Starting phenix.real_space_refine on Fri Mar 15 06:22:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ovb_13083/03_2024/7ovb_13083.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ovb_13083/03_2024/7ovb_13083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ovb_13083/03_2024/7ovb_13083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ovb_13083/03_2024/7ovb_13083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ovb_13083/03_2024/7ovb_13083.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ovb_13083/03_2024/7ovb_13083.pdb" } resolution = 3.61 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= 1.000 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 Zn 1 6.06 5 S 48 5.16 5 C 6889 2.51 5 N 1870 2.21 5 O 2046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 112": "NH1" <-> "NH2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 161": "OD1" <-> "OD2" Residue "A TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ASP 286": "OD1" <-> "OD2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A ARG 570": "NH1" <-> "NH2" Residue "A PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "B ASP 148": "OD1" <-> "OD2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "C ARG 30": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ASP 156": "OD1" <-> "OD2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D ARG 171": "NH1" <-> "NH2" Residue "D PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 197": "OD1" <-> "OD2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ARG 282": "NH1" <-> "NH2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 86": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10854 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3665 Classifications: {'peptide': 473} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 19, 'TRANS': 453} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2085 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 241} Chain: "C" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1615 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 197} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2284 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 275} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1204 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 74} Link IDs: {'PTRANS': 5, 'TRANS': 182} Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 197 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 117 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6091 SG CYS C 46 68.490 32.143 59.833 1.00 53.64 S ATOM 6117 SG CYS C 49 71.848 32.551 59.854 1.00 45.97 S ATOM 6346 SG CYS C 78 70.020 35.728 59.140 1.00 54.09 S ATOM 6369 SG CYS C 81 70.418 33.055 56.514 1.00 52.98 S Time building chain proxies: 6.33, per 1000 atoms: 0.58 Number of scatterers: 10854 At special positions: 0 Unit cell: (142.8, 111.3, 124.95, 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) Zn 1 29.99 S 48 16.00 O 2046 8.00 N 1870 7.00 C 6889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 49 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 78 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 46 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 81 " Number of angles added : 6 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 4 sheets defined 57.1% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.810A pdb=" N THR A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.543A pdb=" N SER A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 removed outlier: 3.674A pdb=" N ARG A 177 " --> pdb=" O PHE A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 218 through 228 removed outlier: 3.816A pdb=" N VAL A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 262 removed outlier: 3.670A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 removed outlier: 4.169A pdb=" N ASP A 276 " --> pdb=" O ASN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 303 through 316 removed outlier: 4.259A pdb=" N THR A 307 " --> pdb=" O PRO A 303 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Proline residue: A 309 - end of helix removed outlier: 3.608A pdb=" N LEU A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 353 removed outlier: 4.272A pdb=" N GLN A 328 " --> pdb=" O LYS A 324 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N GLN A 335 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LEU A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASP A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 373 Processing helix chain 'A' and resid 387 through 392 Processing helix chain 'A' and resid 395 through 405 removed