Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 05:04:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7anz_11835/04_2023/7anz_11835.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7anz_11835/04_2023/7anz_11835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7anz_11835/04_2023/7anz_11835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7anz_11835/04_2023/7anz_11835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7anz_11835/04_2023/7anz_11835.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7anz_11835/04_2023/7anz_11835.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 10787 2.51 5 N 2772 2.21 5 O 3136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 51": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B ARG 116": "NH1" <-> "NH2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A ARG 116": "NH1" <-> "NH2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A GLU 439": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "C GLU 94": "OE1" <-> "OE2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C GLU 233": "OE1" <-> "OE2" Residue "C GLU 330": "OE1" <-> "OE2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C GLU 492": "OE1" <-> "OE2" Residue "C GLU 519": "OE1" <-> "OE2" Residue "C GLU 526": "OE1" <-> "OE2" Residue "C GLU 530": "OE1" <-> "OE2" Residue "C GLU 603": "OE1" <-> "OE2" Residue "C GLU 676": "OE1" <-> "OE2" Residue "C ARG 762": "NH1" <-> "NH2" Residue "C GLU 764": "OE1" <-> "OE2" Residue "C GLU 800": "OE1" <-> "OE2" Residue "C GLU 816": "OE1" <-> "OE2" Residue "C ARG 853": "NH1" <-> "NH2" Residue "C GLU 866": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D GLU 321": "OE1" <-> "OE2" Residue "D GLU 377": "OE1" <-> "OE2" Residue "D GLU 464": "OE1" <-> "OE2" Residue "D GLU 516": "OE1" <-> "OE2" Residue "D GLU 529": "OE1" <-> "OE2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D ARG 576": "NH1" <-> "NH2" Residue "D GLU 599": "OE1" <-> "OE2" Residue "D GLU 611": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16751 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3269 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 16, 'TRANS': 393} Chain breaks: 6 Chain: "A" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 16, 'TRANS': 383} Chain breaks: 6 Chain: "C" Number of atoms: 5142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 5142 Classifications: {'peptide': 618} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 606} Chain breaks: 6 Chain: "D" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 5155 Classifications: {'peptide': 613} Link IDs: {'CIS': 3, 'PTRANS': 12, 'TRANS': 597} Chain breaks: 4 Time building chain proxies: 8.87, per 1000 atoms: 0.53 Number of scatterers: 16751 At special positions: 0 Unit cell: (176.55, 169.06, 86.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 3136 8.00 N 2772 7.00 C 10787 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: 6.39 Conformation dependent library (CDL) restraints added in 2.4 seconds 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3922 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 8 sheets defined 59.8% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'B' and resid 11 through 30 removed outlier: 3.891A pdb=" N GLN B 16 " --> pdb=" O GLN B 12 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 removed outlier: 4.063A pdb=" N LEU B 79 " --> pdb=" O HIS B 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 76 through 79' Processing helix chain 'B' and resid 100 through 108 removed outlier: 3.697A pdb=" N SER B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.791A pdb=" N GLU B 141 " --> pdb=" O TYR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.603A pdb=" N LEU B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 removed outlier: 3.531A pdb=" N LYS B 179 " --> pdb=" O GLY B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 189 removed outlier: 3.583A pdb=" N ASP B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 224 removed outlier: 3.657A pdb=" N THR B 216 " --> pdb=" O GLN B 212 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 218 " --> pdb=" O TYR B 214 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS B 221 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.813A pdb=" N ILE B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 268 " --> pdb=" O ASN B 264 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 269 " --> pdb=" O LYS B 265 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 287 through 293 removed outlier: 3.572A pdb=" N ILE B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 329 removed outlier: 3.702A pdb=" N LEU B 326 " --> pdb=" O TYR B 322 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 371 removed outlier: 4.083A pdb=" N GLN B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 427 removed outlier: 3.973A pdb=" N VAL B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 422 " --> pdb=" O LYS B 418 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 423 " --> pdb=" O GLN B 419 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG B 426 " --> pdb=" O LEU B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 463 removed outlier: 3.709A pdb=" N VAL B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 455 " --> pdb=" O ARG B 451 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER B 456 " --> pdb=" O GLU B 452 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 457 " --> pdb=" O SER B 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 removed outlier: 3.615A pdb=" N GLY A 14 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 removed outlier: 3.982A pdb=" N LEU A 79 " --> pdb=" O HIS A 76 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 