Starting phenix.real_space_refine on Wed Feb 14 12:58:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiu_33864/02_2024/7yiu_33864_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiu_33864/02_2024/7yiu_33864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiu_33864/02_2024/7yiu_33864.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiu_33864/02_2024/7yiu_33864.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiu_33864/02_2024/7yiu_33864_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yiu_33864/02_2024/7yiu_33864_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 52 5.16 5 C 5994 2.51 5 N 1561 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 369": "OD1" <-> "OD2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B GLU 464": "OE1" <-> "OE2" Residue "B ASP 465": "OD1" <-> "OD2" Residue "B ARG 489": "NH1" <-> "NH2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B ARG 541": "NH1" <-> "NH2" Residue "E TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A ASP 150": "OD1" <-> "OD2" Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A ARG 445": "NH1" <-> "NH2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 458": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A GLU 466": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9285 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 3940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3940 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 481} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 341 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1236 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "C" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 411 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain: "A" Number of atoms: 3285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3285 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 401} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {'6CM': 1, 'R16': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 5.50, per 1000 atoms: 0.59 Number of scatterers: 9285 At special positions: 0 Unit cell: (91.8, 85.32, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 1 15.00 O 1677 8.00 N 1561 7.00 C 5994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 2.0 seconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 5 sheets defined 38.2% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'B' and resid 68 through 72 Processing helix chain 'B' and resid 74 through 92 removed outlier: 3.610A pdb=" N LEU B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 88 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.717A pdb=" N GLU B 220 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 264 through 273 removed outlier: 3.630A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.643A pdb=" N ALA B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 330 No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 394 through 397 No H-bonds generated for 'chain 'B' and resid 394 through 397' Processing helix chain 'B' and resid 403 through 407 Processing helix chain 'B' and resid 413 through 426 removed outlier: 3.524A pdb=" N GLN B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 426 " --> pdb=" O SER B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 454 removed outlier: 3.633A pdb=" N CYS B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 444 " --> pdb=" O GLN B 440 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B 445 " --> pdb=" O GLN B 441 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 489 removed outlier: 4.326A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 481 " --> pdb=" O ALA B 477 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 484 " --> pdb=" O GLY B 480 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 487 " --> pdb=" O GLY B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 534 Processing helix chain 'E' and resid 11 through 15 Processing helix chain 'E' and resid 22 through 39 removed outlier: 3.543A pdb=" N LEU E 27 " --> pdb=" O TYR E 23 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP E 34 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 27 through 37 removed outlier: 3.519A pdb=" N VAL D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 65 removed outlier: 3.672A pdb=" N ASN D 53 " --> pdb=" O TRP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 removed outlier: 6.119A pdb=" N ASP D 90 " --> pdb=" O TRP D 86 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TYR D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 115 removed outlier: 3.595A pdb=" N PHE D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) Proline residue: D 106 - end of helix removed outlier: 3.531A pdb=" N THR D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 135 removed outlier: 3.991A pdb=" N LEU D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN D 127 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL D 129 " --> pdb=" O VAL D 125 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER D 133 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 