Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 23:28:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owt_20217/10_2023/6owt_20217.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owt_20217/10_2023/6owt_20217.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owt_20217/10_2023/6owt_20217.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owt_20217/10_2023/6owt_20217.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owt_20217/10_2023/6owt_20217.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6owt_20217/10_2023/6owt_20217.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 32 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 7498 2.51 5 N 1975 2.21 5 O 2130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 17": "OE1" <-> "OE2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 385": "OE1" <-> "OE2" Residue "B GLU 476": "OE1" <-> "OE2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 137": "NH1" <-> "NH2" Residue "N ARG 138": "NH1" <-> "NH2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 11649 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4255 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 22, 'TRANS': 567} Unresolved non-hydrogen bonds: 418 Unresolved non-hydrogen angles: 512 Unresolved non-hydrogen dihedrals: 344 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 234 Chain: "B" Number of atoms: 4242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4242 Classifications: {'peptide': 578} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 26, 'TRANS': 551} Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 17, 'TYR:plan': 1, 'ASN:plan1': 11, 'HIS:plan': 2, 'GLU:plan': 16, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 202 Chain: "M" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 932 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 5, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "T" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 74 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1047 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "S" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1099 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 139} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 60 Time building chain proxies: 6.55, per 1000 atoms: 0.56 Number of scatterers: 11649 At special positions: 0 Unit cell: (98.814, 105.708, 127.539, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 2130 8.00 N 1975 7.00 C 7498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS N 193 " - pdb=" SG CYS S 97 " distance=2.03 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: 4.56 Conformation dependent library (CDL) restraints added in 2.0 seconds 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 4 sheets defined 68.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 51 through 68 Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 82 through 85 removed outlier: 3.677A pdb=" N SER A 85 " --> pdb=" O LEU A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 106 through 122 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 149 through 156 removed outlier: 3.748A pdb=" N LYS A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 179 removed outlier: 3.814A pdb=" N LYS A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 194 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.764A pdb=" N THR A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 222 through 238 removed outlier: 3.749A pdb=" N VAL A 226 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.622A pdb=" N CYS A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 293 Processing helix chain 'A' and resid 299 through 321 removed outlier: 4.264A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 310 " --> pdb=" O LYS A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 3.556A pdb=" N ARG A 329 " --> pdb=" O ASN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 removed outlier: 4.311A pdb=" N LEU A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.533A pdb=" N SER A 358 " --> pdb=" O CYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 382 through 397 Processing helix chain 'A' and resid 401 through 414 Processing helix chain 'A' and resid 420 through 435 removed outlier: 3.840A pdb=" N ILE A 424 " --> pdb=" O ILE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 removed outlier: 4.115A pdb=" N TYR A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 472 removed outlier: 4.104A pdb=" N TRP A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 466 " --> pdb=" O TRP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 512 removed outlier: 3.593A pdb=" N ALA A 512 " --> pdb=" O ASN A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 512' Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 3.913A pdb=" N LEU A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.585A pdb=" N LEU A 542 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 565 removed outlier: 3.684A pdb=" N ILE A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 573 through 587 Processing helix chain 'A' and resid 591 through 599 Processing helix chain 'A' and resid 610 through 620 Processing helix chain 'B' and resid 17 through 24 removed outlier: 3.705A pdb=" N GLU B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 44 Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 62 through 76 Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 87 through 93 Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'B' and