100 through 110 removed outlier: 3.723A pdb=" N ALA A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 141 removed outlier: 3.569A pdb=" N LYS A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.526A pdb=" N LEU A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 189 removed outlier: 4.131A pdb=" N VAL A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 184 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.824A pdb=" N ASN A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 216 " --> pdb=" O GLN A 212 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU A 218 " --> pdb=" O TYR A 214 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR A 226 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 removed outlier: 3.789A pdb=" N ASN A 239 " --> pdb=" O ASN A 235 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 240 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 274 removed outlier: 3.707A pdb=" N LYS A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.587A pdb=" N ASN A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.838A pdb=" N LEU A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 326 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 368 removed outlier: 3.590A pdb=" N LYS A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 427 removed outlier: 3.920A pdb=" N PHE A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.689A pdb=" N VAL A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE A 457 " --> pdb=" O SER A 453 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 458 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 470 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 150 through 162 removed outlier: 3.977A pdb=" N LEU C 154 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 155 " --> pdb=" O TYR C 151 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 187 removed outlier: 3.704A pdb=" N LYS C 172 " --> pdb=" O LYS C 168 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 173 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 197 removed outlier: 3.617A pdb=" N PHE C 197 " --> pdb=" O HIS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.693A pdb=" N LEU C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 235 removed outlier: 4.391A pdb=" N HIS C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 222 " --> pdb=" O MET C 218 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 223 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE C 228 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU C 234 " --> pdb=" O ARG C 230 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 290 removed outlier: 3.596A pdb=" N ILE C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN C 284 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C 290 " --> pdb=" O ARG C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 308 removed outlier: 3.910A pdb=" N ASP C 298 " --> pdb=" O PRO C 294 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N PHE C 299 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 300 " --> pdb=" O SER C 296 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN C 302 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.645A pdb=" N GLY C 313 " --> pdb=" O SER C 309 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 365 removed outlier: 4.174A pdb=" N LEU C 365 " --> pdb=" O ILE C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 392 removed outlier: 3.554A pdb=" N LYS C 377 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY C 382 " --> pdb=" O ILE C 378 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE C 388 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR C 392 " --> pdb=" O PHE C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 436 removed outlier: 3.809A pdb=" N ASP C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 430 " --> pdb=" O ALA C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 445 removed outlier: 3.570A pdb=" N ASN C 445 " --> pdb=" O PRO C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 451 Processing helix chain 'C' and resid 456 through 464 removed outlier: 3.504A pdb=" N ASN C 461 " --> pdb=" O PHE C 457 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP C 464 " --> pdb=" O ASP C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 removed outlier: 3.618A pdb=" N LYS C 471 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 491 removed outlier: 3.889A pdb=" N LEU C 482 " --> pdb=" O SER C 478 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 488 " --> pdb=" O LYS C 484 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 489 " --> pdb=" O GLN C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 509 removed outlier: 3.562A pdb=" N LEU C 508 " --> pdb=" O VAL C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 529 removed outlier: 3.657A pdb=" N VAL C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU C 526 " --> pdb=" O TYR C 522 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET C 529 " --> pdb=" O VAL C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 594 removed outlier: 4.241A pdb=" N VAL C 593 " --> pdb=" O PRO C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 628 removed outlier: 3.741A pdb=" N GLN C 601 " --> pdb=" O GLN C 597 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE C 604 " --> pdb=" O TYR C 600 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N MET C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE C 606 " --> pdb=" O TYR C 602 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 624 " --> pdb=" O SER C 620 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN C 627 " --> pdb=" O TRP C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 