Starting phenix.real_space_refine on Tue Jul 23 15:43:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptn_17875/07_2024/8ptn_17875_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptn_17875/07_2024/8ptn_17875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptn_17875/07_2024/8ptn_17875.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptn_17875/07_2024/8ptn_17875.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptn_17875/07_2024/8ptn_17875_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ptn_17875/07_2024/8ptn_17875_neut.cif" } resolution = 3.3 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= 0.006 sd= 0.040 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: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 14431 2.51 5 N 4050 2.21 5 O 4378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "E GLU 414": "OE1" <-> "OE2" Residue "F GLU 244": "OE1" <-> "OE2" Residue "F GLU 414": "OE1" <-> "OE2" Residue "b GLU 59": "OE1" <-> "OE2" Residue "c GLU 83": "OE1" <-> "OE2" Residue "d GLU 17": "OE1" <-> "OE2" Residue "e GLU 17": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 22976 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "B" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "C" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "D" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "E" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "F" Number of atoms: 3291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3291 Classifications: {'peptide': 418} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain: "a" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "b" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "c" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "d" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "e" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Time building chain proxies: 12.20, per 1000 atoms: 0.53 Number of scatterers: 22976 At special positions: 0 Unit cell: (130.624, 141.44, 163.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 4378 8.00 N 4050 7.00 C 14431 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=0, symmetry=0 Time building additional restraints: 8.65 Conformation dependent library (CDL) restraints added in 4.1 seconds 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5458 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 28 sheets defined 44.8% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.69 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.636A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 22 Processing helix chain 'A' and resid 30 through 46 removed outlier: 3.823A pdb=" N ILE A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.627A pdb=" N ILE A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'A' and resid 212 through 223 Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.501A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.534A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.598A pdb=" N ALA A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.090A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 Processing helix chain 'A' and resid 392 through 405 removed outlier: 4.502A pdb=" N MET A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 removed outlier: 3.767A pdb=" N MET A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 9 removed outlier: 3.940A pdb=" N THR B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 Processing helix chain 'B' and resid 30 through 45 Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.628A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 153 through 166 removed outlier: 3.888A pdb=" N THR B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 Processing helix chain 'B' and resid 212 through 223 removed outlier: 3.714A pdb=" N VAL B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 256 removed outlier: 3.573A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 removed outlier: 3.613A pdb=" N LEU B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 289 removed outlier: 3.734A pdb=" N VAL B 289 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 346 through 352 removed outlier: 3.648A pdb=" N LYS B 352 " --> pdb=" O LYS B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.608A pdb=" N LEU B 370 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 Processing helix chain 'B' and resid 391 through 406 removed outlier: 4.509A pdb=" N MET B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 406 " --> pdb=" O LYS B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.647A pdb=" N ARG B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 10 through 22 Processing helix chain 'C' and resid 30 through 46 Processing helix chain 'C' and resid 82 through 89 removed outlier: 3.535A pdb=" N ILE C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 128 removed outlier: 3.771A pdb=" N ARG C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.265A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 223 Processing helix chain 'C' and resid 235 through 255 removed outlier: 3.546A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 294 through 302 removed outlier: 3.565A pdb=" N LYS C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 405 removed outlier: 3.644A pdb=" N MET C 405 " --> pdb=" O ASN C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 418 Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.563A pdb=" N LEU D 6 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.804A pdb=" N SER D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 89 removed outlier: 3.766A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.228A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.568A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 294 through 303 removed outlier: 3.956A pdb=" N LYS D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG D 299 " --> pdb=" O HIS D 295 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE D 300 " --> pdb=" O ARG D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 Processing helix chain 'D' and resid 346 through 352 removed outlier: 3.695A pdb=" N ALA D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS D 352 " --> pdb=" O LYS D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 363 removed outlier: 3.526A pdb=" N SER D 363 " --> pdb=" O TYR D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 403 Processing helix chain 'D' and resid 409 through 418 Processing helix chain 'E' and resid 2 through 9 removed outlier: 3.654A pdb=" N ASN E 8 " --> pdb=" O THR E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 22 Processing helix chain 'E' and resid 30 through 46 Processing