Starting phenix.real_space_refine (version: dev) on Sun Feb 19 22:17:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hra_14916/02_2023/6hra_14916_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hra_14916/02_2023/6hra_14916.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hra_14916/02_2023/6hra_14916.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hra_14916/02_2023/6hra_14916.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hra_14916/02_2023/6hra_14916_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hra_14916/02_2023/6hra_14916_updated.pdb" } resolution = 3.7 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= 0.005 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 Process input model Symmetric amino acids flipped Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 172": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 293": "NH1" <-> "NH2" Residue "B PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 475": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10818 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1413 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 13, 'TRANS': 173} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5047 Classifications: {'peptide': 679} Link IDs: {'PTRANS': 26, 'TRANS': 652} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.49, per 1000 atoms: 0.60 Number of scatterers: 10818 At special positions: 0 Unit cell: (98.164, 113.344, 152.812, 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) K 3 19.00 S 61 16.00 P 1 15.00 O 1962 8.00 N 1823 7.00 C 6968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.78 Conformation dependent library (CDL) restraints added in 1.7 seconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 65 helices and 5 sheets defined 49.7% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 3 through 31 removed outlier: 3.639A pdb=" N LEU A 7 " --> pdb=" O ALA A 3 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 8 " --> pdb=" O GLN A 4 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) Proline residue: A 22 - end of helix removed outlier: 3.534A pdb=" N SER A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.587A pdb=" N CYS A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 66 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY A 68 " --> pdb=" O CYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.738A pdb=" N VAL A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 77 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.544A pdb=" N PHE A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 133 removed outlier: 3.692A pdb=" N ALA A 131 " --> pdb=" O PHE A 127 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 156 removed outlier: 3.627A pdb=" N LEU A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.874A pdb=" N ARG A 172 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 182 No H-bonds generated for 'chain 'A' and resid 179 through 182' Processing helix chain 'A' and resid 184 through 192 removed outlier: 3.618A pdb=" N PHE A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 228 removed outlier: 4.377A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 273 removed outlier: 3.670A pdb=" N PHE A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 4.387A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 273 " --> pdb=" O ALA A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 303 removed outlier: 4.385A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 289 " --> pdb=" O TRP A 285 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.606A pdb=" N LEU A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 removed outlier: 3.703A pdb=" N VAL A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.844A pdb=" N MET A 366 " --> pdb=" O PRO A 362 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 367 " --> pdb=" O MET A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 390 removed outlier: 4.028A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 395 No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 415 through 434 removed outlier: 3.868A pdb=" N LEU A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix removed outlier: 3.581A pdb=" N VAL A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 429 " --> pdb=" O PRO A 425 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 4.446A pdb=" N ALA A 444 " --> pdb=" O ALA A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.684A pdb=" N VAL A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 removed outlier: 3.511A pdb=" N CYS A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 492 " --> pdb=" O CYS A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 508 removed outlier: 3.875A pdb=" N ILE A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 508 " --> pdb=" O ALA A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 538 removed outlier: 3.713A pdb=" N GLY A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 547 No H-bonds generated for 'chain 'A' and resid 544 through 547' Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.573A pdb=" N PHE C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 19 No H-bonds generated for 'chain 'C' and resid 16 through 19' Processing helix chain 'C' and resid 22 through 33 removed outlier: 3.687A pdb=" N TRP C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 38 No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 92 through 103 removed outlier: 3.528A pdb=" N LYS C 96 " --> pdb=" O PRO C 92 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 118 through 121 No H-bonds generated for 'chain 'C' and resid 118 through 121' Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 148 removed outlier: 3.606A pdb=" N LYS C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 161 removed outlier: 3.845A pdb=" N GLN C 157 " --> pdb=" O GLU C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 189 removed outlier: 3.591A pdb=" N LYS C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 23 removed outlier: 3.668A pdb=" N THR D 7 " --> pdb=" O ALA D 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 22 removed outlier: 4.249A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 34 through 55 removed