667 removed outlier: 3.767A pdb=" N TRP C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 657 " --> pdb=" O SER C 653 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE C 658 " --> pdb=" O ARG C 654 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 659 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN C 664 " --> pdb=" O HIS C 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 690 removed outlier: 4.319A pdb=" N GLU C 677 " --> pdb=" O HIS C 673 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE C 678 " --> pdb=" O ASN C 674 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS C 683 " --> pdb=" O LYS C 679 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 684 " --> pdb=" O ASN C 680 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N THR C 685 " --> pdb=" O LEU C 681 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN C 688 " --> pdb=" O THR C 684 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 690 " --> pdb=" O ALA C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 758 removed outlier: 3.540A pdb=" N ILE C 744 " --> pdb=" O VAL C 740 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN C 745 " --> pdb=" O GLU C 741 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 758 " --> pdb=" O LEU C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 787 removed outlier: 3.555A pdb=" N LYS C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C 782 " --> pdb=" O HIS C 778 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 784 " --> pdb=" O ASN C 780 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN C 785 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 786 " --> pdb=" O TYR C 782 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS C 787 " --> pdb=" O ILE C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 801 removed outlier: 3.509A pdb=" N GLU C 800 " --> pdb=" O GLU C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 851 removed outlier: 3.673A pdb=" N GLN C 832 " --> pdb=" O THR C 828 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 841 " --> pdb=" O GLY C 837 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 842 " --> pdb=" O GLU C 838 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 848 " --> pdb=" O LEU C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 869 removed outlier: 3.868A pdb=" N LEU C 859 " --> pdb=" O ASN C 855 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU C 860 " --> pdb=" O GLN C 856 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 866 " --> pdb=" O SER C 862 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C 867 " --> pdb=" O ASN C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 159 removed outlier: 3.588A pdb=" N LEU D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 209 removed outlier: 4.562A pdb=" N LEU D 188 " --> pdb=" O SER D 184 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N PHE D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 196 " --> pdb=" O VAL D 192 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL D 205 " --> pdb=" O GLN D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 242 removed outlier: 3.996A pdb=" N TYR D 221 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 223 " --> pdb=" O THR D 219 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN D 234 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN D 238 " --> pdb=" O ASN D 234 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 255 removed outlier: 3.636A pdb=" N TYR D 251 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER D 253 " --> pdb=" O VAL D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 269 removed outlier: 3.838A pdb=" N PHE D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 4.239A pdb=" N LEU D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 301 removed outlier: 3.612A pdb=" N THR D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 316 removed outlier: 4.230A pdb=" N TYR D 309 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 313 " --> pdb=" O TYR D 309 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS D 315 " --> pdb=" O ASN D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 351 Processing helix chain 'D' and resid 361 through 371 removed outlier: 4.603A pdb=" N THR D 367 " --> pdb=" O GLN D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 389 removed outlier: 3.662A pdb=" N SER D 389 " --> pdb=" O ASN D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 394 Processing helix chain 'D' and resid 403 through 423 removed outlier: 3.505A pdb=" N SER D 413 " --> pdb=" O LYS D 409 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU D 417 " --> pdb=" O SER D 413 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE D 421 " --> pdb=" O GLU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 removed outlier: 3.892A pdb=" N PHE D 442 " --> pdb=" O ASN D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 457 removed outlier: 3.913A pdb=" N ILE D 451 " --> pdb=" O THR D 447 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET D 455 " --> pdb=" O ILE D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 485 Processing helix chain 'D' and resid 486 through 489 removed outlier: 3.761A pdb=" N ASN D 489 " --> pdb=" O SER D 486 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 486 through 489' Processing helix chain 'D' and resid 529 through 532 Processing helix chain 'D' and resid 533 through 552 removed outlier: 3.767A pdb=" N MET D 539 " --> pdb=" O GLN D 535 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE D 540 " --> pdb=" O TYR D 536 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 546 " --> pdb=" O PHE D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 