helix chain 'E' and resid 82 through 89 removed outlier: 3.570A pdb=" N ILE E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 129 removed outlier: 3.696A pdb=" N ASN E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 223 Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.528A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 290 through 302 removed outlier: 3.967A pdb=" N ARG E 296 " --> pdb=" O ASN E 292 " (cutoff:3.500A) Proline residue: E 297 - end of helix Processing helix chain 'E' and resid 326 through 335 removed outlier: 4.371A pdb=" N VAL E 330 " --> pdb=" O LYS E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.861A pdb=" N LEU E 370 " --> pdb=" O LYS E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 388 Processing helix chain 'E' and resid 391 through 404 Processing helix chain 'E' and resid 408 through 418 Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 10 through 21 Processing helix chain 'F' and resid 30 through 46 removed outlier: 3.573A pdb=" N GLY F 46 " --> pdb=" O HIS F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 89 removed outlier: 3.629A pdb=" N ILE F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 129 Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 184 through 199 Processing helix chain 'F' and resid 212 through 223 removed outlier: 3.697A pdb=" N VAL F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 256 Processing helix chain 'F' and resid 266 through 278 removed outlier: 3.590A pdb=" N LEU F 270 " --> pdb=" O SER F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 289 removed outlier: 3.850A pdb=" N VAL F 289 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 302 removed outlier: 3.640A pdb=" N ARG F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Proline residue: F 297 - end of helix Processing helix chain 'F' and resid 325 through 336 Processing helix chain 'F' and resid 337 through 339 No H-bonds generated for 'chain 'F' and resid 337 through 339' Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 367 through 372 Processing helix chain 'F' and resid 373 through 388 Processing helix chain 'F' and resid 394 through 406 removed outlier: 4.097A pdb=" N THR F 406 " --> pdb=" O LYS F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 415 removed outlier: 4.232A pdb=" N PHE F 412 " --> pdb=" O THR F 408 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 23 removed outlier: 3.537A pdb=" N TYR a 13 " --> pdb=" O ASN a 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 23 removed outlier: 3.541A pdb=" N HIS b 23 " --> pdb=" O ALA b 19 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 23 Processing helix chain 'c' and resid 56 through 59 Processing helix chain 'd' and resid 9 through 23 Processing helix chain 'e' and resid 9 through 23 Processing helix chain 'e' and resid 45 through 49 removed outlier: 3.523A pdb=" N ASN e 48 " --> pdb=" O SER e 45 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 57 removed outlier: 3.785A pdb=" N ILE A 79 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LEU A 114 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARG A 102 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N VAL A 116 " --> pdb=" O LYS A 100 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS A 100 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 231 removed outlier: 6.328A pdb=" N LEU A 204 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL A 228 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N VAL A 206 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N SER A 230 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 208 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ILE A 316 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 262 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR A 318 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ARG A 173 " --> pdb=" O MET A 341 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU A 343 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 175 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 57 removed outlier: 3.524A pdb=" N LEU B 113 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 112 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS B 100 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL B 116 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N SER B 98 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLU B 118 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N THR B 96 " --> pdb=" O GLU B 118 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.600A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.489A pdb=" N ILE B 168 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 226 through 231 removed outlier: 7.012A pdb=" N LEU B 204 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE B 209 " --> pdb=" O ASP B 265 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY B 174 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA B 319 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ILE B 176 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG B 173 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU B 343 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU B 175 " --> pdb=" O LEU B 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 57 removed outlier: 3.845A pdb=" N ILE C 79 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS C 100 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N VAL C 116 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER C 98 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU C 118 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR C 96 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.723A pdb=" N ASN C 306 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 226 through 231 removed outlier: 6.593A pdb=" N LEU C 204 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL C 228 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL C 206 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER C 230 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU C 208 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE C 316 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE C 262 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR C 318 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU C 264 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N LEU C 320 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.824A pdb=" N VAL C 289 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 49 through 57 removed outlier: 3.959A pdb=" N ILE D 79 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 113 " --> pdb=" O TYR D 80 