Starting phenix.real_space_refine (version: dev) on Tue Dec 13 17:59:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d83_7453/12_2022/6d83_7453_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d83_7453/12_2022/6d83_7453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d83_7453/12_2022/6d83_7453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d83_7453/12_2022/6d83_7453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d83_7453/12_2022/6d83_7453_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d83_7453/12_2022/6d83_7453_updated.pdb" } resolution = 4.27 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= 0.000 sd= 0.003 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "T ARG 10": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 345": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H ARG 109": "NH1" <-> "NH2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "M ARG 243": "NH1" <-> "NH2" Residue "M TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 33": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 16588 Number of models: 1 Model: "" Number of chains: 10 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "L" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 70 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4513 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 25, 'TRANS': 544} Chain: "C" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1330 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "G" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4633 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 13, 'TRANS': 571} Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Chain: "M" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3362 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Chain: "S" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1197 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.04, per 1000 atoms: 0.54 Number of scatterers: 16588 At special positions: 0 Unit cell: (164.318, 133.375, 126.973, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 99 16.00 P 6 15.00 Mg 2 11.99 O 3122 8.00 N 2821 7.00 C 10538 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: 6.51 Conformation dependent library (CDL) restraints added in 2.5 seconds 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 11 sheets defined 48.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'B' and resid 15 through 22 Processing helix chain 'B' and resid 27 through 43 removed outlier: 4.224A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.564A pdb=" N PHE B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) Proline residue: B 52 - end of helix No H-bonds generated for 'chain 'B' and resid 48 through 54' Processing helix chain 'B' and resid 66 through 75 Processing helix chain 'B' and resid 84 through 94 removed outlier: 3.769A pdb=" N ALA B 87 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 88 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASN B 89 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 112 removed outlier: 4.022A pdb=" N CYS B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 135 through 151 removed outlier: 3.555A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.743A pdb=" N ILE B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 190 Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 218 through 221 No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 235 through 249 removed outlier: 3.934A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Proline residue: B 246 - end of helix removed outlier: 4.725A pdb=" N SER B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 4.587A pdb=" N GLU B 268 " --> pdb=" O MET B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 293 removed outlier: 4.022A pdb=" N ALA B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Proline residue: B 286 - end of helix removed outlier: 4.479A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.606A pdb=" N TYR B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 311 " --> pdb=" O ASN B 307 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 332 through 345 removed outlier: 4.276A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 388 through 401 removed outlier: 3.950A pdb=" N THR B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 removed outlier: 4.415A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 442 through 454 removed outlier: 3.773A pdb=" N ALA B 446 " --> pdb=" O PRO B 442 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 479 through 494 removed outlier: 3.691A pdb=" N VAL B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 511 removed outlier: 3.785A pdb=" N GLN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 533 Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 557 through 565 removed outlier: 3.868A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 75 through 82 removed outlier: 3.673A pdb=" N TRP C 78 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG C 79 " --> pdb=" O PRO C 76 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS C 80 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 110 removed outlier: 4.296A pdb=" N ASN C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 166 through 177 Processing helix chain 'G' and resid 7 through 15 Processing helix chain 'G' and resid 20 through 38 removed outlier: 4.659A pdb=" N GLU G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 59 removed outlier: 3.686A pdb=" N LEU G 59 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 74 Processing helix chain 'G' and resid 79 through 92 Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 100 through 112 removed outlier: 4.370A pdb=" N ASN G 105 " --> pdb=" O