mtm) cc_final: 0.8213 (mtm) REVERT: E 9 VAL cc_start: 0.4836 (OUTLIER) cc_final: 0.4421 (t) REVERT: D 19 SER cc_start: 0.9050 (m) cc_final: 0.8775 (m) REVERT: A 423 SER cc_start: 0.8657 (m) cc_final: 0.8103 (p) REVERT: A 434 LYS cc_start: 0.8497 (mmtm) cc_final: 0.8163 (mmpt) REVERT: A 435 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7220 (mm-30) outliers start: 25 outliers final: 10 residues processed: 135 average time/residue: 1.5586 time to fit residues: 222.0703 Evaluate side-chains 133 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9457 Z= 0.243 Angle : 0.575 6.894 12787 Z= 0.303 Chirality : 0.046 0.200 1428 Planarity : 0.005 0.053 1619 Dihedral : 7.896 71.060 1331 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.15 % Allowed : 14.42 % Favored : 82.44 % 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: 0.26 (0.25), residues: 1154 helix: 1.63 (0.24), residues: 509 sheet: 0.03 (0.46), residues: 125 loop : -1.31 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 134 HIS 0.003 0.001 HIS A 91 PHE 0.016 0.002 PHE A 209 TYR 0.016 0.002 TYR B 235 ARG 0.006 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 0.968 Fit side-chains REVERT: B 93 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6577 (m-10) REVERT: B 109 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8210 (mmtt) REVERT: B 152 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7786 (pm20) REVERT: B 189 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.6924 (mm-40) REVERT: B 197 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7760 (tp30) REVERT: B 281 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8015 (mtmt) REVERT: B 427 MET cc_start: 0.8646 (mtm) cc_final: 0.8331 (mtm) REVERT: B 436 LYS cc_start: 0.8464 (mtmm) cc_final: 0.7671 (mtpt) REVERT: E 9 VAL cc_start: 0.4976 (OUTLIER) cc_final: 0.4610 (t) REVERT: E 13 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6058 (mtt) REVERT: D 19 SER cc_start: 0.9097 (m) cc_final: 0.8841 (m) REVERT: A 144 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8368 (p) REVERT: A 423 SER cc_start: 0.8644 (m) cc_final: 0.8079 (p) REVERT: A 434 LYS cc_start: 0.8526 (mmtm) cc_final: 0.8181 (mmpt) REVERT: A 435 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7425 (mm-30) outliers start: 31 outliers final: 15 residues processed: 136 average time/residue: 1.5830 time to fit residues: 226.6176 Evaluate side-chains 140 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 542 HIS Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 205 ASP Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 62 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 0.0270 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 50 optimal weight: 0.4980 chunk 67 optimal weight: 0.9980 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9457 Z= 0.131 Angle : 0.482 6.724 12787 Z= 0.257 Chirality : 0.042 0.185 1428 Planarity : 0.004 0.047 1619 Dihedral : 7.415 80.859 1331 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.94 % Allowed : 14.92 % Favored : 82.13 % 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: 0.55 (0.26), residues: 1154 helix: 1.89 (0.24), residues: 516 sheet: 0.04 (0.46), residues: 125 loop : -1.19 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 134 HIS 0.002 0.000 HIS A 292 PHE 0.013 0.001 PHE A 209 TYR 0.010 0.001 TYR B 235 ARG 0.007 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 120 time to evaluate : 1.086 Fit side-chains REVERT: B 93 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6506 (m-10) REVERT: B 109 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8196 (mmtt) REVERT: B 189 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.6909 (mm-40) REVERT: B 190 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7597 (mt-10) REVERT: B 197 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7747 (tp30) REVERT: B 281 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7851 (mtmt) REVERT: B 427 MET cc_start: 0.8612 (mtm) cc_final: 0.8294 (mtm) REVERT: E 9 VAL cc_start: 0.5005 (OUTLIER) cc_final: 0.4648 (t) REVERT: E 13 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6291 (mtt) REVERT: D 19 SER cc_start: 0.8998 (m) cc_final: 0.8711 (m) REVERT: A 423 SER cc_start: 0.8642 (m) cc_final: 0.8109 (p) REVERT: A 434 LYS cc_start: 0.8509 (mmtm) cc_final: 0.8186 (mmpt) REVERT: A 435 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7484 (mm-30) outliers start: 29 outliers final: 13 residues processed: 137 average time/residue: 1.5465 time to fit residues: 223.5754 Evaluate side-chains 135 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 435 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.0670 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 0.0770 chunk 99 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 HIS ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9457 Z= 0.135 Angle : 0.488 7.443 12787 Z= 0.260 Chirality : 0.042 0.183 1428 Planarity : 0.004 0.047 1619 Dihedral : 6.972 89.677 1325 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.54 % Allowed : 15.94 % Favored : 81.52 % 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: 0.73 (0.26), residues: 1154 helix: 2.02 (0.24), residues: 518 sheet: 0.03 (0.46), residues: 127 loop : -1.05 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.001 0.000 HIS D 34 PHE 0.015 0.001 PHE B 121 TYR 0.010 0.001 TYR B 235 ARG 0.008 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 0.997 Fit side-chains REVERT: B 93 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6566 (m-10) REVERT: B 109 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8213 (mmtt) REVERT: B 189 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.6910 (mm-40) REVERT: B 190 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7575 (mt-10) REVERT: B 197 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7752 (tp30) REVERT: B 281 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7815 (mtmt) REVERT: B 427 MET cc_start: 0.8595 (mtm) cc_final: 0.8287 (mtm) REVERT: B 434 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7037 (tp) REVERT: B 475 MET cc_start: 0.8441 (mpt) cc_final: 0.7958 (mpt) REVERT: E 9 VAL cc_start: 0.5009 (OUTLIER) cc_final: 0.4566 (t) REVERT: D 19 SER cc_start: 0.8981 (m) cc_final: 0.8702 (m) REVERT: A 423 SER cc_start: 0.8638 (m) cc_final: 0.8110 (p) REVERT: A 434 LYS cc_start: 0.8507 (mmtm) cc_final: 0.8194 (mmpt) outliers start: 25 outliers final: 13 residues processed: 134 average time/residue: 1.5336 time to fit residues: 217.0749 Evaluate side-chains 129 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 110 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 365 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 92 optimal weight: 0.3980 chunk 67 optimal weight: 0.0970 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 0.0370 overall best weight: 0.2256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9457 Z= 0.118 Angle : 0.470 8.239 12787 Z= 0.249 Chirality : 0.041 0.180 1428 Planarity : 0.004 0.060 1619 Dihedral : 6.523 79.974 1322 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.93 % Allowed : 16.95 % Favored : 81.12 % 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: 0.87 (0.26), residues: 1154 helix: 2.10 (0.24), residues: 523 sheet: 0.04 (0.47), residues: 127 loop : -0.95 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 32 HIS 0.001 0.000 HIS B 403 PHE 0.012 0.001 PHE B 121 TYR 0.008 0.001 TYR C 27 ARG 0.007 0.000 ARG B 271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.052 Fit side-chains REVERT: B 93 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6581 (m-10) REVERT: B 109 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8229 (mmtt) REVERT: B 189 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6877 (mm-40) REVERT: B 190 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7468 (mt-10) REVERT: B 281 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7833 (mtmt) REVERT: B 427 MET cc_start: 0.8563 (mtm) cc_final: 0.8246 (mtm) REVERT: B 434 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.6945 (tp) REVERT: B 475 MET cc_start: 0.8424 (mpt) cc_final: 0.7964 (mpt) REVERT: E 9 VAL cc_start: 0.4929 (OUTLIER) cc_final: 0.4596 (t) REVERT: E 13 MET cc_start: 0.7038 (mtt) cc_final: 0.6285 (mtt) REVERT: D 19 SER cc_start: 0.8967 (m) cc_final: 0.8677 (m) REVERT: A 423 SER cc_start: 0.8594 (m) cc_final: 0.8085 (p) REVERT: A 434 LYS cc_start: 0.8534 (mmtm) cc_final: 0.8171 (mmpt) outliers start: 19 outliers final: 9 residues processed: 132 average time/residue: 1.5108 time to fit residues: 210.7050 Evaluate side-chains 127 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 326 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 0.0060 chunk 9 optimal weight: 0.0040 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.4808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9457 Z= 0.132 Angle : 0.491 9.720 12787 Z= 0.257 Chirality : 0.042 0.194 1428 Planarity : 0.005 0.108 1619 Dihedral : 6.406 75.146 1322 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.93 % Allowed : 17.06 % Favored : 81.02 % 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: 0.92 (0.26), residues: 1154 helix: 2.14 (0.24), residues: 523 sheet: 0.06 (0.47), residues: 127 loop : -0.92 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 32 HIS 0.001 0.000 HIS D 34 PHE 0.014 0.001 PHE B 121 TYR 0.009 0.001 TYR B 235 ARG 0.007 0.000 ARG B 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2308 Ramachandran restraints generated. 1154 Oldfield, 0 Emsley, 1154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.067 Fit side-chains REVERT: B 93 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6636 (m-10) REVERT: B 109 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8230 (mmtt) REVERT: B 189 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6867 (mm-40) REVERT: B 197 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7746 (tp30) REVERT: B 427 MET cc_start: 0.8562 (mtm) cc_final: 0.8256 (mtm) REVERT: B 434 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.6921 (tp) REVERT: E 9 VAL cc_start: 0.4936 (OUTLIER) cc_final: 0.4530 (t) REVERT: D 19 SER cc_start: 0.8959 (m) cc_final: 0.8670 (m) REVERT: D 118 LYS cc_start: 0.8439 (mttt) cc_final: 0.8178 (mttt) REVERT: A 423 SER cc_start: 0.8599 (m) cc_final: 0.8085 (p) REVERT: A 434 LYS cc_start: 0.8545 (mmtm) cc_final: 0.8181 (mmpt) outliers start: 19 outliers final: 11 residues processed: 129 average time/residue: 1.5093 time to fit residues: 205.9526 Evaluate side-chains 128 residues out of total 997 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 185 THR Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 326 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 0.0170 chunk 65 optimal weight: 4.9990 overall best weight: 1.2622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 490 ASN ** 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 = 0.3272 r_free = 0.3272 target = 0.114990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.093810 restraints weight = 11332.986| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.72 r_work: 0.2814 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9457 Z= 0.211 Angle : 0.570 9.923 12787 Z= 0.298 Chirality : 0.045 0.196 1428 Planarity : 0.005 0.105 1619 Dihedral : 6.964 87.925 1322 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.13 % Allowed : 17.06 % Favored : 80.81 % 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: 0.69 (0.26), residues: 1154 helix: 1.92 (0.24), residues: 522 sheet: 0.09 (0.47), residues: 125 loop : -1.04 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 134 HIS 0.002 0.001 HIS A 292 PHE 0.016 0.001 PHE B 121 TYR 0.016 0.001 TYR B 235 ARG 0.007 0.000 ARG B 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3925.34 seconds wall clock time: 69 minutes 45.30 seconds (4185.30 seconds total)