567 removed outlier: 4.117A pdb=" N GLU D 562 " --> pdb=" O GLU D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 571 removed outlier: 3.522A pdb=" N LEU D 571 " --> pdb=" O VAL D 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 568 through 571' Processing helix chain 'D' and resid 575 through 605 removed outlier: 3.687A pdb=" N LEU D 579 " --> pdb=" O ASN D 575 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS D 581 " --> pdb=" O ARG D 577 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE D 586 " --> pdb=" O SER D 582 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE D 596 " --> pdb=" O HIS D 592 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN D 598 " --> pdb=" O THR D 594 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU D 599 " --> pdb=" O GLN D 595 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 602 " --> pdb=" O ASN D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 617 removed outlier: 3.622A pdb=" N ASN D 612 " --> pdb=" O VAL D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 623 Processing helix chain 'D' and resid 657 through 674 removed outlier: 3.878A pdb=" N GLU D 663 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS D 665 " --> pdb=" O LEU D 661 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 672 " --> pdb=" O TYR D 668 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 708 removed outlier: 3.627A pdb=" N ASN D 707 " --> pdb=" O PHE D 703 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 725 removed outlier: 3.584A pdb=" N LEU D 715 " --> pdb=" O GLU D 711 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 717 " --> pdb=" O TYR D 713 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR D 718 " --> pdb=" O SER D 714 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 721 " --> pdb=" O VAL D 717 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL D 723 " --> pdb=" O PHE D 719 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 724 " --> pdb=" O GLY D 720 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER D 725 " --> pdb=" O LEU D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 768 removed outlier: 3.520A pdb=" N LYS D 749 " --> pdb=" O LEU D 745 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG D 750 " --> pdb=" O HIS D 746 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR D 757 " --> pdb=" O TYR D 753 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 765 " --> pdb=" O TYR D 761 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN D 766 " --> pdb=" O LYS D 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 773 removed outlier: 3.795A pdb=" N ASN D 773 " --> pdb=" O LYS D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 779 through 784 removed outlier: 3.664A pdb=" N LYS D 783 " --> pdb=" O ASP D 780 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 784 " --> pdb=" O LEU D 781 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 118 through 119 removed outlier: 8.130A pdb=" N HIS B 119 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 95 " --> pdb=" O HIS B 119 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU B 4 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N GLN B 163 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE B 6 " --> pdb=" O GLN B 163 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N PHE B 165 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU B 8 " --> pdb=" O PHE B 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.571A pdb=" N THR B 90 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 199 through 200 removed outlier: 4.702A pdb=" N SER B 306 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N HIS B 234 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 11.364A pdb=" N ILE B 308 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 383 " --> pdb=" O MET B 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 removed outlier: 6.886A pdb=" N GLU A 4 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLN A 163 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 6 " --> pdb=" O GLN A 163 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N PHE A 165 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 8 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N SER A 306 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N HIS A 234 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 11.121A pdb=" N ILE A 308 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE A 303 " --> pdb=" O ASN A 406 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN A 406 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 401 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ASN A 349 " --> pdb=" O ILE A 401 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL A 403 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N MET A 347 " --> pdb=" O VAL A 403 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN A 405 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 383 " --> pdb=" O MET A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 83 removed outlier: 3.878A pdb=" N THR A 90 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 334 through 335 removed outlier: 3.617A pdb=" N LEU C 359 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 331 through 332 removed outlier: 3.884A pdb=" N ILE D 332 " --> pdb=" O LYS D 345 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS D 345 " --> pdb=" O ILE D 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 496 through 500 removed outlier: 3.647A pdb=" N ARG D 499 " --> pdb=" O THR D 514 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 6.