LEU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 129 removed outlier: 4.002A pdb=" N LEU G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 removed outlier: 3.670A pdb=" N ARG G 136 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLY G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 146 No H-bonds generated for 'chain 'G' and resid 144 through 146' Processing helix chain 'G' and resid 151 through 167 removed outlier: 3.944A pdb=" N LYS G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS G 156 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU G 159 " --> pdb=" O LYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 173 through 176 No H-bonds generated for 'chain 'G' and resid 173 through 176' Processing helix chain 'G' and resid 188 through 204 Processing helix chain 'G' and resid 206 through 212 removed outlier: 4.011A pdb=" N HIS G 211 " --> pdb=" O ASP G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 227 Processing helix chain 'G' and resid 243 through 255 removed outlier: 3.769A pdb=" N ARG G 248 " --> pdb=" O PHE G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 266 Processing helix chain 'G' and resid 268 through 274 Processing helix chain 'G' and resid 283 through 298 Processing helix chain 'G' and resid 303 through 316 removed outlier: 3.848A pdb=" N LEU G 308 " --> pdb=" O GLY G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 334 Processing helix chain 'G' and resid 340 through 355 removed outlier: 3.806A pdb=" N GLN G 344 " --> pdb=" O HIS G 340 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG G 345 " --> pdb=" O ASN G 341 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N HIS G 346 " --> pdb=" O ALA G 342 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG G 347 " --> pdb=" O VAL G 343 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER G 348 " --> pdb=" O GLN G 344 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR G 349 " --> pdb=" O ARG G 345 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 354 " --> pdb=" O ILE G 350 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS G 355 " --> pdb=" O VAL G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 371 Processing helix chain 'G' and resid 378 through 390 removed outlier: 3.596A pdb=" N MET G 382 " --> pdb=" O ILE G 378 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS G 383 " --> pdb=" O ARG G 379 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU G 384 " --> pdb=" O GLY G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 410 removed outlier: 3.631A pdb=" N PHE G 405 " --> pdb=" O ALA G 401 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS G 410 " --> pdb=" O LEU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 428 Processing helix chain 'G' and resid 437 through 447 Processing helix chain 'G' and resid 453 through 463 removed outlier: 3.962A pdb=" N ARG G 458 " --> pdb=" O TYR G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 487 removed outlier: 4.101A pdb=" N TRP G 478 " --> pdb=" O GLN G 474 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASP G 485 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU G 486 " --> pdb=" O GLU G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 514 removed outlier: 4.030A pdb=" N LEU G 509 " --> pdb=" O VAL G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 536 removed outlier: 3.788A pdb=" N SER G 534 " --> pdb=" O ILE G 530 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR G 535 " --> pdb=" O MET G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 550 Processing helix chain 'G' and resid 557 through 572 removed outlier: 3.737A pdb=" N LEU G 569 " --> pdb=" O GLU G 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 38 Processing helix chain 'H' and resid 75 through 81 removed outlier: 3.708A pdb=" N TRP H 78 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG H 79 " --> pdb=" O PRO H 76 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS H 80 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 110 removed outlier: 3.703A pdb=" N VAL H 100 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASN H 101 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU H 102 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET H 108 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 143 Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing helix chain 'H' and resid 166 through 177 Processing helix chain 'M' and resid 27 through 41 removed outlier: 3.727A pdb=" N VAL M 30 " --> pdb=" O MET M 27 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS M 32 " --> pdb=" O GLU M 29 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N MET M 34 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Proline residue: M 35 - end of helix removed outlier: 3.676A pdb=" N LYS M 40 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 94 Processing helix chain 'M' and resid 100 through 103 No H-bonds generated for 'chain 'M' and resid 100 through 103' Processing helix chain 'M' and resid 107 through 116 removed outlier: 4.056A pdb=" N TYR M 111 " --> pdb=" O PHE M 107 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU M 112 " --> pdb=" O VAL M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 132 Processing helix chain 'M' and resid 151 through 153 No H-bonds generated for 'chain 'M' and resid 151 through 153' Processing helix chain 'M' and resid 217 through 223 Processing helix chain 'M' and resid 244 through 250 Processing helix chain 'S' and resid 25 through 41 removed outlier: 3.564A pdb=" N SER S 41 " --> pdb=" O GLN S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 95 Processing helix chain 'S' and resid 100 through 105 Processing helix chain 'S' and resid 107 through 117 Processing helix chain 