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU D 114 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ARG D 102 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N VAL D 116 " --> pdb=" O LYS D 100 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS D 100 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE D 49 " --> pdb=" O ILE D 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.340A pdb=" N VAL D 260 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE D 316 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE D 262 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N THR D 318 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU D 264 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N LEU D 320 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU D 226 " --> pdb=" O LEU D 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 138 through 139 removed outlier: 6.006A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.657A pdb=" N ILE E 79 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LYS E 100 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL E 116 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER E 98 " --> pdb=" O VAL E 116 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLU E 118 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR E 96 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE E 49 " --> pdb=" O ILE E 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.545A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.545A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL E 260 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N ILE E 316 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE E 262 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR E 318 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU E 264 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N LEU E 320 " --> pdb=" O LEU E 264 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU E 263 " --> pdb=" O MET E 205 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU E 226 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 79 through 81 removed outlier: 3.816A pdb=" N ILE F 49 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR F 96 " --> pdb=" O GLU F 118 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLU F 118 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N SER F 98 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL F 116 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS F 100 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA F 112 " --> pdb=" O ARG F 102 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 260 through 264 removed outlier: 7.232A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ILE F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE F 262 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N THR F 318 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU F 264 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N LEU F 320 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU F 175 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N LEU F 345 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL F 177 " --> pdb=" O LEU F 345 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS F 344 " --> pdb=" O ASP F 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 206 through 211 removed outlier: 6.137A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'a' and resid 26 through 29 Processing sheet with id=AC3, first strand: chain 'a' and resid 40 through 46 removed outlier: 4.139A pdb=" N ASP a 42 " --> pdb=" O VAL a 53 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL a 53 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 61 through 63 removed outlier: 3.670A pdb=" N ASP b 42 " --> pdb=" O VAL b 53 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU b 55 " --> pdb=" O ALA b 40 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA b 40 " --> pdb=" O GLU b 55 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER b 70 " --> pdb=" O GLU b 29 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 35 through 38 removed outlier: 3.992A pdb=" N PHE c 71 " --> pdb=" O VAL c 79 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL c 79 " --> pdb=" O PHE c 71 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 40 through 46 removed outlier: 4.351A pdb=" N ASP c 42 " --> pdb=" O VAL c 53 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL c 53 " --> pdb=" O ASP c 42 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'd' and resid 25 through 29 removed outlier: 5.400A pdb=" N ALA d 40 " --> pdb=" O GLU d 55 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLU d 55 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP d 42 " --> pdb=" O VAL d 53 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 27 through 29 Processing sheet with id=AC9, first strand: chain 'e' and resid 40 through 44 removed outlier: 3.707A pdb=" N ASP e 42 " --> pdb=" O VAL e 53 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'e' and resid 70 through 71 removed outlier: 4.471A pdb=" N PHE e 71 " --> pdb=" O VAL e 79 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL e 79 " --> pdb=" O PHE e 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 1055 hydrogen bonds defined for protein. 3039 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: 8.04 Time building geometry restraints manager: 9.54 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: 7846 1.34 - 1.46: 4497 1.46 - 1.58: 10749 1.58 - 1.70: 0 1.70 - 1.82: 218 Bond restraints: 23310 Sorted by residual: bond pdb=" CB GLU e 17 " pdb=" CG GLU e 17 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.58e+00 bond pdb=" CA ASP B 322 " pdb=" CB ASP B 322 " ideal model delta sigma weight residual 1.530 1.556 -0.026 1.69e-02 3.50e+03 2.42e+00 bond pdb=" CB LYS D 326 " pdb=" CG LYS D 326 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB ASP B 322 " pdb=" CG ASP B 322 " ideal model delta sigma weight residual 1.516 1.547 -0.031 2.50e-02 1.60e+03 1.54e+00 bond pdb=" CB GLU D 329 " pdb=" CG GLU D 329 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.52e+00 ... (remaining 23305 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.44: 441 105.44 - 112.57: 12407 112.57 - 119.71: 7716 119.71 - 126.84: 10648 126.84 - 133.98: 195 Bond angle restraints: 31407 Sorted by residual: angle pdb=" CB MET E 147 " pdb=" CG MET E 147 " pdb=" SD MET E 147 " ideal model delta sigma weight residual 112.70 126.63 -13.93 3.00e+00 1.11e-01 2.15e+01 angle pdb=" N GLU A 333 " pdb=" CA GLU A 333 " pdb=" CB GLU A 333 " ideal model delta sigma weight residual 110.28 117.45 -7.17 1.55e+00 4.16e-01 2.14e+01 