outlier: 4.053A pdb=" N VAL A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.735A pdb=" N SER A 457 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 476 removed outlier: 4.371A pdb=" N SER A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 487 Processing helix chain 'A' and resid 594 through 615 removed outlier: 3.572A pdb=" N MET A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 615 " --> pdb=" O ILE A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.955A pdb=" N ALA A 634 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 635 " --> pdb=" O ILE A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 658 Processing helix chain 'B' and resid 126 through 134 removed outlier: 3.515A pdb=" N ARG B 131 " --> pdb=" O MET B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.518A pdb=" N VAL B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 141 through 146' Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 196 through 208 removed outlier: 3.842A pdb=" N ARG B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 207 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.878A pdb=" N VAL B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 234 " --> pdb=" O MET B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 252 removed outlier: 3.755A pdb=" N ALA B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 246 " --> pdb=" O ASN B 242 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 271 through 279 Processing helix chain 'B' and resid 283 through 296 removed outlier: 3.626A pdb=" N LEU B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 294 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.823A pdb=" N PHE B 306 " --> pdb=" O SER B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 4.106A pdb=" N VAL B 312 " --> pdb=" O TRP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 321 removed outlier: 3.594A pdb=" N ASN B 321 " --> pdb=" O TRP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 346 Processing helix chain 'B' and resid 356 through 364 removed outlier: 3.504A pdb=" N LEU B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'C' and resid 17 through 28 removed outlier: 4.267A pdb=" N LEU C 21 " --> pdb=" O GLY C 17 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.573A pdb=" N TYR C 34 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 86 Processing helix chain 'C' and resid 108 through 118 removed outlier: 3.951A pdb=" N LEU C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 141 removed outlier: 3.514A pdb=" N GLN C 133 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN C 134 " --> pdb=" O SER C 130 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 138 " --> pdb=" O ASN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.810A pdb=" N PHE C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 166 removed outlier: 3.602A pdb=" N GLN C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET C 164 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 187 through 190 removed outlier: 3.758A pdb=" N LYS C 190 " --> pdb=" O SER C 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 187 through 190' Processing helix chain 'C' and resid 191 through 196 removed outlier: 3.546A pdb=" N GLU C 196 " --> pdb=" O ARG C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 removed outlier: 3.530A pdb=" N GLU C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 30 removed outlier: 3.842A pdb=" N LEU D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 40 Processing helix chain 'D' and resid 50 through 87 removed outlier: 4.235A pdb=" N ILE D 55 " --> pdb=" O HIS D 51 " (cutoff:3.500A) Proline residue: D 56 - end of helix removed outlier: 3.549A pdb=" N ASN D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR D 72 " --> pdb=" O GLN D 68 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 80 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER D 86 " --> pdb=" O ASP D 82 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 87 " --> pdb=" O TYR D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 160 removed outlier: 4.359A pdb=" N THR D 100 " --> pdb=" O GLN D 96 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 101 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU D 102 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N SER D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU D 107 " --> pdb=" O SER D 103 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 181 removed outlier: 3.680A pdb=" N LYS D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 203 removed outlier: 3.597A pdb=" N GLN D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 