resid 117 through 122 Processing helix chain 'B' and resid 122 through 128 Processing helix chain 'B' and resid 134 through 149 removed outlier: 3.671A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 170 removed outlier: 3.961A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 188 Processing helix chain 'B' and resid 199 through 213 removed outlier: 4.927A pdb=" N ASN B 205 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 228 removed outlier: 4.221A pdb=" N PHE B 221 " --> pdb=" O TRP B 217 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 245 Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 274 through 291 removed outlier: 3.572A pdb=" N ASN B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Proline residue: B 286 - end of helix Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.746A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.872A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.654A pdb=" N LEU B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 361 removed outlier: 3.793A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU B 357 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 366 through 384 removed outlier: 4.104A pdb=" N GLY B 378 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 400 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.830A pdb=" N GLN B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL B 413 " --> pdb=" O GLU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 436 removed outlier: 4.228A pdb=" N GLU B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 436 " --> pdb=" O LEU B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 461 through 472 removed outlier: 4.121A pdb=" N LEU B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 490 through 495 Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 504 through 512 removed outlier: 3.686A pdb=" N GLN B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 531 removed outlier: 3.745A pdb=" N SER B 531 " --> pdb=" O TRP B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 541 Processing helix chain 'B' and resid 556 through 566 removed outlier: 4.082A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 removed outlier: 4.079A pdb=" N VAL B 573 " --> pdb=" O SER B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 581 removed outlier: 4.008A pdb=" N PHE B 581 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 36 removed outlier: 3.980A pdb=" N PHE M 32 " --> pdb=" O ALA M 28 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG M 33 " --> pdb=" O VAL M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.945A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE M 79 " --> pdb=" O ALA M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 104 Processing helix chain 'M' and resid 104 through 116 removed outlier: 3.577A pdb=" N TYR M 109 " --> pdb=" O PHE M 105 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU M 114 " --> pdb=" O GLU M 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU M 116 " --> pdb=" O LEU M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 22 Processing helix chain 'N' and resid 112 through 127 Processing helix chain 'N' and resid 135 through 150 Processing helix chain 'N' and resid 217 through 221 removed outlier: 3.589A pdb=" N TYR N 221 " --> pdb=" O LYS N 218 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 229 removed outlier: 3.583A pdb=" N TYR N 229 " --> pdb=" O ALA N 225 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 40 removed outlier: 3.598A pdb=" N ILE S 32 " --> pdb=" O LYS S 28 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU S 33 " --> pdb=" O GLN S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 95 removed outlier: 4.084A pdb=" N PHE S 95 " --> pdb=" O LEU S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 117 removed outlier: 3.534A pdb=" N THR S 112 " --> pdb=" O TYR S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 138 Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.423A pdb=" N THR B 8 " --> pdb=" O ASN N 181 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL N 178 " --> pdb=" O ALA N 212 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA N 212 " --> pdb=" O VAL N 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 14 through 16 removed outlier: 6.801A pdb=" N ILE M 7 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.525A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE S 5 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TRP S 19 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N ARG S 3 " --> pdb=" O TRP S 19 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N PHE S 4 " --> pdb=" O CYS S 70 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 118 through 119 677 hydrogen bonds defined for protein. 