angle pdb=" CB MET F 415 " pdb=" CG MET F 415 " pdb=" SD MET F 415 " ideal model delta sigma weight residual 112.70 126.08 -13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" CA ARG A 353 " pdb=" CB ARG A 353 " pdb=" CG ARG A 353 " ideal model delta sigma weight residual 114.10 122.99 -8.89 2.00e+00 2.50e-01 1.98e+01 angle pdb=" CB MET F 396 " pdb=" CG MET F 396 " pdb=" SD MET F 396 " ideal model delta sigma weight residual 112.70 125.33 -12.63 3.00e+00 1.11e-01 1.77e+01 ... (remaining 31402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 12578 17.77 - 35.54: 1470 35.54 - 53.31: 335 53.31 - 71.08: 62 71.08 - 88.85: 25 Dihedral angle restraints: 14470 sinusoidal: 6048 harmonic: 8422 Sorted by residual: dihedral pdb=" CA GLU A 414 " pdb=" C GLU A 414 " pdb=" N MET A 415 " pdb=" CA MET A 415 " ideal model delta harmonic sigma weight residual -180.00 -157.86 -22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA HIS F 388 " pdb=" C HIS F 388 " pdb=" N PRO F 389 " pdb=" CA PRO F 389 " ideal model delta harmonic sigma weight residual 180.00 -162.04 -17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA MET F 29 " pdb=" C MET F 29 " pdb=" N ARG F 30 " pdb=" CA ARG F 30 " ideal model delta harmonic sigma weight residual -180.00 -162.35 -17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 14467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2334 0.033 - 0.065: 801 0.065 - 0.098: 294 0.098 - 0.131: 158 0.131 - 0.163: 10 Chirality restraints: 3597 Sorted by residual: chirality pdb=" CA MET A 396 " pdb=" N MET A 396 " pdb=" C MET A 396 " pdb=" CB MET A 396 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA MET A 186 " pdb=" N MET A 186 " pdb=" C MET A 186 " pdb=" CB MET A 186 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA MET F 21 " pdb=" N MET F 21 " pdb=" C MET F 21 " pdb=" CB MET F 21 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 3594 not shown) Planarity restraints: 4097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 322 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C ASP B 322 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP B 322 " -0.019 2.00e-02 2.50e+03 pdb=" N THR B 323 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 278 " 0.034 5.00e-02 4.00e+02 5.22e-02 4.35e+00 pdb=" N PRO D 279 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 279 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 279 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 322 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ASP C 322 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP C 322 " 0.013 2.00e-02 2.50e+03 pdb=" N THR C 323 " 0.012 2.00e-02 2.50e+03 ... (remaining 4094 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 331 2.64 - 3.21: 21693 3.21 - 3.77: 37204 3.77 - 4.34: 48637 4.34 - 4.90: 78780 Nonbonded interactions: 186645 Sorted by model distance: nonbonded pdb=" OD1 ASP d 42 " pdb=" N LEU d 43 " model vdw 2.077 2.520 nonbonded pdb=" OD1 ASP E 265 " pdb=" OG1 THR E 318 " model vdw 2.101 2.440 nonbonded pdb=" O LEU F 320 " pdb=" OH TYR F 332 " model vdw 2.101 2.440 nonbonded pdb=" O HIS C 42 " pdb=" OG SER C 45 " model vdw 2.115 2.440 nonbonded pdb=" O GLN F 374 " pdb=" NE2 GLN F 378 " model vdw 2.135 2.520 ... (remaining 186640 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } 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=1.00 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: 3.020 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: 0.920 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 59.830 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.003 0.048 23310 Z= 0.203 Angle : 0.710 14.155 31407 Z= 0.352 Chirality : 0.042 0.163 3597 Planarity : 0.004 0.053 4097 Dihedral : 15.969 88.852 9012 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.73 % Favored : 98.24 % Rotamer: Outliers : 0.48 % Allowed : 20.97 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.48 (0.16), residues: 2896 helix: 1.09 (0.15), residues: 1205 sheet: 0.13 (0.26), residues: 400 loop : -0.26 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 381 HIS 0.014 0.001 HIS a 22 PHE 0.020 0.001 PHE F 301 TYR 0.012 0.001 TYR B 332 ARG 0.016 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 407 time to evaluate : 2.497 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: symmetry clash revert: symmetry clash REVERT: E 193 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8625 (tm-30) REVERT: E 390 MET cc_start: 0.9090 (ptp) cc_final: 0.8578 (pmm) REVERT: F 110 TYR cc_start: 0.8745 (p90) cc_final: 0.8385 (p90) REVERT: F 345 LEU cc_start: 0.6270 (tp) cc_final: 0.5865 (tp) REVERT: a 25 MET cc_start: 0.5947 (pmm) cc_final: 0.5138 (tmm) REVERT: b 22 HIS cc_start: 0.8715 (m90) cc_final: 0.8313 (m90) REVERT: b 75 GLU cc_start: 0.9073 (pm20) cc_final: 0.8696 (pm20) REVERT: c 21 GLN cc_start: 0.9049 (mt0) cc_final: 0.8706 (mt0) REVERT: c 51 TYR cc_start: 0.8024 (m-80) cc_final: 0.7789 (m-80) REVERT: c 81 VAL cc_start: 0.9309 (t) cc_final: 0.9099 (m) REVERT: d 51 TYR cc_start: 0.8466 (m-80) cc_final: 0.8177 (m-80) REVERT: d 66 ASP cc_start: 0.8421 (p0) cc_final: 0.7610 (p0) outliers start: 12 outliers final: 6 residues processed: 414 average time/residue: 0.3420 time to fit residues: 219.0081 Evaluate side-chains 369 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 363 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain a residue 22 HIS Chi-restraints excluded: chain b residue 23 HIS Chi-restraints excluded: chain d residue 80 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 40.0000 chunk 216 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 224 optimal weight: 20.0000 chunk 86 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN F 374 GLN ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 GLN ** d 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 15 ASN ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23310 Z= 0.252 Angle : 0.607 12.191 31407 Z= 0.303 Chirality : 0.042 0.156 3597 Planarity : 0.004 0.058 4097 Dihedral : 4.425 55.035 3172 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.18 % Favored : 97.79 % Rotamer: Outliers : 2.70 % Allowed : 19.58 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.58 (0.16), residues: 2896 helix: 1.27 (0.15), residues: 1205 sheet: 0.10 (0.26), residues: 414 loop : -0.28 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 381 HIS 0.004 0.001 HIS A 140 PHE 0.016 0.001 PHE F 398 TYR 0.019 0.002 TYR e 13 ARG 0.011 0.001 ARG a 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 384 time to evaluate : 2.492 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: A 52 