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5336 1.34 - 1.46: 3965 1.46 - 1.58: 7683 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 17082 Sorted by residual: bond pdb=" N CYS C 868 " pdb=" CA CYS C 868 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.45e+00 bond pdb=" N THR C 685 " pdb=" CA THR C 685 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.41e+00 bond pdb=" N ASP D 647 " pdb=" CA ASP D 647 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.54e+00 bond pdb=" N LEU D 522 " pdb=" CA LEU D 522 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.52e+00 bond pdb=" C LEU C 867 " pdb=" N CYS C 868 " ideal model delta sigma weight residual 1.332 1.355 -0.022 1.40e-02 5.10e+03 2.51e+00 ... (remaining 17077 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.72: 334 106.72 - 114.04: 9683 114.04 - 121.37: 9270 121.37 - 128.69: 3676 128.69 - 136.01: 99 Bond angle restraints: 23062 Sorted by residual: angle pdb=" C ASN D 626 " pdb=" N ASP D 627 " pdb=" CA ASP D 627 " ideal model delta sigma weight residual 121.70 131.97 -10.27 1.80e+00 3.09e-01 3.26e+01 angle pdb=" C ASP D 521 " pdb=" N LEU D 522 " pdb=" CA LEU D 522 " ideal model delta sigma weight residual 121.70 131.78 -10.08 1.80e+00 3.09e-01 3.14e+01 angle pdb=" N ILE B 44 " pdb=" CA ILE B 44 " pdb=" C ILE B 44 " ideal model delta sigma weight residual 111.91 106.97 4.94 8.90e-01 1.26e+00 3.08e+01 angle pdb=" C SER D 525 " pdb=" N TYR D 526 " pdb=" CA TYR D 526 " ideal model delta sigma weight residual 121.70 130.64 -8.94 1.80e+00 3.09e-01 2.47e+01 angle pdb=" N PHE D 636 " pdb=" CA PHE D 636 " pdb=" C PHE D 636 " ideal model delta sigma weight residual 114.75 108.49 6.26 1.26e+00 6.30e-01 2.46e+01 ... (remaining 23057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 8993 17.78 - 35.55: 1006 35.55 - 53.33: 212 53.33 - 71.11: 44 71.11 - 88.88: 20 Dihedral angle restraints: 10275 sinusoidal: 4241 harmonic: 6034 Sorted by residual: dihedral pdb=" CA ILE D 343 " pdb=" C ILE D 343 " pdb=" N ILE D 344 " pdb=" CA ILE D 344 " ideal model delta harmonic sigma weight residual -180.00 -138.21 -41.79 0 5.00e+00 4.00e-02 6.99e+01 dihedral pdb=" CA PHE D 329 " pdb=" C PHE D 329 " pdb=" N PHE D 330 " pdb=" CA PHE D 330 " ideal model delta harmonic sigma weight residual 180.00 -145.97 -34.03 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA ILE D 425 " pdb=" C ILE D 425 " pdb=" N ILE D 426 " pdb=" CA ILE D 426 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 ... (remaining 10272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2061 0.054 - 0.107: 464 0.107 - 0.161: 60 0.161 - 0.214: 10 0.214 - 0.268: 4 Chirality restraints: 2599 Sorted by residual: chirality pdb=" CB ILE C 107 " pdb=" CA ILE C 107 " pdb=" CG1 ILE C 107 " pdb=" CG2 ILE C 107 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CB ILE C 324 " pdb=" CA ILE C 324 " pdb=" CG1 ILE C 324 " pdb=" CG2 ILE C 324 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB THR C 408 " pdb=" CA THR C 408 " pdb=" OG1 THR C 408 " pdb=" CG2 THR C 408 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2596 not shown) Planarity restraints: 2919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 867 " -0.031 2.00e-02 2.50e+03 6.01e-02 3.62e+01 pdb=" C LEU C 867 " 0.104 2.00e-02 2.50e+03 pdb=" O LEU C 867 " -0.039 2.00e-02 2.50e+03 pdb=" N CYS C 868 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 684 " -0.029 2.00e-02 2.50e+03 5.65e-02 3.20e+01 pdb=" C THR C 684 " 0.098 2.00e-02 2.50e+03 pdb=" O THR C 684 " -0.036 2.00e-02 2.50e+03 pdb=" N THR C 685 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 869 " -0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO C 870 " 0.138 5.00e-02 4.00e+02 pdb=" CA PRO C 870 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 870 " -0.045 5.00e-02 4.00e+02 ... (remaining 2916 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4750 2.80 - 3.33: 14918 3.33 - 3.85: 26469 3.85 - 4.38: 31679 4.38 - 4.90: 52932 Nonbonded interactions: 130748 Sorted by model distance: nonbonded pdb=" OG1 THR A 82 " pdb=" OG1 THR A 90 " model vdw 2.277 2.440 nonbonded pdb=" O LYS C 377 " pdb=" OG1 THR C 381 " model vdw 2.282 2.440 nonbonded pdb=" O LEU A 181 " pdb=" OG SER A 185 " model vdw 2.284 2.440 nonbonded pdb=" O HIS D 396 " pdb=" OG SER D 401 " model vdw 2.287 2.440 nonbonded pdb=" O TYR D 277 " pdb=" OG1 THR D 281 " model vdw 2.289 2.440 ... (remaining 130743 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 471) selection = (chain 'B' and (resid 2 through 42 or resid 72 through 471)) } 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=0.00 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: 0.010 Extract box with map and model: 4.910 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 42.000 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 17082 Z= 0.206 Angle : 0.775 11.841 23062 Z= 0.410 Chirality : 0.046 0.268 2599 Planarity : 0.005 0.080 2919 Dihedral : 15.891 88.882 6353 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.49 % Favored : 93.36 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -5.88 (0.12), residues: 1989 helix: -4.51 (0.05), residues: 1082 sheet: -1.96 (0.46), residues: 109 loop : -3.01 (0.18), residues: 798 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 449 time to evaluate : 2.