134 " --> pdb=" O SER D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 142 No H-bonds generated for 'chain 'D' and resid 140 through 142' Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'C' and resid 10 through 13 No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 15 through 23 Processing helix chain 'C' and resid 31 through 45 removed outlier: 3.636A pdb=" N VAL C 36 " --> pdb=" O TRP C 32 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 50 No H-bonds generated for 'chain 'C' and resid 47 through 50' Processing helix chain 'A' and resid 54 through 63 removed outlier: 3.811A pdb=" N GLU A 58 " --> pdb=" O VAL A 54 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 125 removed outlier: 3.847A pdb=" N ALA A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.583A pdb=" N ASP A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 214 through 226 removed outlier: 3.678A pdb=" N GLU A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.811A pdb=" N LYS A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 297 through 299 No H-bonds generated for 'chain 'A' and resid 297 through 299' Processing helix chain 'A' and resid 322 through 327 removed outlier: 5.071A pdb=" N HIS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.673A pdb=" N ALA A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 365 through 368 No H-bonds generated for 'chain 'A' and resid 365 through 368' Processing helix chain 'A' and resid 405 through 420 Processing helix chain 'A' and resid 454 through 466 removed outlier: 3.530A pdb=" N THR A 463 " --> pdb=" O ARG A 459 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.445A pdb=" N LEU B 255 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU B 313 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 257 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N GLU B 315 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N ASP B 259 " --> pdb=" O GLU B 315 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR B 276 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N SER B 258 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ARG B 278 " --> pdb=" O SER B 258 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 470 through 472 removed outlier: 3.838A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 92 through 94 Processing sheet with id= D, first strand: chain 'A' and resid 160 through 164 removed outlier: 3.611A pdb=" N GLY A 316 " --> pdb=" O TYR A 164 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 184 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL A 243 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 186 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP A 205 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL A 187 " --> pdb=" O ASP A 205 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS A 207 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 383 through 386 removed outlier: 3.520A pdb=" N VAL A 386 " --> pdb=" O HIS A 395 " (cutoff:3.500A) 221 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.32 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2778 1.33 - 1.45: 1310 1.45 - 1.57: 5308 1.57 - 1.69: 1 1.69 - 1.81: 87 Bond restraints: 9484 Sorted by residual: bond pdb=" C2 PLP B 601 " pdb=" C3 PLP B 601 " ideal model delta sigma weight residual 1.390 1.485 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C4 PLP B 601 " pdb=" C5 PLP B 601 " ideal model delta sigma weight residual 1.390 1.482 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C3 PLP B 601 " pdb=" C4 PLP B 601 " ideal model delta sigma weight residual 1.390 1.480 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C PHE B 498 " pdb=" O PHE B 498 " ideal model delta sigma weight residual 1.244 1.212 0.032 9.10e-03 1.21e+04 1.21e+01 bond pdb=" CA ASN B 120 " pdb=" CB ASN B 120 " ideal model delta sigma weight residual 1.532 1.565 -0.032 1.53e-02 4.27e+03 4.51e+00 ... (remaining 9479 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.50: 258 106.50 - 113.39: 5064 113.39 - 120.28: 3424 120.28 - 127.17: 3989 127.17 - 134.06: 84 Bond angle restraints: 12819 Sorted by residual: angle pdb=" N LYS B 168 " pdb=" CA LYS B 168 " pdb=" C LYS B 168 " ideal model delta sigma weight residual 111.02 119.68 -8.66 1.22e+00 6.72e-01 5.04e+01 angle pdb=" N GLY B 497 " pdb=" CA GLY B 497 " pdb=" C GLY B 497 " ideal model delta sigma weight residual 112.60 121.63 -9.03 1.43e+00 4.89e-01 3.98e+01 angle pdb=" N PRO A 78 " pdb=" CA PRO A 78 " pdb=" CB PRO A 78 " ideal model delta sigma weight residual 103.33 110.19 -6.86 1.10e+00 8.26e-01 3.89e+01 angle pdb=" C GLN B 300 " pdb=" N PRO B 301 " pdb=" CA PRO B 301 " ideal model delta sigma weight residual 119.84 127.47 -7.63 1.25e+00 6.40e-01 3.73e+01 angle pdb=" N MET B 456 " pdb=" CA MET B 456 " pdb=" C MET B 456 " ideal model delta sigma weight residual 113.41 106.08 7.33 1.22e+00 6.72e-01 3.61e+01 ... (remaining 12814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4763 17.64 - 35.28: 549 35.28 - 52.91: 274 52.91 - 70.55: 84 70.55 - 88.19: 10 Dihedral