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.6778 (t0) REVERT: D 320 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8985 (mm) REVERT: E 21 MET cc_start: 0.8798 (ppp) cc_final: 0.8377 (ppp) REVERT: E 193 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8642 (tm-30) REVERT: E 298 LYS cc_start: 0.8390 (tptt) cc_final: 0.7739 (tptp) REVERT: E 390 MET cc_start: 0.9224 (ptp) cc_final: 0.8872 (pmm) REVERT: F 110 TYR cc_start: 0.8747 (p90) cc_final: 0.8349 (p90) REVERT: F 345 LEU cc_start: 0.6019 (tp) cc_final: 0.5646 (tp) REVERT: a 25 MET cc_start: 0.6044 (pmm) cc_final: 0.5243 (tmm) REVERT: b 17 GLU cc_start: 0.8683 (pt0) cc_final: 0.8422 (pt0) REVERT: b 25 MET cc_start: 0.8938 (tpp) cc_final: 0.8673 (tpp) REVERT: b 75 GLU cc_start: 0.9056 (pm20) cc_final: 0.8625 (pm20) REVERT: c 64 ARG cc_start: 0.7971 (ttt180) cc_final: 0.7296 (ttp80) REVERT: d 51 TYR cc_start: 0.8441 (m-80) cc_final: 0.8161 (m-80) REVERT: d 64 ARG cc_start: 0.7929 (mtm180) cc_final: 0.7343 (mtp-110) REVERT: d 76 ILE cc_start: 0.7037 (pt) cc_final: 0.6791 (mt) outliers start: 68 outliers final: 39 residues processed: 422 average time/residue: 0.3258 time to fit residues: 214.8735 Evaluate side-chains 401 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 360 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 8 ILE Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 144 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 260 optimal weight: 0.1980 chunk 281 optimal weight: 30.0000 chunk 231 optimal weight: 4.9990 chunk 258 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 15 ASN ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23310 Z= 0.220 Angle : 0.596 12.487 31407 Z= 0.293 Chirality : 0.042 0.179 3597 Planarity : 0.004 0.098 4097 Dihedral : 4.097 41.842 3163 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.86 % Allowed : 21.09 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.62 (0.16), residues: 2896 helix: 1.29 (0.15), residues: 1220 sheet: 0.08 (0.26), residues: 401 loop : -0.26 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 381 HIS 0.006 0.001 HIS c 73 PHE 0.016 0.001 PHE F 301 TYR 0.016 0.002 TYR B 332 ARG 0.006 0.000 ARG a 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 377 time to evaluate : 2.677 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 52 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.6933 (t0) REVERT: C 354 VAL cc_start: 0.9539 (OUTLIER) cc_final: 0.9337 (m) REVERT: D 320 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8981 (mm) REVERT: D 341 MET cc_start: 0.7621 (tmm) cc_final: 0.7369 (tmm) REVERT: E 21 MET cc_start: 0.8804 (ppp) cc_final: 0.8371 (ppp) REVERT: E 193 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8655 (tm-30) REVERT: F 21 MET cc_start: 0.8016 (pmm) cc_final: 0.7805 (pmm) REVERT: F 110 TYR cc_start: 0.8773 (p90) cc_final: 0.8361 (p90) REVERT: F 390 MET cc_start: 0.5791 (tmm) cc_final: 0.5327 (pmm) REVERT: a 25 MET cc_start: 0.6075 (pmm) cc_final: 0.5143 (tmm) REVERT: b 17 GLU cc_start: 0.8643 (pt0) cc_final: 0.8435 (pt0) REVERT: b 25 MET cc_start: 0.9043 (tpp) cc_final: 0.8818 (tpp) REVERT: b 75 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: c 34 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8709 (tm-30) REVERT: c 36 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8903 (tt) REVERT: c 59 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6552 (pp20) REVERT: d 17 GLU cc_start: 0.9184 (tm-30) cc_final: 0.8840 (pt0) REVERT: d 47 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7308 (mtmm) REVERT: d 51 TYR cc_start: 0.8550 (m-80) cc_final: 0.8263 (m-80) REVERT: d 64 ARG cc_start: 0.7863 (mtm180) cc_final: 0.7522 (mtp-110) REVERT: d 76 ILE cc_start: 0.7108 (pt) cc_final: 0.6894 (mt) outliers start: 72 outliers final: 44 residues processed: 419 average time/residue: 0.3245 time to fit residues: 214.2218 Evaluate side-chains 396 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 345 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 341 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 8 ILE Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 257 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 276 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 247 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 15 ASN ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23310 Z= 0.246 Angle : 0.609 10.049 31407 Z= 0.299 Chirality : 0.042 0.153 3597 Planarity : 0.004 0.076 4097 Dihedral : 4.051 19.438 3160 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.49 % Allowed : 21.56 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.61 (0.16), residues: 2896 helix: 1.34 (0.15), residues: 1214 sheet: 0.00 (0.25), residues: 420 loop : -0.29 (0.17), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 381 HIS 0.007 0.001 HIS d 73 PHE 0.016 0.001 PHE F 301 TYR 0.016 0.001 TYR B 332 ARG 0.007 0.000 ARG a 46 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 360 time to evaluate : 2.575 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 1 MET cc_start: 0.6923 (ppp) cc_final: 0.5899 (ppp) REVERT: D 320 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8975 (mm) REVERT: D 341 MET cc_start: 0.7651 (tmm) cc_final: 0.7437 (tmm) REVERT: E 21 MET cc_start: 0.8806 (ppp) cc_final: 0.8368 (ppp) REVERT: E 193 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8651 (tm-30) REVERT: E 298 LYS cc_start: 0.8506 (tptt) cc_final: 0.7974 (tptp) REVERT: E 390 MET cc_start: 0.9259 (ptp) cc_final: 0.8648 (pmm) REVERT: F 21 MET cc_start: 0.8100 (pmm) cc_final: 0.7874 (pmm) REVERT: F 110 TYR cc_start: 0.8807 (p90) cc_final: 0.8388 (p90) REVERT: F 390 MET cc_start: 0.5767 (tmm) cc_final: 0.5308 (pmm) REVERT: a 25 MET cc_start: 0.6018 (pmm) cc_final: 0.5161 (tmm) REVERT: a 54 VAL cc_start: 0.6162 (OUTLIER) cc_final: 0.5742 (p) REVERT: b 17 GLU cc_start: 0.8706 (pt0) cc_final: 0.8456 (pt0) REVERT: b 75 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: c 13 TYR cc_start: 0.7796 (t80) cc_final: 0.7189 (t80) REVERT: c 59 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6566 (pp20) REVERT: c 64 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7603 (ttt180) REVERT: d 47 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7284 (mtmm) REVERT: d 51 TYR cc_start: 0.8539 (m-80) cc_final: 0.8258 (m-80) REVERT: d 76 ILE cc_start: 0.7076 (pt) cc_final: 0.6787 (mt) outliers start: 88 outliers final: 62 residues processed: 417 average time/residue: 0.3311 time to fit residues: 218.4390 Evaluate side-chains 405 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 338 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 117 ASN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 