217 removed outlier: 3.501A pdb=" N LEU D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 265 removed outlier: 3.973A pdb=" N LEU D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE D 236 " --> pdb=" O LYS D 232 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR D 237 " --> pdb=" O LEU D 233 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N HIS D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 262 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU D 263 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 274 through 282 removed outlier: 3.640A pdb=" N ILE D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 286 removed outlier: 3.744A pdb=" N TYR D 286 " --> pdb=" O GLU D 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 283 through 286' Processing helix chain 'E' and resid 8 through 18 Processing helix chain 'E' and resid 22 through 39 Processing helix chain 'E' and resid 43 through 64 Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 79 through 96 removed outlier: 3.556A pdb=" N THR E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 142 Processing helix chain 'E' and resid 170 through 183 Processing sheet with id=AA1, first strand: chain 'A' and resid 117 through 120 removed outlier: 6.333A pdb=" N PHE A 120 " --> pdb=" O PHE A 107 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE A 107 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN A 110 " --> pdb=" O ARG A 570 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A 558 " --> pdb=" O ALA A 569 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS A 492 " --> pdb=" O HIS A 559 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS A 490 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU A 130 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR A 433 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE A 463 " --> pdb=" O TYR A 433 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS A 435 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA A 465 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 437 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE A 158 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR A 159 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 186 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LEU A 380 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE A 188 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 61 removed outlier: 3.676A pdb=" N ASP C 58 " --> pdb=" O ALA C 77 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 99 through 101 450 hydrogen bonds defined for protein. 1305 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: 2.83 Time building geometry restraints manager: 4.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2323 1.32 - 1.45: 2424 1.45 - 1.57: 6214 1.57 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 11041 Sorted by residual: bond pdb=" CA ASP B 236 " pdb=" CB ASP B 236 " ideal model delta sigma weight residual 1.522 1.479 0.043 1.32e-02 5.74e+03 1.07e+01 bond pdb=" CA SER E 79 " pdb=" CB SER E 79 " ideal model delta sigma weight residual 1.526 1.485 0.041 1.26e-02 6.30e+03 1.04e+01 bond pdb=" C PRO E 77 " pdb=" O PRO E 77 " ideal model delta sigma weight residual 1.233 1.200 0.033 1.23e-02 6.61e+03 7.28e+00 bond pdb=" CB TRP E 71 " pdb=" CG TRP E 71 " ideal model delta sigma weight residual 1.498 1.418 0.080 3.10e-02 1.04e+03 6.73e+00 bond pdb=" N SER E 79 " pdb=" CA SER E 79 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.24e-02 6.50e+03 6.48e+00 ... (remaining 11036 not shown) Histogram of bond angle deviations from ideal: 95.60 - 103.34: 127 103.34 - 111.08: 4205 111.08 - 118.82: 4695 118.82 - 126.55: 5788 126.55 - 134.29: 106 Bond angle restraints: 14921 Sorted by residual: angle pdb=" N PRO E 77 " pdb=" CA PRO E 77 " pdb=" C PRO E 77 " ideal model delta sigma weight residual 111.03 100.29 10.74 1.54e+00 4.22e-01 4.87e+01 angle pdb=" C LEU D 85 " pdb=" N SER D 86 " pdb=" CA SER D 86 " ideal model delta sigma weight residual 122.56 115.64 6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" C PHE A 108 " pdb=" N GLY A 109 " pdb=" CA GLY A 109 " ideal model delta sigma weight residual 120.56 114.22 6.34 1.42e+00 4.96e-01 1.99e+01 angle pdb=" C LYS E 52 " pdb=" N ILE E 53 " pdb=" CA ILE E 53 " ideal model delta sigma weight residual 120.64 113.86 6.78 1.64e+00 3.72e-01 1.71e+01 angle pdb=" N ILE D 179 " pdb=" CA ILE D 179 " pdb=" C ILE D 179 " ideal model delta sigma weight residual 113.42 108.76 4.66 1.17e+00 7.31e-01 1.58e+01 ... (remaining 14916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6012 