outlier: 3.722A pdb=" N ILE B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 39 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 52 " --> pdb=" O CYS B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 101 removed outlier: 4.050A pdb=" N ALA B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ILE B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 201 through 207 removed outlier: 4.056A pdb=" N MET B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 237 removed outlier: 3.822A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 245 removed outlier: 4.105A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.658A pdb=" N ALA B 257 " --> pdb=" O THR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 268 No H-bonds generated for 'chain 'B' and resid 265 through 268' Processing helix chain 'B' and resid 271 through 284 removed outlier: 4.014A pdb=" N VAL B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 299 removed outlier: 3.876A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 354 removed outlier: 3.792A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 424 removed outlier: 3.846A pdb=" N ASP B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 475 through 485 removed outlier: 3.780A pdb=" N ALA B 479 " --> pdb=" O ARG B 475 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 503 removed outlier: 3.661A pdb=" N ILE B 503 " --> pdb=" O LYS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 542 through 545 No H-bonds generated for 'chain 'B' and resid 542 through 545' Processing helix chain 'B' and resid 555 through 565 removed outlier: 4.138A pdb=" N LEU B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 562 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N HIS B 563 " --> pdb=" O GLU B 560 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 565 " --> pdb=" O VAL B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 594 removed outlier: 4.437A pdb=" N ARG B 572 " --> pdb=" O MET B 568 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 575 " --> pdb=" O THR B 571 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 576 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 581 " --> pdb=" O THR B 577 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 588 " --> pdb=" O VAL B 584 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.526A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 637 removed outlier: 4.410A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 655 removed outlier: 3.956A pdb=" N ARG B 651 " --> pdb=" O SER B 647 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 654 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP B 655 " --> pdb=" O ARG B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 678 Proline residue: B 665 - end of helix removed outlier: 4.260A pdb=" N LYS B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'B' and resid 131 through 134 removed outlier: 6.718A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 287 through 289 Processing sheet with id= D, first strand: chain 'B' and resid 303 through 307 removed outlier: 6.410A pdb=" N LYS B 466 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU B 306 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B 468 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP B 489 " --> pdb=" O MET B 469 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 394 through 396 removed outlier: 4.645A pdb=" N ARG B 394 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL B 434 " --> pdb=" O ARG B 394 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 978 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: 3.10 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3056 1.33 - 1.45: 1681 1.45 - 1.57: 6164 1.57 - 1.69: 4 1.69 - 1.81: 110 Bond restraints: 11015 Sorted by residual: bond pdb=" C ASN B 26 " pdb=" N PRO B 27 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.42e+00 bond pdb=" CG LEU A 422 " pdb=" CD2 LEU A 422 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.76e+00 bond pdb=" CB PRO A 425 " pdb=" CG PRO A 425 " ideal model delta sigma weight residual 1.492 1.410 0.082 5.00e-02 4.00e+02 2.68e+00 bond pdb=" CG1 ILE B 267 " pdb=" CD1 ILE B 267 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.65e+00 bond pdb=" CB VAL B 231 " pdb=" CG2 VAL B 231 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.45e+00 ... (remaining 11010 not shown) Histogram of bond angle deviations from ideal: 95.60 - 103.28: 126 103.28 - 110.96: 4175 110.96 - 118.64: 4661 118.64 - 126.33: 5868 126.33 - 134.01: 163 Bond angle restraints: 14993 Sorted by residual: angle pdb=" N ILE A 398 " pdb=" CA ILE A 398 " pdb=" C ILE A 398 " ideal model delta sigma weight residual 113.71 105.24 8.47 9.50e-01 1.11e+00 7.94e+01 angle pdb=" N ILE D 24 " pdb=" CA ILE D 24 " pdb=" C ILE D 24 " ideal model delta sigma weight residual 112.29 107.96 4.33 9.40e-01 1.13e+00 2.12e+01 angle pdb=" C PRO B 11 " pdb=" N THR B 12 " pdb=" CA THR B 12 " ideal model delta sigma weight residual 121.54 130.31 -8.77 1.91e+00 2.74e-01 2.11e+01 angle pdb=" C PHE A 260 " pdb=" CA PHE A 260 " pdb=" CB PHE A 260 " ideal model delta sigma weight residual 111.22 106.62 4.60 1.23e+00 6.61e-01 1.40e+01 angle pdb=" C ASN B 316 " pdb=" N ARG B 317 " pdb=" CA ARG B 317 " ideal model delta sigma weight residual 122.07 127.36 -5.29 1.43e+00 4.89e-01 1.37e+01 ... (remaining 14988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.27: 6240 15.27 - 30.54: 245 30.54 - 45.81: 55 45.81 - 61.09: 6 61.09 - 76.36: 8 Dihedral angle restraints: 6554 sinusoidal: 2446 harmonic: 4108 Sorted by residual: dihedral pdb=" CA VAL B 449 " pdb=" C VAL B 449 " pdb=" N LYS B 450 " pdb=" CA LYS B 450 " ideal model delta harmonic sigma weight residual -180.00 -151.47 -28.53 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ASP B 447 " pdb=" C ASP B 447 " pdb=" N ILE B 448 " pdb=" CA ILE B 448 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA PHE B 412 " pdb=" C PHE B 412 " pdb=" N PRO B 413 " pdb=" CA PRO B 413 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 6551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1659 0.092 - 0.183: 144 0.183 - 0.275: 5 0.275 - 0.367: 0 0.367 - 0.458: 1 