63 LEU Chi-restraints excluded: chain b residue 16 LEU Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 71 PHE Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 230 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 205 optimal weight: 20.0000 chunk 114 optimal weight: 5.9990 chunk 235 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 141 optimal weight: 0.7980 chunk 248 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23310 Z= 0.294 Angle : 0.630 14.836 31407 Z= 0.310 Chirality : 0.042 0.155 3597 Planarity : 0.004 0.059 4097 Dihedral : 4.141 20.062 3160 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.05 % Allowed : 22.08 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.56 (0.16), residues: 2896 helix: 1.28 (0.15), residues: 1215 sheet: -0.01 (0.26), residues: 405 loop : -0.30 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 381 HIS 0.006 0.001 HIS d 73 PHE 0.017 0.001 PHE D 62 TYR 0.019 0.001 TYR B 332 ARG 0.010 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 367 time to evaluate : 2.600 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 1 MET cc_start: 0.7071 (ppp) cc_final: 0.6077 (ppp) REVERT: A 329 GLU cc_start: 0.8348 (mp0) cc_final: 0.8134 (mp0) REVERT: D 294 LEU cc_start: 0.9096 (tp) cc_final: 0.8813 (tt) REVERT: D 320 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8989 (mm) REVERT: E 21 MET cc_start: 0.8806 (ppp) cc_final: 0.8367 (ppp) REVERT: E 193 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8624 (tm-30) REVERT: E 298 LYS cc_start: 0.8509 (tptt) cc_final: 0.8169 (tptp) REVERT: E 390 MET cc_start: 0.9283 (ptp) cc_final: 0.8811 (pmm) REVERT: F 30 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8540 (tpp80) REVERT: F 110 TYR cc_start: 0.8856 (p90) cc_final: 0.8418 (p90) REVERT: F 345 LEU cc_start: 0.6217 (mm) cc_final: 0.5592 (tp) REVERT: F 390 MET cc_start: 0.5574 (tmm) cc_final: 0.5161 (pmm) REVERT: F 415 MET cc_start: 0.9292 (tpp) cc_final: 0.9070 (ppp) REVERT: a 25 MET cc_start: 0.6028 (pmm) cc_final: 0.5219 (tmm) REVERT: a 54 VAL cc_start: 0.6133 (OUTLIER) cc_final: 0.5726 (p) REVERT: b 17 GLU cc_start: 0.8738 (pt0) cc_final: 0.8538 (pt0) REVERT: b 75 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8711 (pm20) REVERT: c 59 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6627 (pp20) REVERT: c 61 ARG cc_start: 0.7760 (ptm-80) cc_final: 0.7302 (ptm-80) REVERT: c 65 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8284 (mm) REVERT: d 47 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7283 (mtmm) REVERT: d 51 TYR cc_start: 0.8584 (m-80) cc_final: 0.8265 (m-80) REVERT: d 64 ARG cc_start: 0.8003 (mtm180) cc_final: 0.7608 (mtp-110) REVERT: d 76 ILE cc_start: 0.7147 (pt) cc_final: 0.6925 (mt) outliers start: 102 outliers final: 63 residues processed: 440 average time/residue: 0.3278 time to fit residues: 225.1550 Evaluate side-chains 415 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 345 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 117 ASN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 267 ILE Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 65 LEU Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 65 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 93 optimal weight: 1.9990 chunk 248 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 128 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 145 optimal weight: 0.1980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 HIS B 172 GLN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 198 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 HIS ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23310 Z= 0.242 Angle : 0.631 11.433 31407 Z= 0.307 Chirality : 0.042 0.187 3597 Planarity : 0.004 0.059 4097 Dihedral : 4.119 21.616 3160 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.73 % Allowed : 22.60 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.56 (0.16), residues: 2896 helix: 1.30 (0.15), residues: 1215 sheet: -0.07 (0.26), residues: 404 loop : -0.29 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 381 HIS 0.007 0.001 HIS A 295 PHE 0.018 0.001 PHE F 398 TYR 0.017 0.001 TYR B 332 ARG 0.009 0.000 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 349 time to evaluate : 2.605 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: A 1 MET cc_start: 0.7156 (ppp) cc_final: 0.6089 (ppp) REVERT: A 415 MET cc_start: 0.9181 (ppp) cc_final: 0.8838 (ppp) REVERT: D 198 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8551 (m110) REVERT: D 294 LEU cc_start: 0.9100 (tp) cc_final: 0.8861 (tt) REVERT: D 320 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8950 (mm) REVERT: E 21 MET cc_start: 0.8837 (ppp) cc_final: 0.8404 (ppp) REVERT: E 193 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8626 (tm-30) REVERT: E 390 MET cc_start: 0.9302 (ptp) cc_final: 0.8841 (pmm) REVERT: F 30 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8546 (tpp80) REVERT: F 110 TYR cc_start: 0.8863 (p90) cc_final: 0.8426 (p90) REVERT: F 390 MET cc_start: 0.5446 (tmm) cc_final: 0.5029 (pmm) REVERT: F 415 MET cc_start: 0.9280 (tpp) cc_final: 0.9071 (ppp) REVERT: a 25 MET cc_start: 0.6162 (pmm) cc_final: 0.5332 (tmm) REVERT: a 54 VAL cc_start: 0.6021 (OUTLIER) cc_final: 0.5628 (p) REVERT: b 75 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8729 (pm20) REVERT: c 13 TYR cc_start: 0.7927 (t80) cc_final: 0.7383 (t80) REVERT: c 59 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6684 (pp20) REVERT: c 65 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8380 (mm) REVERT: d 6 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8318 (mm-40) REVERT: d 47 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7296 (mtmm) REVERT: d 51 TYR cc_start: 0.8612 (m-80) cc_final: 0.8295 (m-80) REVERT: d 64 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7574 (mtp-110) outliers start: 94 outliers final: 68 residues processed: 415 average time/residue: 0.3340 time to fit residues: 219.8209 Evaluate side-chains 416 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 340 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 381 TRP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 117 ASN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain a residue 43 LEU Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain b residue 23 HIS Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 30 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 65 LEU Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Chi-restraints excluded: chain e residue 52 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 266 optimal weight: 0.1980 chunk 31 