angle restraints: 5680 sinusoidal: 2304 harmonic: 3376 Sorted by residual: dihedral pdb=" C ASN B 120 " pdb=" N ASN B 120 " pdb=" CA ASN B 120 " pdb=" CB ASN B 120 " ideal model delta harmonic sigma weight residual -122.60 -137.95 15.35 0 2.50e+00 1.60e-01 3.77e+01 dihedral pdb=" N ASN B 120 " pdb=" C ASN B 120 " pdb=" CA ASN B 120 " pdb=" CB ASN B 120 " ideal model delta harmonic sigma weight residual 122.80 136.47 -13.67 0 2.50e+00 1.60e-01 2.99e+01 dihedral pdb=" N LEU A 111 " pdb=" C LEU A 111 " pdb=" CA LEU A 111 " pdb=" CB LEU A 111 " ideal model delta harmonic sigma weight residual 122.80 133.25 -10.45 0 2.50e+00 1.60e-01 1.75e+01 ... (remaining 5677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1248 0.098 - 0.196: 163 0.196 - 0.294: 14 0.294 - 0.392: 3 0.392 - 0.490: 2 Chirality restraints: 1430 Sorted by residual: chirality pdb=" CA ASN B 120 " pdb=" N ASN B 120 " pdb=" C ASN B 120 " pdb=" CB ASN B 120 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" CA LEU A 111 " pdb=" N LEU A 111 " pdb=" C LEU A 111 " pdb=" CB LEU A 111 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" CA LYS B 168 " pdb=" N LYS B 168 " pdb=" C LYS B 168 " pdb=" CB LYS B 168 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 1427 not shown) Planarity restraints: 1622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C19 6CM D 801 " -0.084 2.00e-02 2.50e+03 2.81e-01 9.90e+02 pdb=" C2 6CM D 801 " 0.331 2.00e-02 2.50e+03 pdb=" C20 6CM D 801 " 0.171 2.00e-02 2.50e+03 pdb=" N2 6CM D 801 " -0.495 2.00e-02 2.50e+03 pdb=" O19 6CM D 801 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 501 " -0.059 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO B 502 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 502 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 502 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 501 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.34e+00 pdb=" C THR B 501 " -0.036 2.00e-02 2.50e+03 pdb=" O THR B 501 " 0.014 2.00e-02 2.50e+03 pdb=" N PRO B 502 " 0.012 2.00e-02 2.50e+03 ... (remaining 1619 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 32 2.53 - 3.12: 6284 3.12 - 3.71: 13074 3.71 - 4.31: 20151 4.31 - 4.90: 33862 Nonbonded interactions: 73403 Sorted by model distance: nonbonded pdb=" O THR B 66 " pdb=" NH1 ARG D 20 " model vdw 1.932 2.520 nonbonded pdb=" NH2 ARG A 151 " pdb=" OD1 ASN A 354 " model vdw 1.966 2.520 nonbonded pdb=" OH TYR A 128 " pdb=" OD1 ASP A 143 " model vdw 1.991 2.440 nonbonded pdb=" O LEU B 473 " pdb=" O SER B 506 " model vdw 2.002 3.040 nonbonded pdb=" O ALA B 201 " pdb=" OG SER B 412 " model vdw 2.011 2.440 ... (remaining 73398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 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: 3.790 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 27.660 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.007 0.095 9484 Z= 0.455 Angle : 1.076 10.505 12819 Z= 0.718 Chirality : 0.070 0.490 1430 Planarity : 0.009 0.281 1622 Dihedral : 19.632 88.187 3520 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 1.21 % Allowed : 6.49 % Favored : 92.30 % Rotamer: Outliers : 16.13 % Allowed : 10.14 % Favored : 73.73 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.20), residues: 1156 helix: -4.19 (0.14), residues: 506 sheet: -1.58 (0.44), residues: 123 loop : -2.41 (0.24), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 32 HIS 0.006 0.001 HIS B 263 PHE 0.025 0.002 PHE A 138 TYR 0.021 0.002 TYR A 166 ARG 0.005 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 127 time to evaluate : 1.099 Fit side-chains REVERT: B 57 ARG cc_start: 0.7612 (mtm110) cc_final: 0.7011 (ptp-170) REVERT: B 68 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8862 (tpt) REVERT: B 92 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8212 (ptt180) REVERT: B 111 PHE cc_start: 0.9408 (OUTLIER) cc_final: 0.9016 (m-80) REVERT: B 150 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: B 165 ASN cc_start: 0.7754 (p0) cc_final: 0.7172 (p0) REVERT: B 190 GLU cc_start: 0.8005 (tt0) cc_final: 0.7755 (tp30) REVERT: B 197 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: B 271 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8267 (mtt-85) REVERT: B 305 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.8053 (mmt-90) REVERT: B 423 MET cc_start: 0.9117 (ttp) cc_final: 0.8830 (ttp) REVERT: B 463 ASN cc_start: 0.8754 (OUTLIER) cc_final: 0.8517 (t0) REVERT: B 475 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.7463 (mtt) REVERT: B 521 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8935 (mp) REVERT: B 543 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6294 (ttm170) REVERT: E 10 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6475 (tm) REVERT: E 13 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7475 (mtp) REVERT: E 15 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7294 (tt0) REVERT: E 37 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6944 (tpt-90) REVERT: E 42 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7752 (mttm) REVERT: D 152 LYS cc_start: 0.8898 (tptm) cc_final: 0.8529 (tmtm) REVERT: C 12 GLN cc_start: 0.7805 (tt0) cc_final: 0.7553 (tt0) REVERT: C 53 TYR cc_start: 0.7671 (t80) cc_final: 0.7449 (t80) REVERT: A 77 HIS cc_start: 0.6181 (OUTLIER) cc_final: 0.5604 (m90) REVERT: A 236 ARG cc_start: 0.8061 (mtm-85) cc_final: 0.7727 (mtt180) REVERT: A 249 MET cc_start: 0.8678 (ttm) cc_final: 0.8459 (ttt) REVERT: A 268 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8861 (mmtp) REVERT: A 287 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8441 (mtt180) REVERT: A 368 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8336 (pp20) REVERT: A 375 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8637 (tttm) REVERT: A 407 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: A 419 CYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8107 (m) REVERT: A 427 THR cc_start: 0.8972 (p) cc_final: 0.8658 (t) REVERT: A 464 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9009 (mt) outliers start: 159 outliers final: 79 residues processed: 251 average time/residue: 1.3072 time to fit residues: 348.9231 Evaluate side-chains 211 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 109 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 161 LYS Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 271 ARG Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 373 MET Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 402 SER Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 454 LYS Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 519 GLU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 526 LYS Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 15 GLN Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 17 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 11 LYS Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 405 ARG Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN B 242 ASN D 7 HIS ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 18 ASN C 38 ASN A 285 HIS A 327 HIS A 407 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9484 Z= 0.194 Angle : 0.612 10.504 12819 Z= 0.325 Chirality : 0.045 0.191 1430 Planarity : 0.005 0.058 1622 Dihedral : 13.610 86.948 1556 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.14 % Favored : 93.77 % Rotamer: Outliers : 7.20 % Allowed : 17.34 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.22), residues: 1156 helix: -2.70 (0.19), residues: 501 sheet: -1.27 (0.45), residues: 126 loop : -2.11 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 134 HIS 0.003 0.001 HIS B 100 PHE 0.018 0.002 PHE B 121 TYR 0.015 0.001 TYR C 50 ARG 0.004 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 117 time to evaluate : 1.064 Fit side-chains REVERT: B 50 GLN cc_start: 0.5765 (OUTLIER) cc_final: 0.5100 (pm20) REVERT: B 57 ARG cc_start: 0.7547 (mtm110) cc_final: 0.6925 (ptp-170) REVERT: B 110 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: B 126 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8246 (mp) REVERT: B 149 MET cc_start: 0.8305 (mtp) cc_final: 0.8104 (mtp) REVERT: B 150 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: B 165 ASN cc_start: 0.7676 (p0) cc_final: 0.7114 (p0) REVERT: B 183 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7714 (ptt90) REVERT: B 190 GLU cc_start: 0.7979 (tt0) cc_final: 0.7771 (tp30) REVERT: B 197 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7410 (tm-30) REVERT: B 440 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7962 (pp30) REVERT: E 18 TYR cc_start: 0.4256 (OUTLIER) cc_final: 0.4005 (t80) REVERT: D 152 LYS cc_start: 0.8895 (tptm) cc_final: 0.8564 (tmtm) REVERT: A 62 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7430 (mm-30) REVERT: A 77 HIS cc_start: 0.6092 (OUTLIER) cc_final: 0.5523 (m90) REVERT: A 236 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7700 (mtt180) REVERT: A 360 PRO cc_start: 0.8898 (Cg_endo) cc_final: 0.8552 (Cg_exo) REVERT: A 368 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8146 (pp20) REVERT: A 427 THR cc_start: 0.8842 (p) cc_final: 0.8564 (t) REVERT: A 464 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8693 (mt) outliers start: 71 outliers final: 37 residues processed: 172 average time/residue: 1.2772 time to fit residues: 234.2943 Evaluate side-chains 158 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 110 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 150 GLU Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 0.0770 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS D 11 ASN A 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9484 Z= 0.269 Angle : 0.604 9.939 12819 Z= 0.314 Chirality : 0.045 0.197 1430 Planarity : 0.004 0.041 1622 Dihedral : 10.451 59.025 1405 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.98 % Allowed : 20.49 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.23), residues: 1156 helix: -1.67 (0.21), residues: 511 sheet: -1.21 (0.45), residues: 126 loop : -1.96 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 94 HIS 0.004 0.001 HIS A 145 PHE 0.018 