'S' and resid 130 through 141 Processing sheet with id= A, first strand: chain 'C' and resid 19 through 22 removed outlier: 7.143A pdb=" N ILE C 20 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR C 64 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET C 22 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP C 66 " --> pdb=" O MET C 22 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 90 through 93 removed outlier: 3.667A pdb=" N PHE C 124 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN C 126 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 153 through 157 removed outlier: 6.444A pdb=" N LEU H 121 " --> pdb=" O TYR H 154 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN H 156 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL H 123 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLY H 24 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'M' and resid 49 through 52 removed outlier: 3.627A pdb=" N SER M 71 " --> pdb=" O ARG M 56 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR M 66 " --> pdb=" O LEU M 9 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA M 5 " --> pdb=" O THR M 70 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'M' and resid 381 through 383 removed outlier: 3.890A pdb=" N MET M 265 " --> pdb=" O ILE M 198 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N MET M 200 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU M 263 " --> pdb=" O MET M 200 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL M 202 " --> pdb=" O GLU M 261 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU M 261 " --> pdb=" O VAL M 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'M' and resid 192 through 194 removed outlier: 3.537A pdb=" N VAL M 183 " --> pdb=" O GLN M 419 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 395 through 398 removed outlier: 3.588A pdb=" N ARG M 211 " --> pdb=" O LYS M 396 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE M 253 " --> pdb=" O LEU M 212 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'M' and resid 277 through 280 Processing sheet with id= I, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= J, first strand: chain 'M' and resid 310 through 315 removed outlier: 3.510A pdb=" N ILE M 314 " --> pdb=" O ILE M 341 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 49 through 51 removed outlier: 4.288A pdb=" N PHE S 4 " --> pdb=" O ALA S 70 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 1896 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: 4.92 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5389 1.34 - 1.46: 2858 1.46 - 1.58: 8455 1.58 - 1.69: 10 1.69 - 1.81: 161 Bond restraints: 16873 Sorted by residual: bond pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 1.337 1.371 -0.034 1.11e-02 8.12e+03 9.54e+00 bond pdb=" C ILE H 46 " pdb=" N PRO H 47 " ideal model delta sigma weight residual 1.333 1.354 -0.020 1.01e-02 9.80e+03 4.11e+00 bond pdb=" CA GLN B 400 " pdb=" C GLN B 400 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.34e-02 5.57e+03 3.40e+00 bond pdb=" C VAL G 216 " pdb=" N PRO G 217 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.25e-02 6.40e+03 3.24e+00 bond pdb=" CA VAL M 273 " pdb=" CB VAL M 273 " ideal model delta sigma weight residual 1.542 1.563 -0.021 1.26e-02 6.30e+03 2.76e+00 ... (remaining 16868 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.29: 296 105.29 - 112.49: 8620 112.49 - 119.69: 6065 119.69 - 126.89: 7684 126.89 - 134.09: 162 Bond angle restraints: 22827 Sorted by residual: angle pdb=" N VAL B 334 " pdb=" CA VAL B 334 " pdb=" C VAL B 334 " ideal model delta sigma weight residual 112.96 106.91 6.05 1.00e+00 1.00e+00 3.66e+01 angle pdb=" N ARG G 543 " pdb=" CA ARG G 543 " pdb=" C ARG G 543 " ideal model delta sigma weight residual 114.04 106.62 7.42 1.24e+00 6.50e-01 3.58e+01 angle pdb=" C LYS H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta sigma weight residual 121.54 130.76 -9.22 1.91e+00 2.74e-01 2.33e+01 angle pdb=" C ASN M 308 " pdb=" N ASN M 309 " pdb=" CA ASN M 309 " ideal model delta sigma weight residual 121.54 130.18 -8.64 1.91e+00 2.74e-01 2.05e+01 angle pdb=" CA GLN B 400 " pdb=" C GLN B 400 " pdb=" N THR B 401 " ideal model delta sigma weight residual 116.84 123.65 -6.81 1.71e+00 3.42e-01 1.59e+01 ... (remaining 22822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.15: 10206 30.15 - 60.30: 119 60.30 - 90.45: 14 90.45 - 120.61: 2 120.61 - 150.76: 7 Dihedral angle restraints: 10348 sinusoidal: 4265 harmonic: 6083 Sorted by residual: dihedral pdb=" O5' GTP H1001 " pdb=" O3A GTP H1001 " pdb=" PA GTP H1001 " pdb=" PB GTP H1001 " ideal model delta sinusoidal sigma weight residual -85.88 64.88 -150.76 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" CA GLU B 295 " pdb=" C GLU B 295 " pdb=" N PRO B 296 " pdb=" CA PRO B 296 " ideal model delta harmonic sigma weight residual 180.00 -146.57 -33.43 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" O3B GTP C1001 " pdb=" O3A GTP C1001 " pdb=" PB GTP C1001 " pdb=" PA GTP C1001 " ideal model delta sinusoidal sigma weight residual 291.08 146.93 144.15 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 10345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2215 0.071 - 0.143: 390 0.143 - 0.214: 25 0.214 - 0.285: 3 0.285 - 0.356: 1 Chirality restraints: 2634 Sorted by residual: chirality pdb=" CB VAL B 47 " pdb=" CA VAL B 47 " pdb=" CG1 VAL B 47 " pdb=" CG2 VAL B 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CG LEU B 197 " pdb=" CB LEU B 197 " pdb=" CD1 LEU B 197 " pdb=" CD2 LEU B 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ASN H 60 " pdb=" N ASN H 60 " pdb=" C ASN H 60 " pdb=" CB ASN H 60 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2631 