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 232 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 275 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23310 Z= 0.265 Angle : 0.644 12.747 31407 Z= 0.313 Chirality : 0.043 0.181 3597 Planarity : 0.004 0.059 4097 Dihedral : 4.148 21.402 3160 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.69 % Allowed : 22.88 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.53 (0.16), residues: 2896 helix: 1.26 (0.15), residues: 1215 sheet: -0.13 (0.25), residues: 404 loop : -0.28 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 381 HIS 0.007 0.001 HIS A 295 PHE 0.019 0.001 PHE F 398 TYR 0.017 0.001 TYR B 332 ARG 0.007 0.000 ARG C 109 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 351 time to evaluate : 2.976 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 415 MET cc_start: 0.9199 (ppp) cc_final: 0.8867 (ppp) REVERT: D 320 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8956 (mm) REVERT: E 21 MET cc_start: 0.8871 (ppp) cc_final: 0.8446 (ppp) REVERT: E 193 GLN cc_start: 0.8876 (tm-30) cc_final: 0.8618 (tm-30) REVERT: E 298 LYS cc_start: 0.8498 (tptt) cc_final: 0.8275 (tptp) REVERT: F 30 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8546 (tpp80) REVERT: F 110 TYR cc_start: 0.8908 (p90) cc_final: 0.8460 (p90) REVERT: F 390 MET cc_start: 0.5444 (tmm) cc_final: 0.5033 (pmm) REVERT: F 415 MET cc_start: 0.9267 (tpp) cc_final: 0.9061 (ppp) REVERT: a 17 GLU cc_start: 0.7776 (mt-10) cc_final: 0.6853 (tm-30) REVERT: a 54 VAL cc_start: 0.6018 (OUTLIER) cc_final: 0.5633 (p) REVERT: b 75 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8741 (pm20) REVERT: c 59 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.6832 (pp20) REVERT: c 65 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8439 (mm) REVERT: d 47 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7274 (mtmm) REVERT: d 51 TYR cc_start: 0.8624 (m-80) cc_final: 0.8302 (m-80) REVERT: d 64 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7633 (mtp-110) outliers start: 93 outliers final: 73 residues processed: 418 average time/residue: 0.3250 time to fit residues: 213.4696 Evaluate side-chains 429 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 349 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 186 MET Chi-restraints excluded: chain C residue 193 GLN Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 TYR Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 117 ASN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain a residue 43 LEU Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain b residue 23 HIS Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain c residue 65 LEU Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 170 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 164 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 175 optimal weight: 7.9990 chunk 187 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 216 optimal weight: 8.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 198 ASN A 306 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS ** b 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23310 Z= 0.198 Angle : 0.654 12.788 31407 Z= 0.313 Chirality : 0.043 0.205 3597 Planarity : 0.004 0.058 4097 Dihedral : 4.092 20.889 3160 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.38 % Allowed : 23.47 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.57 (0.16), residues: 2896 helix: 1.30 (0.15), residues: 1221 sheet: -0.11 (0.26), residues: 403 loop : -0.26 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 381 HIS 0.004 0.001 HIS d 73 PHE 0.023 0.001 PHE F 398 TYR 0.020 0.001 TYR d 13 ARG 0.012 0.000 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 360 time to evaluate : 2.831 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: A 1 MET cc_start: 0.7197 (ppp) cc_final: 0.6068 (ppp) REVERT: A 56 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7245 (tm-30) REVERT: A 353 ARG cc_start: 0.8075 (mmm160) cc_final: 0.7661 (mmp-170) REVERT: A 415 MET cc_start: 0.9196 (ppp) cc_final: 0.8870 (ppp) REVERT: C 221 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7336 (mtt90) REVERT: D 320 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8941 (mm) REVERT: D 329 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7909 (tm-30) REVERT: E 21 MET cc_start: 0.8921 (ppp) cc_final: 0.8533 (ppp) REVERT: E 193 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8611 (tm-30) REVERT: F 110 TYR cc_start: 0.8918 (p90) cc_final: 0.8455 (p90) REVERT: F 390 MET cc_start: 0.5428 (tmm) cc_final: 0.5014 (pmm) REVERT: a 17 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7078 (tm-30) REVERT: a 54 VAL cc_start: 0.5947 (OUTLIER) cc_final: 0.5571 (p) REVERT: b 75 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8752 (pm20) REVERT: c 59 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.6801 (pp20) REVERT: c 61 ARG cc_start: 0.7837 (ptm-80) cc_final: 0.7081 (ptm-80) REVERT: d 51 TYR cc_start: 0.8647 (m-80) cc_final: 0.8336 (m-80) REVERT: d 64 ARG cc_start: 0.7970 (mtm180) cc_final: 0.7584 (mtp-110) outliers start: 85 outliers final: 70 residues processed: 420 average time/residue: 0.3327 time to fit residues: 219.0744 Evaluate side-chains 411 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 336 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 221 ARG Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 274 TYR Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 117 ASN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain a residue 23 HIS Chi-restraints excluded: chain a residue 43 LEU Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain b residue 23 HIS Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 75 GLU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 250 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 242 optimal weight: 20.0000 chunk 255 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 198 ASN D 374 GLN E 85 GLN E 120 ASN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 23310 Z= 0.525 Angle : 0.792 13.835 31407 Z= 0.392 Chirality : 0.046 0.313 3597 Planarity : 0.005 0.064 4097 Dihedral : 4.558 22.121 3160 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.65 % Allowed : 23.63 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.18 (0.15), residues: 2896 helix: 0.91 (0.15), residues: 1226 sheet: -0.45 (0.25), residues: 422 loop : -0.34 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 381 HIS 0.008 0.001 HIS d 73 PHE 0.022 0.002 PHE F 398 TYR 0.022 0.002 TYR e 51 ARG 0.012 0.001 ARG A 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 343 time to evaluate : 2.793 