0.002 PHE A 138 TYR 0.016 0.002 TYR B 342 ARG 0.004 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 110 time to evaluate : 1.168 Fit side-chains REVERT: B 93 TYR cc_start: 0.6645 (OUTLIER) cc_final: 0.6199 (m-80) REVERT: B 149 MET cc_start: 0.8231 (mtp) cc_final: 0.7998 (mtp) REVERT: B 165 ASN cc_start: 0.7546 (p0) cc_final: 0.7062 (p0) REVERT: B 183 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7746 (ptt90) REVERT: B 190 GLU cc_start: 0.8023 (tt0) cc_final: 0.7751 (tp30) REVERT: B 197 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7466 (tm-30) REVERT: B 440 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7868 (pp30) REVERT: E 13 MET cc_start: 0.7965 (mtp) cc_final: 0.7534 (mtt) REVERT: E 18 TYR cc_start: 0.4284 (OUTLIER) cc_final: 0.4062 (t80) REVERT: D 152 LYS cc_start: 0.8988 (tptm) cc_final: 0.8548 (tmtm) REVERT: A 52 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6726 (mm) REVERT: A 77 HIS cc_start: 0.6430 (OUTLIER) cc_final: 0.6024 (m90) REVERT: A 360 PRO cc_start: 0.8900 (Cg_endo) cc_final: 0.8568 (Cg_exo) REVERT: A 368 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8178 (pp20) REVERT: A 464 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8744 (mt) outliers start: 59 outliers final: 32 residues processed: 156 average time/residue: 1.2891 time to fit residues: 214.8787 Evaluate side-chains 145 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 105 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 83 ASN Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN A 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9484 Z= 0.255 Angle : 0.580 10.174 12819 Z= 0.301 Chirality : 0.045 0.195 1430 Planarity : 0.004 0.046 1622 Dihedral : 9.429 59.860 1381 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 5.98 % Allowed : 21.20 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.24), residues: 1156 helix: -1.12 (0.22), residues: 517 sheet: -1.16 (0.46), residues: 130 loop : -1.89 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 134 HIS 0.003 0.001 HIS A 327 PHE 0.017 0.002 PHE A 138 TYR 0.015 0.002 TYR B 342 ARG 0.003 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 103 time to evaluate : 1.145 Fit side-chains REVERT: B 50 GLN cc_start: 0.5719 (OUTLIER) cc_final: 0.5072 (pm20) REVERT: B 93 TYR cc_start: 0.6598 (OUTLIER) cc_final: 0.5996 (m-10) REVERT: B 106 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6843 (tt0) REVERT: B 110 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7569 (m-30) REVERT: B 183 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7733 (ptt90) REVERT: B 190 GLU cc_start: 0.8015 (tt0) cc_final: 0.7748 (tp30) REVERT: B 197 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7479 (tm-30) REVERT: B 440 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7889 (pp30) REVERT: E 13 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7722 (mtt) REVERT: E 18 TYR cc_start: 0.4244 (OUTLIER) cc_final: 0.4019 (t80) REVERT: A 52 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6756 (mm) REVERT: A 58 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: A 62 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7391 (tm-30) REVERT: A 151 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7396 (mtp-110) REVERT: A 277 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8872 (mp) REVERT: A 367 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8258 (ptpp) REVERT: A 368 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8266 (pp20) REVERT: A 464 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8692 (mt) outliers start: 59 outliers final: 30 residues processed: 147 average time/residue: 1.3014 time to fit residues: 204.0017 Evaluate side-chains 145 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 100 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.0870 chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 108 GLN D 11 ASN D 13 ASN D 141 GLN A 77 HIS A 83 ASN A 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9484 Z= 0.236 Angle : 0.561 9.904 12819 Z= 0.291 Chirality : 0.045 0.190 1430 Planarity : 0.004 0.046 1622 Dihedral : 8.789 59.235 1367 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 6.19 % Allowed : 20.69 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.24), residues: 1156 helix: -0.72 (0.23), residues: 514 sheet: -1.02 (0.46), residues: 128 loop : -1.84 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 134 HIS 0.003 0.001 HIS A 327 PHE 0.017 0.001 PHE A 138 TYR 0.014 0.001 TYR B 342 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 101 time to evaluate : 0.958 Fit side-chains REVERT: B 106 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6906 (tt0) REVERT: B 110 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: B 183 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7819 (mtt90) REVERT: B 190 GLU cc_start: 0.8013 (tt0) cc_final: 0.7763 (tp30) REVERT: B 197 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7443 (tm-30) REVERT: B 440 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7884 (pp30) REVERT: B 444 