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 455 average time/residue: 0.3270 time to fit residues: 213.7011 Evaluate side-chains 318 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 317 time to evaluate : 2.010 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1509 time to fit residues: 3.1585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 82 optimal weight: 0.0470 chunk 159 optimal weight: 0.0270 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 118 optimal weight: 0.7980 chunk 184 optimal weight: 0.5980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 117 ASN B 161 ASN B 195 ASN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 294 ASN A 16 GLN A 32 GLN A 264 ASN A 294 ASN A 419 GLN C 132 ASN C 159 GLN C 185 GLN C 200 ASN C 202 ASN ** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 GLN C 483 GLN C 611 ASN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 652 HIS C 660 HIS C 742 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 ASN D 237 ASN D 252 ASN D 272 ASN D 341 ASN ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN D 700 GLN D 766 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 17082 Z= 0.168 Angle : 0.606 8.946 23062 Z= 0.311 Chirality : 0.040 0.175 2599 Planarity : 0.004 0.064 2919 Dihedral : 4.731 37.166 2188 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer Outliers : 2.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.70 (0.15), residues: 1989 helix: -2.27 (0.12), residues: 1105 sheet: -1.46 (0.46), residues: 120 loop : -2.70 (0.20), residues: 764 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 350 time to evaluate : 2.037 Fit side-chains outliers start: 48 outliers final: 26 residues processed: 374 average time/residue: 0.2839 time to fit residues: 161.3269 Evaluate side-chains 317 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 291 time to evaluate : 1.836 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1546 time to fit residues: 10.1013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 0.0970 chunk 57 optimal weight: 0.3980 chunk 153 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 148 optimal weight: 0.0020 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN A 15 ASN A 32 GLN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 GLN C 223 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN D 252 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 17082 Z= 0.150 Angle : 0.566 11.213 23062 Z= 0.284 Chirality : 0.040 0.169 2599 Planarity : 0.003 0.056 2919 Dihedral : 4.471 35.620 2188 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.43 (0.17), residues: 1989 helix: -0.97 (0.15), residues: 1103 sheet: -1.35 (0.45), residues: 120 loop : -2.53 (0.20), residues: 766 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 311 time to evaluate : 2.023 Fit side-chains outliers start: 30 outliers final: 14 residues processed: 328 average time/residue: 0.2786 time to fit residues: 141.1180 Evaluate side-chains 295 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 281 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2123 time to fit residues: 7.7771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 185 optimal weight: 0.8980 chunk 196 optimal weight: 0.5980 chunk 96 optimal weight: 0.3980 chunk 175 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN A 15 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 HIS ** C 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN D 272 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 17082 Z= 0.189 Angle : 0.575 9.930 23062 Z= 0.288 Chirality : 0.041 0.185 2599 Planarity : 0.003 0.053 2919 Dihedral : 4.426 34.838 2188 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.82 (0.18), residues: 1989 helix: -0.42 (0.15), residues: 1121 sheet: -1.20 (0.46), residues: 121 loop : -2.36 (0.21), residues: 747 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 302 time to evaluate : 2.039 Fit side-chains outliers start: 44 outliers final: 27 residues processed: 326 average time/residue: 0.2691 time to fit residues: 135.9912 Evaluate side-chains 309 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 282 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1624 time to fit residues: 10.9644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN ** B 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 634 ASN C 794 ASN D 238 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 GLN ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 17082 Z= 0.225 Angle : 0.604 9.385 23062 Z= 0.302 Chirality : 0.042 0.213 2599 Planarity : 0.003 0.054 2919 Dihedral : 4.480 29.683 2188 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % 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: -1.52 (0.18), residues: 1989 helix: -0.12 (0.15), residues: 1122 sheet: -1.20 (0.44), residues: 132 loop : -2.31 (0.21), residues: 735 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 308 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 14 residues processed: 327 average time/residue: 0.2808 time to fit residues: 143.4703 Evaluate side-chains 298 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 284 time to evaluate : 2.165 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1667 time to fit residues: 7.3842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 6.9990 chunk 176 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 196 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN B 212 GLN B 294 ASN A 355 ASN A 358 GLN C 302 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 17082 Z= 0.191 Angle : 0.590 10.304 23062 Z= 0.295 Chirality : 0.041 0.233 2599 Planarity : 0.003 0.052 2919 Dihedral : 4.460 33.361 2188 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.23 (0.19), residues: 1989 helix: 0.16 (0.16), residues: 1118 sheet: -1.13 (0.44), residues: 132 loop : -2.26 (0.22), residues: 739 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 312 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 26 residues processed: 333 average time/residue: 0.2775 time to fit residues: 143.6953 Evaluate side-chains 304 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 