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 56 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7309 (tm-30) REVERT: A 353 ARG cc_start: 0.8250 (mmm160) cc_final: 0.7963 (mmp-170) REVERT: A 415 MET cc_start: 0.9212 (ppp) cc_final: 0.8885 (ppp) REVERT: D 320 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9006 (mm) REVERT: E 21 MET cc_start: 0.8761 (ppp) cc_final: 0.8555 (ppp) REVERT: E 390 MET cc_start: 0.8829 (pmm) cc_final: 0.8589 (pmm) REVERT: F 110 TYR cc_start: 0.8935 (p90) cc_final: 0.8472 (p90) REVERT: F 390 MET cc_start: 0.5329 (tmm) cc_final: 0.4946 (pmm) REVERT: a 54 VAL cc_start: 0.6034 (OUTLIER) cc_final: 0.5643 (p) REVERT: b 67 LYS cc_start: 0.9379 (mtmm) cc_final: 0.9134 (pttp) REVERT: b 75 GLU cc_start: 0.9150 (pm20) cc_final: 0.8822 (pm20) REVERT: c 13 TYR cc_start: 0.7847 (t80) cc_final: 0.7518 (t80) REVERT: c 59 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.6689 (pp20) REVERT: c 61 ARG cc_start: 0.8032 (ptm-80) cc_final: 0.7283 (ptm-80) REVERT: d 51 TYR cc_start: 0.8671 (m-80) cc_final: 0.8422 (m-80) REVERT: d 64 ARG cc_start: 0.8071 (mtm180) cc_final: 0.7663 (mtp-110) outliers start: 92 outliers final: 75 residues processed: 414 average time/residue: 0.3254 time to fit residues: 212.3956 Evaluate side-chains 412 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 334 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 117 ASN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain a residue 23 HIS Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 12 ASP Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 47 LYS Chi-restraints excluded: chain d residue 79 VAL Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 20 CYS Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 168 optimal weight: 0.8980 chunk 271 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 284 optimal weight: 9.9990 chunk 262 optimal weight: 0.9980 chunk 226 optimal weight: 4.9990 chunk 23 optimal weight: 0.0020 chunk 175 optimal weight: 4.9990 chunk 139 optimal weight: 0.9980 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 374 GLN E 85 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 15 ASN ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 23 HIS ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23310 Z= 0.188 Angle : 0.711 13.934 31407 Z= 0.339 Chirality : 0.044 0.278 3597 Planarity : 0.004 0.060 4097 Dihedral : 4.265 22.496 3160 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.82 % Allowed : 24.90 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.41 (0.16), residues: 2896 helix: 1.16 (0.15), residues: 1215 sheet: -0.31 (0.25), residues: 411 loop : -0.29 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 381 HIS 0.007 0.001 HIS b 22 PHE 0.029 0.001 PHE F 398 TYR 0.021 0.002 TYR e 13 ARG 0.015 0.000 ARG A 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5792 Ramachandran restraints generated. 2896 Oldfield, 0 Emsley, 2896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 363 time to evaluate : 2.623 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: A 353 ARG cc_start: 0.8206 (mmm160) cc_final: 0.7962 (mmp-170) REVERT: A 415 MET cc_start: 0.9122 (ppp) cc_final: 0.8808 (ppp) REVERT: B 322 ASP cc_start: 0.7814 (t70) cc_final: 0.7508 (t0) REVERT: D 320 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8892 (mm) REVERT: E 21 MET cc_start: 0.8828 (ppp) cc_final: 0.8444 (ppp) REVERT: F 110 TYR cc_start: 0.8907 (p90) cc_final: 0.8440 (p90) REVERT: F 322 ASP cc_start: 0.9036 (m-30) cc_final: 0.8573 (t70) REVERT: F 390 MET cc_start: 0.5318 (tmm) cc_final: 0.4935 (pmm) REVERT: b 17 GLU cc_start: 0.8521 (pt0) cc_final: 0.8300 (pt0) REVERT: b 67 LYS cc_start: 0.9360 (mtmm) cc_final: 0.9139 (pttp) REVERT: b 68 ILE cc_start: 0.9077 (mm) cc_final: 0.8717 (mm) REVERT: b 75 GLU cc_start: 0.9126 (pm20) cc_final: 0.8809 (pm20) REVERT: c 59 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.6869 (pp20) REVERT: d 51 TYR cc_start: 0.8558 (m-80) cc_final: 0.8215 (m-80) REVERT: d 64 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7608 (mtp-110) outliers start: 71 outliers final: 63 residues processed: 414 average time/residue: 0.3266 time to fit residues: 211.0957 Evaluate side-chains 417 residues out of total 2518 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 352 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 52 ASP Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 410 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 410 ASP Chi-restraints excluded: chain D residue 418 ARG Chi-restraints excluded: chain E residue 52 ASP Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 394 ASP Chi-restraints excluded: chain E residue 401 ASN Chi-restraints excluded: chain E residue 410 ASP Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 117 ASN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 197 TYR Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 318 THR Chi-restraints excluded: chain F residue 353 ARG Chi-restraints excluded: chain F residue 354 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain a residue 23 HIS Chi-restraints excluded: chain b residue 23 HIS Chi-restraints excluded: chain b residue 24 LEU Chi-restraints excluded: chain b residue 79 VAL Chi-restraints excluded: chain c residue 59 GLU Chi-restraints excluded: chain d residue 15 ASN Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain e residue 27 THR Chi-restraints excluded: chain e residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 180 optimal weight: 3.9990 chunk 241 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 GLN D 374 GLN ** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 9 ASN d 23 HIS ** e 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.106761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.072402 restraints weight = 73778.076| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.39 r_work: 0.3076 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23310 Z= 0.228 Angle : 0.702 13.848 31407 Z= 0.338 Chirality : 0.044 0.269 3597 Planarity : 0.004 0.059 4097 Dihedral : 4.209 23.430 3160 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.78 % Allowed : 24.82 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.18 % 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: 0.46 (0.16), residues: 2896 helix: 1.19 (0.15), residues: 1215 sheet: -0.20 (0.25), residues: 407 loop : -0.29 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 381 HIS 0.005 0.001 HIS d 73 PHE 0.027 0.001 PHE F 398 TYR 0.044 0.002 TYR c 13 ARG 0.014 0.000 ARG A 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5482.77 seconds wall clock time: 98 minutes 18.85 seconds (5898.85 seconds total)