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7199 (mt-10) REVERT: E 13 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7717 (mtt) REVERT: E 18 TYR cc_start: 0.4203 (OUTLIER) cc_final: 0.3959 (t80) REVERT: C 29 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.7909 (mp) REVERT: A 52 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.6796 (mm) REVERT: A 58 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: A 62 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7348 (tm-30) REVERT: A 151 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7454 (mtp-110) REVERT: A 277 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8831 (mp) REVERT: A 360 PRO cc_start: 0.8883 (Cg_endo) cc_final: 0.8585 (Cg_exo) REVERT: A 367 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8244 (ptpp) REVERT: A 368 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8254 (pp20) REVERT: A 464 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8646 (mt) outliers start: 61 outliers final: 33 residues processed: 148 average time/residue: 1.3109 time to fit residues: 206.6116 Evaluate side-chains 147 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 100 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 183 ARG Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN E 15 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN A 77 HIS A 83 ASN A 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9484 Z= 0.281 Angle : 0.587 9.652 12819 Z= 0.303 Chirality : 0.046 0.191 1430 Planarity : 0.004 0.048 1622 Dihedral : 8.798 59.880 1367 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 6.80 % Allowed : 19.88 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.24), residues: 1156 helix: -0.60 (0.23), residues: 523 sheet: -1.02 (0.47), residues: 127 loop : -1.88 (0.25), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 134 HIS 0.003 0.001 HIS A 327 PHE 0.019 0.002 PHE A 138 TYR 0.015 0.002 TYR B 342 ARG 0.003 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 103 time to evaluate : 1.069 Fit side-chains REVERT: B 93 TYR cc_start: 0.6600 (OUTLIER) cc_final: 0.5993 (m-80) REVERT: B 106 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6976 (tt0) REVERT: B 110 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: B 190 GLU cc_start: 0.7996 (tt0) cc_final: 0.7764 (tp30) REVERT: B 197 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7474 (tm-30) REVERT: B 252 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8215 (tttm) REVERT: B 305 ARG cc_start: 0.8308 (mmt-90) cc_final: 0.8071 (mmt-90) REVERT: B 440 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7835 (pp30) REVERT: B 444 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7215 (mt-10) REVERT: E 13 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7733 (mtt) REVERT: E 18 TYR cc_start: 0.4213 (OUTLIER) cc_final: 0.3971 (t80) REVERT: C 29 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.7922 (mp) REVERT: A 52 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.6817 (mm) REVERT: A 58 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: A 62 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7326 (tm-30) REVERT: A 151 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7474 (mtp-110) REVERT: A 277 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8824 (mp) REVERT: A 360 PRO cc_start: 0.8888 (Cg_endo) cc_final: 0.8591 (Cg_exo) REVERT: A 367 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8240 (ptpp) REVERT: A 368 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8249 (pp20) REVERT: A 423 SER cc_start: 0.8049 (m) cc_final: 0.7715 (t) REVERT: A 464 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8644 (mt) outliers start: 67 outliers final: 35 residues processed: 154 average time/residue: 1.2872 time to fit residues: 211.2845 Evaluate side-chains 151 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 101 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 44 TYR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 72 PHE Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 0.0770 chunk 62 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 109 optimal weight: 0.0270 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 GLN B 108 GLN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN D 141 GLN A 77 HIS A 83 ASN A 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9484 Z= 0.173 Angle : 0.513 8.607 12819 Z= 0.267 Chirality : 0.043 0.178 1430 Planarity : 0.004 0.046 1622 Dihedral : 8.373 58.831 1363 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.17 % Allowed : 22.11 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.24), residues: 1156 helix: -0.19 (0.23), residues: 525 sheet: -0.93 (0.47), residues: 127 loop : -1.75 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 134 HIS 0.002 0.000 HIS A 327 PHE 0.012 0.001 PHE A 138 TYR 0.011 0.001 TYR B 342 ARG 0.001 0.000 ARG A 239 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 108 time to evaluate : 1.039 Fit side-chains REVERT: B 93 TYR cc_start: 0.6596 (OUTLIER) cc_final: 0.5924 (m-80) REVERT: B 106 