Chirality restraints: 1809 Sorted by residual: chirality pdb=" CB ILE A 368 " pdb=" CA ILE A 368 " pdb=" CG1 ILE A 368 " pdb=" CG2 ILE A 368 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CG LEU A 133 " pdb=" CB LEU A 133 " pdb=" CD1 LEU A 133 " pdb=" CD2 LEU A 133 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 1806 not shown) Planarity restraints: 1902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 447 " -0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO A 448 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 448 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 448 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 215 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO B 216 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 216 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 216 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 523 " 0.037 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO B 524 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 524 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 524 " 0.032 5.00e-02 4.00e+02 ... (remaining 1899 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 3243 2.81 - 3.39: 11827 3.39 - 3.97: 20568 3.97 - 4.56: 28878 4.56 - 5.14: 41948 Nonbonded interactions: 106464 Sorted by model distance: nonbonded pdb=" OG SER B 175 " pdb=" O GLY B 538 " model vdw 2.227 2.440 nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.241 2.440 nonbonded pdb=" O LEU A 541 " pdb=" OH TYR B 587 " model vdw 2.264 2.440 nonbonded pdb=" OG SER B 192 " pdb=" OE1 GLN B 540 " model vdw 2.278 2.440 nonbonded pdb=" OG SER A 343 " pdb=" O ASN A 466 " model vdw 2.298 2.440 ... (remaining 106459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 1 5.49 5 S 61 5.16 5 C 6968 2.51 5 N 1823 2.21 5 O 1962 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.920 Check model and map are aligned: 0.160 Process input model: 30.980 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2539 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.082 11015 Z= 0.435 Angle : 0.926 9.600 14993 Z= 0.488 Chirality : 0.054 0.458 1809 Planarity : 0.007 0.069 1902 Dihedral : 9.853 76.358 3914 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer Outliers : 0.18 % 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: -5.34 (0.16), residues: 1439 helix: -4.02 (0.10), residues: 737 sheet: -2.86 (0.50), residues: 70 loop : -2.85 (0.21), residues: 632 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 248 average time/residue: 0.2760 time to fit residues: 92.2032 Evaluate side-chains 128 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1271 time to fit residues: 2.0119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 59 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 192 GLN ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN A 279 GLN A 447 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN B 30 GLN B 80 ASN B 316 ASN B 528 GLN B 554 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3079 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 11015 Z= 0.202 Angle : 0.654 8.696 14993 Z= 0.332 Chirality : 0.042 0.175 1809 Planarity : 0.005 0.047 1902 Dihedral : 5.774 34.884 1527 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.19), residues: 1439 helix: -2.55 (0.15), residues: 741 sheet: -2.50 (0.46), residues: 95 loop : -2.34 (0.23), residues: 603 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 165 average time/residue: 0.2445 time to fit residues: 56.9873 Evaluate side-chains 127 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 1.115 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1137 time to fit residues: 3.6739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 0.0870 chunk 40 optimal weight: 0.0060 chunk 107 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 115 optimal weight: 40.0000 chunk 128 optimal weight: 0.3980 chunk 44 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3315 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 11015 Z= 0.190 Angle : 0.629 9.457 14993 Z= 0.314 Chirality : 0.041 0.153 1809 Planarity : 0.004 0.039 1902 Dihedral : 5.246 33.074 1527 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.20), residues: 1439 helix: -1.73 (0.17), residues: 754 sheet: -2.21 (0.48), residues: 92 loop : -2.09 (0.24), residues: 593 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 154 average time/residue: 0.2078 time to fit residues: 48.1913 Evaluate side-chains 125 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1185 time to fit residues: 3.8747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 0.0370 chunk 86 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 0.1980 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3508 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 11015 Z= 0.176 Angle : 0.585 7.720 14993 Z= 0.289 Chirality : 0.040 0.141 1809 Planarity : 0.004 0.066 1902 Dihedral : 4.892 29.282 1527 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.21), residues: 1439 helix: -1.19 (0.18), residues: 756 sheet: -2.04 (0.49), residues: 92 loop : -1.92 (0.24), residues: 591 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 142 average time/residue: 0.2173 time to fit residues: 46.9928 Evaluate side-chains 118 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.386 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1127 time to fit residues: 3.4743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.0040 chunk 1 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 123 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 212 GLN A 239 ASN A 367 GLN C 130 ASN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 GLN ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN B 653 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4239 moved from start: 0.7242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 11015 Z= 0.246 Angle : 0.718 10.930 14993 Z= 0.356 Chirality : 0.045 0.249 1809 Planarity : 0.005 0.050 1902 Dihedral : 5.177 26.074 1527 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 2.