278 time to evaluate : 2.040 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1780 time to fit residues: 10.9887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 143 optimal weight: 0.0020 chunk 165 optimal weight: 0.4980 chunk 109 optimal weight: 0.2980 chunk 195 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 0.0870 chunk 121 optimal weight: 0.6980 overall best weight: 0.3166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 294 ASN ** A 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 17082 Z= 0.143 Angle : 0.574 9.443 23062 Z= 0.285 Chirality : 0.040 0.204 2599 Planarity : 0.003 0.050 2919 Dihedral : 4.290 31.056 2188 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.93 (0.19), residues: 1989 helix: 0.47 (0.16), residues: 1114 sheet: -0.96 (0.45), residues: 127 loop : -2.23 (0.21), residues: 748 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 300 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 309 average time/residue: 0.2832 time to fit residues: 135.3693 Evaluate side-chains 281 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 274 time to evaluate : 1.946 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1656 time to fit residues: 5.0325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 chunk 58 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 18 optimal weight: 0.0270 chunk 153 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 HIS D 238 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 758 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 17082 Z= 0.166 Angle : 0.590 12.361 23062 Z= 0.293 Chirality : 0.040 0.175 2599 Planarity : 0.003 0.048 2919 Dihedral : 4.270 30.352 2188 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.74 (0.19), residues: 1989 helix: 0.61 (0.16), residues: 1115 sheet: -0.69 (0.46), residues: 124 loop : -2.17 (0.21), residues: 750 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 285 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 297 average time/residue: 0.2710 time to fit residues: 124.7038 Evaluate side-chains 282 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 270 time to evaluate : 1.938 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1599 time to fit residues: 6.2882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 1.9990 chunk 171 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 164 optimal weight: 0.6980 chunk 172 optimal weight: 0.8980 chunk 181 optimal weight: 0.5980 chunk 119 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 17082 Z= 0.189 Angle : 0.617 12.677 23062 Z= 0.304 Chirality : 0.041 0.211 2599 Planarity : 0.003 0.048 2919 Dihedral : 4.306 29.338 2188 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.19), residues: 1989 helix: 0.65 (0.16), residues: 1116 sheet: -0.64 (0.47), residues: 124 loop : -2.15 (0.22), residues: 749 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 284 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 294 average time/residue: 0.2824 time to fit residues: 128.9974 Evaluate side-chains 287 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 277 time to evaluate : 1.986 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1519 time to fit residues: 5.5363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 0.7980 chunk 117 optimal weight: 0.0470 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 202 optimal weight: 10.0000 chunk 186 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN B 50 GLN B 161 ASN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN C 316 ASN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN D 385 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 17082 Z= 0.186 Angle : 0.620 12.796 23062 Z= 0.307 Chirality : 0.041 0.222 2599 Planarity : 0.003 0.048 2919 Dihedral : 4.342 30.304 2188 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.67 (0.19), residues: 1989 helix: 0.68 (0.16), residues: 1116 sheet: -0.74 (0.46), residues: 130 loop : -2.15 (0.22), residues: 743 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 287 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 289 average time/residue: 0.2868 time to fit residues: 127.3495 Evaluate side-chains 282 residues out of total 1910 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 278 time to evaluate : 1.882 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1664 time to fit residues: 3.9158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 148 optimal weight: 0.0370 chunk 23 optimal weight: 0.4980 chunk 44 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 67 optimal weight: 0.0670 chunk 165 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN ** C 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN ** D 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.158803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.131918 restraints weight = 26978.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.133189 restraints weight = 17728.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.133679 restraints weight = 14801.207| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 17082 Z= 0.160 Angle : 0.619 12.451 23062 Z= 0.304 Chirality : 0.040 0.201 2599 Planarity : 0.003 0.047 2919 Dihedral : 4.252 29.606 2188 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.15 % 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: -0.60 (0.19), residues: 1989 helix: 0.77 (0.16), residues: 1109 sheet: -0.78 (0.46), residues: 130 loop : -2.15 (0.22), residues: 750 =============================================================================== Job complete usr+sys time: 3347.98 seconds wall clock time: 61 minutes 53.72 seconds (3713.72 seconds total)