17.78 - 35.57: 615 35.57 - 53.35: 75 53.35 - 71.13: 17 71.13 - 88.92: 21 Dihedral angle restraints: 6740 sinusoidal: 2652 harmonic: 4088 Sorted by residual: dihedral pdb=" CA GLU D 235 " pdb=" C GLU D 235 " pdb=" N PHE D 236 " pdb=" CA PHE D 236 " ideal model delta harmonic sigma weight residual 180.00 -150.15 -29.85 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA GLN D 253 " pdb=" C GLN D 253 " pdb=" N PHE D 254 " pdb=" CA PHE D 254 " ideal model delta harmonic sigma weight residual 180.00 153.08 26.92 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLU A 591 " pdb=" C GLU A 591 " pdb=" N PRO A 592 " pdb=" CA PRO A 592 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 6737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1273 0.067 - 0.134: 372 0.134 - 0.201: 35 0.201 - 0.268: 3 0.268 - 0.335: 2 Chirality restraints: 1685 Sorted by residual: chirality pdb=" CA THR E 78 " pdb=" N THR E 78 " pdb=" C THR E 78 " pdb=" CB THR E 78 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB ILE D 31 " pdb=" CA ILE D 31 " pdb=" CG1 ILE D 31 " pdb=" CG2 ILE D 31 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ARG E 76 " pdb=" N ARG E 76 " pdb=" C ARG E 76 " pdb=" CB ARG E 76 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1682 not shown) Planarity restraints: 1936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 75 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C GLU E 75 " 0.061 2.00e-02 2.50e+03 pdb=" O GLU E 75 " -0.023 2.00e-02 2.50e+03 pdb=" N ARG E 76 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 62 " -0.033 2.00e-02 2.50e+03 2.51e-02 1.10e+01 pdb=" CG PHE E 62 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE E 62 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE E 62 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 62 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 62 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 62 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 19 " -0.007 2.00e-02 2.50e+03 1.79e-02 7.99e+00 pdb=" CG TRP C 19 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP C 19 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C 19 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP C 19 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 19 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 19 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 19 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 19 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 19 " -0.001 2.00e-02 2.50e+03 ... (remaining 1933 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 140 2.55 - 3.14: 9749 3.14 - 3.72: 16082 3.72 - 4.31: 22737 4.31 - 4.90: 36136 Nonbonded interactions: 84844 Sorted by model distance: nonbonded pdb=" O ALA A 150 " pdb=" OG SER A 155 " model vdw 1.960 2.440 nonbonded pdb=" O MET A 175 " pdb=" OG SER A 178 " model vdw 2.038 2.440 nonbonded pdb=" NH2 ARG D 101 " pdb=" OE2 GLU D 102 " model vdw 2.062 2.520 nonbonded pdb=" OH TYR B 283 " pdb=" O LEU B 350 " model vdw 2.070 2.440 nonbonded pdb=" OG SER A 387 " pdb=" OD1 ASP A 389 " model vdw 2.076 2.440 ... (remaining 84839 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.000 Extract box with map and model: 5.910 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 33.050 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.013 0.080 11041 Z= 0.841 Angle : 1.129 11.586 14921 Z= 0.632 Chirality : 0.059 0.335 1685 Planarity : 0.006 0.066 1936 Dihedral : 15.016 88.916 4094 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 0.09 % Allowed : 0.44 % Favored : 99.47 % 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: -4.16 (0.20), residues: 1389 helix: -2.73 (0.16), residues: 711 sheet: -2.05 (0.58), residues: 71 loop : -2.76 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.004 TRP C 19 HIS 0.006 0.002 HIS A 128 PHE 0.055 0.004 PHE E 62 TYR 0.030 0.004 TYR A 433 ARG 0.011 0.001 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.284 Fit side-chains REVERT: A 169 TYR cc_start: 0.8411 (t80) cc_final: 0.8191 (t80) REVERT: A 258 MET cc_start: 0.8032 (tpt) cc_final: 0.7796 (tmm) REVERT: E 29 MET cc_start: 0.7698 (tmm) cc_final: 0.7017 (tmm) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.2166 time to fit residues: 31.9175 Evaluate side-chains 81 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11041 Z= 0.231 Angle : 0.658 12.970 14921 Z= 0.344 Chirality : 0.043 0.172 1685 Planarity : 0.005 0.054 1936 Dihedral : 5.622 23.486 1513 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.35 % Allowed : 8.15 % Favored : 91.50 % 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: -2.94 (0.21), residues: 1389 helix: -1.44 (0.18), residues: 733 sheet: -1.86 (0.58), residues: 70 loop : -2.55 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 317 HIS 0.017 0.002 HIS D 180 PHE 0.040 0.002 PHE E 62 TYR 0.028 0.002 TYR A 313 ARG 0.005 0.001 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.288 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.7867 (tpt) cc_final: 0.7509 (tmm) REVERT: A 372 LEU cc_start: 0.8565 (tp) cc_final: 0.8107 (mt) REVERT: B 248 ASP cc_start: 0.6713 (m-30) cc_final: 0.6439 (m-30) REVERT: B 375 MET cc_start: 0.8390 (tpt) cc_final: 0.7950 (tpp) REVERT: C 79 CYS cc_start: 0.8370 (t) cc_final: 0.8077 (t) outliers start: 4 outliers final: 2 residues processed: 105 average time/residue: 0.2023 time to fit residues: 32.3596 Evaluate side-chains 93 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain D residue 94 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 135 optimal weight: 50.0000 chunk 111 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11041 Z= 0.307 Angle : 0.623 9.825 14921 Z= 0.324 Chirality : 0.043 0.152 1685 Planarity : 0.004 0.048 1936 Dihedral : 5.337 23.017 1513 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.97 % Allowed : 12.40 % Favored : 86.63 % 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: -2.55 (0.22), residues: 1389 helix: -1.01 (0.19), residues: 753 sheet: -1.48 (0.62), residues: 72 loop : -2.62 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.018 0.002 HIS D 180 PHE 0.035 0.002 PHE E 62 TYR 0.026 0.002 TYR A 169 ARG 0.006 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 258 MET cc_start: 0.7883 (tpt) cc_final: 0.7599 (tmm) REVERT: B 248 ASP cc_start: 0.6778 (m-30) cc_final: 0.6526 (m-30) REVERT: B 353 MET cc_start: 0.7383 (mtm) cc_final: 0.7125 (mtp) REVERT: C 79 CYS cc_start: 0.8411 (t) cc_final: 0.8173 (t) REVERT: E 86 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6133 (tp30) outliers start: 11 outliers final: 7 residues processed: 104 average time/residue: 0.1993 time to fit residues: 31.6208 Evaluate side-chains 93 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 53 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 chunk 119 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11041 Z= 0.225 Angle : 0.561 8.858 14921 Z= 0.293 Chirality : 0.041 0.159 1685 Planarity : 0.004 0.042 1936 Dihedral : 4.934 21.649 1513 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.77 % Allowed : 14.44 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.22), residues: 1389 helix: -0.66 (0.19), residues: 739 sheet: -1.26 (0.59), residues: 83 loop : -2.40 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 212 HIS 0.018 0.002 HIS D 180 PHE 0.028 0.001 PHE E 62 TYR 0.041 0.002 TYR A 313 ARG 0.003 0.000 ARG E 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: C 19 TRP cc_start: 0.8731 (t-100) cc_final: 0.8152 (t60) REVERT: C 79 CYS cc_start: 0.8343 (t) cc_final: 0.8120 (t) REVERT: E 53 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7377 (mt) REVERT: E 62 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: E 86 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6292 (tp30) outliers start: 20 outliers final: 8 residues processed: 110 average time/residue: 0.1979 time to fit residues: 33.2174 Evaluate side-chains 98 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 88 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN D 54 GLN ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11041 Z= 0.241 Angle : 0.559 9.373 14921 Z= 0.290 Chirality : 0.041 0.175 1685 Planarity : 0.004 0.041 1936 Dihedral : 4.793 21.498 1513 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.13 % Allowed : 16.21 % Favored : 81.67 % 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: -1.88 (0.22), residues: 1389 helix: -0.46 (0.19), residues: 739 sheet: -1.19 (0.58), residues: 83 loop : -2.27 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 212 HIS 0.018 0.002 HIS D 180 PHE 0.030 0.001 PHE E 62 TYR 0.020 0.002 TYR A 169 ARG 0.004 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 91 time to evaluate : 1.303 Fit side-chains revert: symmetry clash REVERT: A 214 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6638 (pp30) REVERT: A 240 TRP cc_start: 0.4783 (m-10) cc_final: 0.3429 (p90) REVERT: B 319 MET cc_start: 0.8655 (tpp) cc_final: 0.8408 (tpp) REVERT: C 19 TRP cc_start: 0.8762 (t-100) cc_final: 0.8179 (t60) REVERT: E 29 MET cc_start: 0.7670 (tmm) cc_final: 0.7066 (tmm) REVERT: E 62 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: E 