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.21), residues: 1439 helix: -1.04 (0.18), residues: 760 sheet: -1.78 (0.57), residues: 83 loop : -2.07 (0.24), residues: 596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 137 time to evaluate : 1.265 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 158 average time/residue: 0.2357 time to fit residues: 53.9301 Evaluate side-chains 114 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.240 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1138 time to fit residues: 4.2107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 33 optimal weight: 0.6980 chunk 137 optimal weight: 5.9990 chunk 114 optimal weight: 0.1980 chunk 63 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN C 154 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4260 moved from start: 0.7647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 11015 Z= 0.172 Angle : 0.605 8.390 14993 Z= 0.297 Chirality : 0.041 0.154 1809 Planarity : 0.004 0.051 1902 Dihedral : 4.714 28.359 1527 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 1.23 % 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: -1.81 (0.22), residues: 1439 helix: -0.57 (0.19), residues: 759 sheet: -1.56 (0.56), residues: 85 loop : -1.89 (0.25), residues: 595 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 119 average time/residue: 0.2315 time to fit residues: 40.3551 Evaluate side-chains 103 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 1.112 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1097 time to fit residues: 2.8716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4655 moved from start: 0.8872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 11015 Z= 0.223 Angle : 0.657 12.696 14993 Z= 0.325 Chirality : 0.043 0.184 1809 Planarity : 0.004 0.072 1902 Dihedral : 4.866 29.549 1527 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.70 % 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: -1.72 (0.22), residues: 1439 helix: -0.52 (0.19), residues: 753 sheet: -1.34 (0.56), residues: 85 loop : -1.85 (0.25), residues: 601 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 1.142 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 126 average time/residue: 0.2193 time to fit residues: 41.9829 Evaluate side-chains 105 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1226 time to fit residues: 2.0976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.0470 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 124 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 GLN A 255 GLN A 351 HIS ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5164 moved from start: 1.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.084 11015 Z= 0.309 Angle : 0.764 13.570 14993 Z= 0.378 Chirality : 0.047 0.213 1809 Planarity : 0.005 0.063 1902 Dihedral : 5.297 33.392 1527 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.21), residues: 1439 helix: -0.77 (0.19), residues: 746 sheet: -1.43 (0.59), residues: 81 loop : -2.03 (0.24), residues: 612 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 126 time to evaluate : 1.233 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 138 average time/residue: 0.2265 time to fit residues: 46.4686 Evaluate side-chains 110 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1541 time to fit residues: 3.6770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 76 optimal weight: 0.0670 chunk 55 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN C 154 GLN ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5246 moved from start: 1.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 11015 Z= 0.225 Angle : 0.673 13.110 14993 Z= 0.328 Chirality : 0.043 0.182 1809 Planarity : 0.004 0.051 1902 Dihedral : 5.022 36.349 1527 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.22), residues: 1439 helix: -0.44 (0.19), residues: 749 sheet: -1.53 (0.57), residues: 82 loop : -1.95 (0.24), residues: 608 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 122 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 126 average time/residue: 0.2251 time to fit residues: 42.4608 Evaluate side-chains 107 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1260 time to fit residues: 2.2171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 141 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 112 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5288 moved from start: 1.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 11015 Z= 0.199 Angle : 0.648 12.774 14993 Z= 0.319 Chirality : 0.043 0.170 1809 Planarity : 0.004 0.043 1902 Dihedral : 4.880 38.024 1527 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.35 % 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: -1.47 (0.22), residues: 1439 helix: -0.20 (0.20), residues: 730 sheet: -1.37 (0.58), residues: 82 loop : -1.80 (0.24), residues: 627 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 114 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 116 average time/residue: 0.2238 time to fit residues: 39.4450 Evaluate side-chains 103 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1064 time to fit residues: 1.9022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 112 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 99 optimal weight: 7.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.194396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.165563 restraints weight = 23144.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.167259 restraints weight = 17022.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.168447 restraints weight = 13945.688| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 1.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11015 Z= 0.182 Angle : 0.641 12.627 14993 Z= 0.310 Chirality : 0.042 0.163 1809 Planarity : 0.004 0.042 1902 Dihedral : 4.772 38.690 1527 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.18 % 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: -1.28 (0.23), residues: 1439 helix: -0.05 (0.20), residues: 736 sheet: -1.45 (0.58), residues: 84 loop : -1.69 (0.25), residues: 619 =============================================================================== Job complete usr+sys time: 2209.83 seconds wall clock time: 41 minutes 30.70 seconds (2490.70 seconds total)