not shown) Planarity restraints: 2890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO M 374 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO M 375 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO M 375 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO M 375 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 75 " 0.038 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO H 76 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 76 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 76 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 97 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO B 98 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " 0.031 5.00e-02 4.00e+02 ... (remaining 2887 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 91 2.50 - 3.10: 11378 3.10 - 3.70: 25528 3.70 - 4.30: 36448 4.30 - 4.90: 59111 Nonbonded interactions: 132556 Sorted by model distance: nonbonded pdb=" O2G GTP C1001 " pdb="MG MG C1002 " model vdw 1.904 2.170 nonbonded pdb=" O2G GTP H1001 " pdb="MG MG H1002 " model vdw 1.907 2.170 nonbonded pdb=" O1G GTP H1001 " pdb="MG MG H1002 " model vdw 1.954 2.170 nonbonded pdb=" CG2 THR H 31 " pdb="MG MG H1002 " model vdw 2.113 2.590 nonbonded pdb=" PG GTP H1001 " pdb="MG MG H1002 " model vdw 2.192 2.530 ... (remaining 132551 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 'C' and (resid 17 through 179 or resid 1001 through 1002)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 99 5.16 5 C 10538 2.51 5 N 2821 2.21 5 O 3122 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.590 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: 5.240 Check model and map are aligned: 0.220 Convert atoms to be neutral: 0.130 Process input model: 42.590 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.005 0.061 16873 Z= 0.318 Angle : 0.922 9.855 22827 Z= 0.525 Chirality : 0.053 0.356 2634 Planarity : 0.006 0.071 2890 Dihedral : 11.341 150.758 6394 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -4.30 (0.15), residues: 2045 helix: -2.79 (0.11), residues: 1039 sheet: -3.08 (0.30), residues: 246 loop : -2.53 (0.19), residues: 760 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 724 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 725 average time/residue: 0.3323 time to fit residues: 343.5414 Evaluate side-chains 332 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 2.093 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 173 ASN B 205 ASN B 319 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN B 483 GLN B 505 GLN B 575 HIS C 128 GLN C 150 HIS ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN G 235 HIS ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN G 447 ASN G 452 HIS ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 GLN H 128 GLN H 150 HIS H 156 GLN H 176 GLN M 239 HIS M 240 GLN M 270 ASN M 300 GLN S 3 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 16873 Z= 0.206 Angle : 0.666 14.848 22827 Z= 0.337 Chirality : 0.045 0.202 2634 Planarity : 0.006 0.190 2890 Dihedral : 10.194 141.902 2272 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.79 (0.17), residues: 2045 helix: -1.33 (0.14), residues: 1035 sheet: -2.77 (0.29), residues: 259 loop : -2.00 (0.21), residues: 751 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 477 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 478 average time/residue: 0.3004 time to fit residues: 209.0032 Evaluate side-chains 274 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.875 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 184 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 GLN C 128 GLN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 ASN G 323 ASN ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 HIS M 249 ASN M 270 ASN M 288 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 16873 Z= 0.329 Angle : 0.709 14.225 22827 Z= 0.365 Chirality : 0.046 0.208 2634 Planarity : 0.006 0.160 2890 Dihedral : 10.177 138.617 2272 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -2.12 (0.18), residues: 2045 helix: -0.68 (0.15), residues: 1038 sheet: -2.49 (0.31), residues: 244 loop : -1.88 (0.21), residues: 763 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 407 time to evaluate : 1.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 408 average time/residue: 0.2833 time to fit residues: 174.1848 Evaluate side-chains 251 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.103 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 124 optimal weight: 0.0470 chunk 186 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 overall best weight: 2.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 319 HIS ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS M 308 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 16873 Z= 0.294 Angle : 0.672 13.812 22827 Z= 0.342 Chirality : 0.046 0.216 2634 Planarity : 0.005 0.143 2890 Dihedral : 10.095 141.104 2272 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.18), residues: 2045 helix: -0.48 (0.16), residues: 1048 sheet: -2.23 (0.32), residues: 251 loop : -1.75 (0.22), residues: 746 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.2657 time to fit residues: 160.8095 Evaluate side-chains 260 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 9.9990 chunk 111 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 146 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 319 HIS ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.092 16873 Z= 0.294 Angle : 0.691 15.270 22827 Z= 0.347 Chirality : 0.046 0.282 2634 Planarity : 0.005 0.120 2890 Dihedral : 10.076 140.774 2272 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 0.05 % 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: -1.59 (0.18), residues: 2045 helix: -0.33 (0.16), residues: 1052 sheet: -2.00 (0.32), residues: 252 loop : -1.59 (0.22), residues: 741 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 388 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 389 average time/residue: 0.2693 time to fit residues: 158.8552 Evaluate side-chains 259 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 2.172 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1960 time to fit residues: 3.1315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 38 optimal weight: 0.3980 chunk 115 optimal weight: 0.9980 chunk 48 optimal weight: 0.0170 chunk 197 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 319 HIS ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 470 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 16873 Z= 0.187 Angle : 0.659 14.441 22827 Z= 0.322 Chirality : 0.044 0.280 2634 Planarity : 0.005 0.107 2890 Dihedral : 9.855 142.119 2272 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.31 (0.19), residues: 2045 helix: -0.13 (0.16), residues: 1053 sheet: -1.93 (0.32), residues: 257 loop : -1.37 (0.23), residues: 735 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 392 time to evaluate : 2.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 393 average time/residue: 0.2744 time to fit residues: 163.7283 Evaluate side-chains 263 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.8980 chunk 22 optimal weight: 0.0470 chunk 112 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN G 97 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 16873 Z= 0.220 Angle : 0.663 14.709 22827 Z= 0.329 Chirality : 0.045 0.308 2634 Planarity : 0.005 0.102 2890 Dihedral : 9.790 141.024 2272 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.20 (0.19), residues: 2045 helix: -0.07 (0.16), residues: 1064 sheet: -1.88 (0.32), residues: 256 loop : -1.29 (0.24), residues: 725 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 368 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 369 average time/residue: 0.2819 time to fit residues: 157.5705 Evaluate side-chains 260 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 154 optimal weight: 2.9990 chunk 178 optimal weight: 0.0060 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS M 249 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 16873 Z= 0.182 Angle : 0.654 14.566 22827 Z= 0.319 Chirality : 0.044 0.305 2634 Planarity : 0.004 0.067 2890 Dihedral : 9.637 140.697 2272 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.04 (0.19), residues: 2045 helix: 0.06 (0.16), residues: 1064 sheet: -1.74 (0.33), residues: 251 loop : -1.22 (0.24), residues: 730 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 382 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 383 average time/residue: 0.2688 time to fit residues: 158.4701 Evaluate side-chains 254 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.212 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.0010 chunk 171 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 56 optimal weight: 0.0570 chunk 165 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 overall best weight: 0.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 GLN B 319 HIS ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS G 97 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 16873 Z= 0.175 Angle : 0.673 14.263 22827 Z= 0.325 Chirality : 0.045 0.273 2634 Planarity : 0.004 0.075 2890 Dihedral : 9.514 140.791 2272 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.01 (0.19), residues: 2045 helix: 0.03 (0.16), residues: 1059 sheet: -1.66 (0.33), residues: 250 loop : -1.16 (0.24), residues: 736 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.2703 time to fit residues: 156.3157 Evaluate side-chains 269 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 2.084 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 128 optimal weight: 0.0970 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS B 435 ASN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** G 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 119 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 16873 Z= 0.276 Angle : 0.719 15.130 22827 Z= 0.355 Chirality : 0.047 0.351 2634 Planarity : 0.005 0.101 2890 Dihedral : 9.584 141.296 2272 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -1.02 (0.19), residues: 2045 helix: 0.03 (0.16), residues: 1053 sheet: -1.69 (0.33), residues: 249 loop : -1.15 (0.24), residues: 743 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 357 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.2917 time to fit residues: 160.1589 Evaluate side-chains 257 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.959 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 119 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.091625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.078814 restraints weight = 55103.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.080407 restraints weight = 35795.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.081531 restraints weight = 24392.106| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 16873 Z= 0.206 Angle : 0.691 14.720 22827 Z= 0.339 Chirality : 0.046 0.314 2634 Planarity : 0.004 0.077 2890 Dihedral : 9.463 143.508 2272 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % 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: -0.99 (0.19), residues: 2045 helix: 0.07 (0.16), residues: 1054 sheet: -1.72 (0.32), residues: 252 loop : -1.15 (0.24), residues: 739 =============================================================================== Job complete usr+sys time: 3706.39 seconds wall clock time: 67 minutes 59.50 seconds (4079.50 seconds total)