86 GLU cc_start: 0.6739 (mm-30) cc_final: 0.6304 (tp30) outliers start: 24 outliers final: 13 residues processed: 109 average time/residue: 0.1936 time to fit residues: 32.4340 Evaluate side-chains 100 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 0.0050 chunk 32 optimal weight: 0.4980 chunk 133 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN D 155 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11041 Z= 0.169 Angle : 0.521 7.874 14921 Z= 0.270 Chirality : 0.040 0.167 1685 Planarity : 0.003 0.038 1936 Dihedral : 4.524 20.597 1513 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.86 % Allowed : 16.56 % Favored : 81.58 % 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: -1.60 (0.23), residues: 1389 helix: -0.27 (0.20), residues: 741 sheet: -1.16 (0.59), residues: 81 loop : -2.07 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 212 HIS 0.004 0.001 HIS A 559 PHE 0.029 0.001 PHE E 62 TYR 0.018 0.001 TYR A 313 ARG 0.003 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.6839 (tpt) cc_final: 0.6527 (tpt) REVERT: B 319 MET cc_start: 0.8598 (tpp) cc_final: 0.8315 (tpp) REVERT: C 19 TRP cc_start: 0.8741 (t-100) cc_final: 0.8296 (t60) REVERT: C 208 ASP cc_start: 0.5445 (t0) cc_final: 0.5144 (p0) REVERT: D 155 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.7104 (m-40) REVERT: E 29 MET cc_start: 0.7681 (tmm) cc_final: 0.7055 (tmm) REVERT: E 62 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7374 (m-80) REVERT: E 86 GLU cc_start: 0.6594 (mm-30) cc_final: 0.6249 (tp30) outliers start: 21 outliers final: 11 residues processed: 110 average time/residue: 0.1974 time to fit residues: 33.4717 Evaluate side-chains 101 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 75 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11041 Z= 0.174 Angle : 0.527 7.797 14921 Z= 0.271 Chirality : 0.040 0.207 1685 Planarity : 0.003 0.038 1936 Dihedral : 4.401 19.995 1513 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.86 % Allowed : 16.92 % Favored : 81.22 % 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: -1.42 (0.23), residues: 1389 helix: -0.09 (0.20), residues: 742 sheet: -0.98 (0.59), residues: 81 loop : -2.05 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 212 HIS 0.004 0.001 HIS A 559 PHE 0.029 0.001 PHE E 62 TYR 0.018 0.001 TYR A 313 ARG 0.003 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 1.414 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.6814 (tpt) cc_final: 0.6608 (tpt) REVERT: A 214 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6588 (pp30) REVERT: A 366 ASP cc_start: 0.7147 (p0) cc_final: 0.6918 (p0) REVERT: B 182 LEU cc_start: 0.8051 (mm) cc_final: 0.7247 (tt) REVERT: B 319 MET cc_start: 0.8600 (tpp) cc_final: 0.8373 (tpp) REVERT: C 19 TRP cc_start: 0.8742 (t-100) cc_final: 0.8338 (t60) REVERT: C 35 GLU cc_start: 0.6252 (tt0) cc_final: 0.6039 (tt0) REVERT: E 29 MET cc_start: 0.7647 (tmm) cc_final: 0.7054 (tmm) REVERT: E 62 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7412 (m-80) REVERT: E 86 GLU cc_start: 0.6579 (mm-30) cc_final: 0.6211 (tp30) outliers start: 21 outliers final: 14 residues processed: 111 average time/residue: 0.1986 time to fit residues: 33.4359 Evaluate side-chains 107 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 0.0020 chunk 40 optimal weight: 0.1980 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 84 optimal weight: 0.0470 chunk 90 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 0.3286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 ASN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11041 Z= 0.148 Angle : 0.514 9.127 14921 Z= 0.263 Chirality : 0.039 0.147 1685 Planarity : 0.003 0.038 1936 Dihedral : 4.249 19.314 1513 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.51 % Allowed : 17.71 % Favored : 80.78 % 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: -1.18 (0.23), residues: 1389 helix: 0.10 (0.20), residues: 744 sheet: -0.69 (0.61), residues: 81 loop : -1.97 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 212 HIS 0.004 0.001 HIS A 559 PHE 0.028 0.001 PHE E 62 TYR 0.019 0.001 TYR A 313 ARG 0.003 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 MET cc_start: 0.6886 (tpt) cc_final: 0.6673 (tpt) REVERT: A 214 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.6757 (pp30) REVERT: A 366 ASP cc_start: 0.7111 (p0) cc_final: 0.6862 (p0) REVERT: B 182 LEU cc_start: 0.7988 (mm) cc_final: 0.7198 (tt) REVERT: C 19 TRP cc_start: 0.8734 (t-100) cc_final: 0.8387 (t60) REVERT: E 29 MET cc_start: 0.7640 (tmm) cc_final: 0.7162 (tmm) REVERT: E 62 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: E 86 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6278 (tp30) outliers start: 17 outliers final: 12 residues processed: 110 average time/residue: 0.2003 time to fit residues: 33.6682 Evaluate side-chains 103 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 131 optimal weight: 30.