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6965 (tt0) REVERT: B 165 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.7408 (p0) REVERT: B 190 GLU cc_start: 0.7971 (tt0) cc_final: 0.7765 (tp30) REVERT: B 197 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: B 252 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8191 (tttm) REVERT: B 305 ARG cc_start: 0.8257 (mmt-90) cc_final: 0.8010 (mmt-90) REVERT: B 422 SER cc_start: 0.8891 (p) cc_final: 0.8682 (m) REVERT: B 440 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7935 (pp30) REVERT: B 444 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7283 (mt-10) REVERT: E 13 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7734 (mtt) REVERT: E 18 TYR cc_start: 0.4319 (OUTLIER) cc_final: 0.4055 (t80) REVERT: A 62 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7291 (tm-30) REVERT: A 360 PRO cc_start: 0.8844 (Cg_endo) cc_final: 0.8576 (Cg_exo) REVERT: A 367 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8462 (ptmt) REVERT: A 368 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8256 (pp20) REVERT: A 423 SER cc_start: 0.7955 (m) cc_final: 0.7653 (t) REVERT: A 427 THR cc_start: 0.8842 (p) cc_final: 0.8574 (t) REVERT: A 464 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8630 (mt) outliers start: 51 outliers final: 27 residues processed: 147 average time/residue: 1.3743 time to fit residues: 214.6952 Evaluate side-chains 139 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 101 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 105 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: B 108 GLN D 11 ASN D 141 GLN A 83 ASN A 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9484 Z= 0.219 Angle : 0.538 8.870 12819 Z= 0.278 Chirality : 0.044 0.177 1430 Planarity : 0.004 0.048 1622 Dihedral : 8.161 58.838 1355 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 5.38 % Allowed : 22.01 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.24), residues: 1156 helix: -0.06 (0.23), residues: 526 sheet: -0.94 (0.47), residues: 127 loop : -1.73 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 134 HIS 0.003 0.001 HIS A 327 PHE 0.016 0.001 PHE A 138 TYR 0.013 0.001 TYR B 342 ARG 0.002 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 101 time to evaluate : 1.182 Fit side-chains REVERT: B 93 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5839 (m-80) REVERT: B 106 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6969 (tt0) REVERT: B 110 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: B 197 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: B 252 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8197 (tttm) REVERT: B 305 ARG cc_start: 0.8305 (mmt-90) cc_final: 0.8073 (mmt-90) REVERT: B 440 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7926 (pp30) REVERT: B 444 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 475 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.7114 (mmm) REVERT: E 13 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7750 (mtt) REVERT: E 18 TYR cc_start: 0.4320 (OUTLIER) cc_final: 0.4063 (t80) REVERT: C 29 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.7872 (mp) REVERT: A 52 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6698 (mm) REVERT: A 58 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7728 (mt-10) REVERT: A 62 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7281 (tm-30) REVERT: A 277 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8895 (mp) REVERT: A 360 PRO cc_start: 0.8858 (Cg_endo) cc_final: 0.8579 (Cg_exo) REVERT: A 367 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8462 (ptmt) REVERT: A 368 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8248 (pp20) REVERT: A 423 SER cc_start: 0.7908 (m) cc_final: 0.7609 (t) REVERT: A 427 THR cc_start: 0.8868 (p) cc_final: 0.8574 (t) REVERT: A 464 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8687 (mt) outliers start: 53 outliers final: 30 residues processed: 142 average time/residue: 1.3485 time to fit residues: 203.9566 Evaluate side-chains 144 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 98 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 425 CYS Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 GLN Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 475 MET Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.0020 chunk 102 optimal weight: 0.2980 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 0.0670 chunk 44 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 92 optimal weight: 0.0980 chunk 67 optimal weight: 0.0470 chunk 108 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 GLN D 11 ASN ** D 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN A 83 ASN A 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9484 Z= 0.119 Angle : 0.466 9.006 12819 Z= 0.243 Chirality : 0.041 0.163 1430 Planarity : 0.003 0.041 1622 Dihedral : 7.488 59.186 1355 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.14 % Allowed : 24.34 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.25), residues: 1156 helix: 0.57 (0.24), residues: 