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11041 Z= 0.196 Angle : 0.534 8.074 14921 Z= 0.273 Chirality : 0.040 0.148 1685 Planarity : 0.003 0.038 1936 Dihedral : 4.253 19.303 1513 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.86 % Allowed : 17.80 % Favored : 80.34 % 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: -1.10 (0.23), residues: 1389 helix: 0.16 (0.20), residues: 745 sheet: -0.47 (0.63), residues: 81 loop : -1.97 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 119 HIS 0.004 0.001 HIS D 51 PHE 0.029 0.001 PHE E 62 TYR 0.028 0.001 TYR A 169 ARG 0.005 0.000 ARG B 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 214 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.6870 (pp30) REVERT: A 366 ASP cc_start: 0.7128 (p0) cc_final: 0.6907 (p0) REVERT: B 182 LEU cc_start: 0.8055 (mm) cc_final: 0.7285 (tt) REVERT: E 29 MET cc_start: 0.7723 (tmm) cc_final: 0.7145 (tmm) REVERT: E 62 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: E 86 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6331 (tp30) outliers start: 21 outliers final: 15 residues processed: 108 average time/residue: 0.1917 time to fit residues: 31.3481 Evaluate side-chains 107 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 90 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 137 optimal weight: 20.0000 chunk 126 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 11 optimal weight: 0.0770 chunk 84 optimal weight: 5.9990 chunk 67 optimal weight: 0.1980 chunk 86 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11041 Z= 0.162 Angle : 0.520 8.110 14921 Z= 0.270 Chirality : 0.040 0.214 1685 Planarity : 0.003 0.037 1936 Dihedral : 4.125 18.956 1513 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.51 % Allowed : 18.33 % Favored : 80.16 % 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: -0.97 (0.23), residues: 1389 helix: 0.28 (0.20), residues: 743 sheet: -0.33 (0.63), residues: 81 loop : -1.95 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 119 HIS 0.004 0.001 HIS A 559 PHE 0.028 0.001 PHE E 62 TYR 0.023 0.001 TYR A 169 ARG 0.003 0.000 ARG A 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2778 Ramachandran restraints generated. 1389 Oldfield, 0 Emsley, 1389 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8236 (mmm) cc_final: 0.7750 (tpp) REVERT: A 214 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6741 (pp30) REVERT: A 366 ASP cc_start: 0.7041 (p0) cc_final: 0.6826 (p0) REVERT: B 182 LEU cc_start: 0.7978 (mm) cc_final: 0.7251 (tt) REVERT: C 76 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8327 (t) REVERT: E 29 MET cc_start: 0.7692 (tmm) cc_final: 0.7216 (tmm) REVERT: E 62 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: E 86 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6313 (tp30) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.1961 time to fit residues: 31.9430 Evaluate side-chains 106 residues out of total 1213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 90 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 ASN Chi-restraints excluded: chain C residue 139 PHE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 32 ARG Chi-restraints excluded: chain E residue 62 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** C 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.107994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.087437 restraints weight = 27410.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089548 restraints weight = 16671.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.090972 restraints weight = 12047.612| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11041 Z= 0.185 Angle : 0.523 7.807 14921 Z= 0.270 Chirality : 0.040 0.201 1685 Planarity : 0.003 0.036 1936 Dihedral : 4.104 18.916 1513 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.68 % Allowed : 18.16 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1389 helix: 0.36 (0.20), residues: 743 sheet: -0.32 (0.64), residues: 81 loop : -1.92 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 308 HIS 0.003 0.001 HIS D 51 PHE 0.028 0.001 PHE E 62 TYR 0.024 0.001 TYR A 169 ARG 0.004 0.000 ARG B 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1914.32 seconds wall clock time: 35 minutes 43.33 seconds (2143.33 seconds total)