525 sheet: -0.73 (0.48), residues: 127 loop : -1.50 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 32 HIS 0.002 0.000 HIS A 91 PHE 0.010 0.001 PHE B 121 TYR 0.007 0.001 TYR E 23 ARG 0.001 0.000 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.046 Fit side-chains REVERT: B 93 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.6145 (m-80) REVERT: B 185 THR cc_start: 0.8322 (p) cc_final: 0.8066 (t) REVERT: B 252 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8159 (tttm) REVERT: B 305 ARG cc_start: 0.8224 (mmt-90) cc_final: 0.7989 (mmt-90) REVERT: E 13 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7740 (mtt) REVERT: E 18 TYR cc_start: 0.4530 (OUTLIER) cc_final: 0.4245 (t80) REVERT: D 9 GLU cc_start: 0.7721 (tp30) cc_final: 0.7278 (tp30) REVERT: D 152 LYS cc_start: 0.9059 (tptm) cc_final: 0.8755 (tmtm) REVERT: C 23 VAL cc_start: 0.8388 (t) cc_final: 0.8187 (t) REVERT: C 29 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.7716 (mp) REVERT: A 52 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6560 (mm) REVERT: A 58 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: A 62 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7262 (tm-30) REVERT: A 106 PHE cc_start: 0.8922 (m-80) cc_final: 0.8701 (m-80) REVERT: A 367 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8463 (ptmt) REVERT: A 368 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8251 (pp20) REVERT: A 464 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8577 (mt) outliers start: 31 outliers final: 14 residues processed: 137 average time/residue: 1.3855 time to fit residues: 201.7661 Evaluate side-chains 130 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 13 MET Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 0.0020 chunk 27 optimal weight: 4.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS D 11 ASN D 127 ASN A 83 ASN A 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9484 Z= 0.200 Angle : 0.533 8.685 12819 Z= 0.272 Chirality : 0.044 0.174 1430 Planarity : 0.004 0.075 1622 Dihedral : 7.174 59.736 1344 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.54 % Allowed : 25.56 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1156 helix: 0.53 (0.24), residues: 535 sheet: -0.80 (0.48), residues: 127 loop : -1.49 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 134 HIS 0.003 0.001 HIS A 327 PHE 0.014 0.001 PHE A 138 TYR 0.011 0.001 TYR B 342 ARG 0.002 0.000 ARG A 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 99 time to evaluate : 1.067 Fit side-chains REVERT: B 93 TYR cc_start: 0.6502 (OUTLIER) cc_final: 0.5859 (m-80) REVERT: B 185 THR cc_start: 0.8421 (p) cc_final: 0.8153 (t) REVERT: B 252 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8167 (tttm) REVERT: B 305 ARG cc_start: 0.8230 (mmt-90) cc_final: 0.7994 (mmt-90) REVERT: E 13 MET cc_start: 0.8138 (mtp) cc_final: 0.7776 (mtt) REVERT: E 18 TYR cc_start: 0.4370 (OUTLIER) cc_final: 0.4112 (t80) REVERT: D 152 LYS cc_start: 0.9117 (tptm) cc_final: 0.8811 (tmtm) REVERT: C 29 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.7817 (mp) REVERT: A 52 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6742 (mm) REVERT: A 62 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7269 (tm-30) REVERT: A 367 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8512 (ptmt) REVERT: A 464 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8608 (mt) outliers start: 25 outliers final: 13 residues processed: 119 average time/residue: 1.3002 time to fit residues: 165.1700 Evaluate side-chains 118 residues out of total 999 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 TYR Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 189 GLN Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 496 VAL Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 18 TYR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 3.9990 chunk 13 optimal weight: 0.0370 chunk 25 optimal weight: 0.0030 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 65 optimal weight: 3.9990 overall best weight: 0.3426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS D 11 ASN D 57 ASN A 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.089546 restraints weight = 11951.446| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.78 r_work: 0.2791 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2672 r_free = 0.2672 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9484 Z= 0.125 Angle : 0.489 11.167 12819 Z= 0.248 Chirality : 0.042 0.166 1430 Planarity : 0.004 0.059 1622 Dihedral : 6.669 57.870 1341 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.93 % Allowed : 26.17 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.26), residues: 1156 helix: 0.88 (0.24), residues: 529 sheet: -0.73 (0.48), residues: 127 loop : -1.36 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 32 HIS 0.001 0.000 HIS A 91 PHE 0.010 0.001 PHE B 121 TYR 0.007 0.001 TYR B 342 ARG 0.001 0.000 ARG B 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.73 seconds wall clock time: 69 minutes 9.19 seconds (4149.19 seconds total)