2001 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: 3.23 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3820 1.34 - 1.46: 2333 1.46 - 1.58: 5653 1.58 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 11872 Sorted by residual: bond pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.92e+00 bond pdb=" C PRO B 286 " pdb=" N PRO B 287 " ideal model delta sigma weight residual 1.336 1.353 -0.017 1.20e-02 6.94e+03 2.11e+00 bond pdb=" C GLU B 124 " pdb=" N PRO B 125 " ideal model delta sigma weight residual 1.336 1.352 -0.016 1.25e-02 6.40e+03 1.71e+00 bond pdb=" CA THR B 245 " pdb=" C THR B 245 " ideal model delta sigma weight residual 1.522 1.538 -0.016 1.26e-02 6.30e+03 1.70e+00 bond pdb=" C ILE A 151 " pdb=" N PRO A 152 " ideal model delta sigma weight residual 1.336 1.352 -0.016 1.23e-02 6.61e+03 1.69e+00 ... (remaining 11867 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.33: 288 106.33 - 113.27: 6628 113.27 - 120.22: 4381 120.22 - 127.16: 4818 127.16 - 134.10: 113 Bond angle restraints: 16228 Sorted by residual: angle pdb=" C ARG M 60 " pdb=" N SER M 61 " pdb=" CA SER M 61 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" N ASN B 200 " pdb=" CA ASN B 200 " pdb=" C ASN B 200 " ideal model delta sigma weight residual 109.81 117.66 -7.85 2.21e+00 2.05e-01 1.26e+01 angle pdb=" CA PRO B 286 " pdb=" C PRO B 286 " pdb=" N PRO B 287 " ideal model delta sigma weight residual 117.93 121.99 -4.06 1.20e+00 6.94e-01 1.15e+01 angle pdb=" CA LEU B 482 " pdb=" CB LEU B 482 " pdb=" CG LEU B 482 " ideal model delta sigma weight residual 116.30 127.75 -11.45 3.50e+00 8.16e-02 1.07e+01 angle pdb=" CA ALA B 285 " pdb=" C ALA B 285 " pdb=" N PRO B 286 " ideal model delta sigma weight residual 118.44 123.05 -4.61 1.59e+00 3.96e-01 8.39e+00 ... (remaining 16223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6658 17.86 - 35.71: 364 35.71 - 53.57: 89 53.57 - 71.42: 9 71.42 - 89.28: 7 Dihedral angle restraints: 7127 sinusoidal: 2450 harmonic: 4677 Sorted by residual: dihedral pdb=" CB CYS N 193 " pdb=" SG CYS N 193 " pdb=" SG CYS S 97 " pdb=" CB CYS S 97 " ideal model delta sinusoidal sigma weight residual 93.00 137.83 -44.83 1 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" CA ILE B 488 " pdb=" C ILE B 488 " pdb=" N VAL B 489 " pdb=" CA VAL B 489 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ASN B 62 " pdb=" C ASN B 62 " pdb=" N LEU B 63 " pdb=" CA LEU B 63 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 7124 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1360 0.039 - 0.077: 479 0.077 - 0.116: 109 0.116 - 0.155: 20 0.155 - 0.193: 1 Chirality restraints: 1969 Sorted by residual: chirality pdb=" CB VAL A 555 " pdb=" CA VAL A 555 " pdb=" CG1 VAL A 555 " pdb=" CG2 VAL A 555 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ASN B 200 " pdb=" N ASN B 200 " pdb=" C ASN B 200 " pdb=" CB ASN B 200 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA THR B 245 " pdb=" N THR B 245 " pdb=" C THR B 245 " pdb=" CB THR B 245 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1966 not shown) Planarity restraints: 2071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 285 " 0.044 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO B 286 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 576 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO B 577 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 577 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 577 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS N 196 " 0.033 5.00e-02 4.00e+02 5.00e-02 3.99e+00 pdb=" N PRO N 197 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO N 197 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO N 197 " 0.028 5.00e-02 4.00e+02 ... (remaining 2068 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3690 2.82 - 3.34: 10608 3.34 - 3.86: 19388 3.86 - 4.38: 20741 4.38 - 4.90: 36282 Nonbonded interactions: 90709 Sorted by model distance: nonbonded pdb=" O SER A 234 " pdb=" OG1 THR A 238 " model vdw 2.304 2.440 nonbonded pdb=" O VAL A 204 " pdb=" OG1 THR A 208 " model vdw 2.305 2.440 nonbonded pdb=" OD2 ASP A 382 " pdb=" OG SER A 384 " model vdw 2.317 2.440 nonbonded pdb=" O HIS S 36 " pdb=" OG1 THR S 40 " model vdw 2.320 2.440 nonbonded pdb=" O TYR A 478 " pdb=" OG1 THR A 482 " model vdw 2.320 2.440 ... (remaining 90704 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 4.010 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.300 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 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: 41.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11872 Z= 0.213 Angle : 0.613 11.446 16228 Z= 0.349 Chirality : 0.041 0.193 1969 Planarity : 0.006 0.066 2071 Dihedral : 12.403 89.277 4076 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.31 % Allowed : 9.78 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.15), residues: 1561 helix: -2.32 (0.11), residues: 978 sheet: -1.54 (0.67), residues: 54 loop : -3.10 (0.22), residues: 529 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 332 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 8 residues processed: 350 average time/residue: 0.2652 time to fit residues: 126.8934 Evaluate side-chains 217 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 209 time to evaluate : 1.394 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1121 time to fit residues: 3.4979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 216 GLN A 266 GLN A 333 GLN A 387 GLN A 488 GLN A 495 ASN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 ASN B 59 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN B 278 ASN B 504 GLN B 505 GLN M 35 ASN M 123 ASN N 121 HIS ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 202 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11872 Z= 0.235 Angle : 0.601 8.482 16228 Z= 0.304 Chirality : 0.041 0.205 1969 Planarity : 0.004 0.049 2071 Dihedral : 4.319 24.543 1686 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.84 % Allowed : 17.33 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.20), residues: 1561 helix: -0.25 (0.15), residues: 975 sheet: -0.99 (0.69), residues: 54 loop : -2.50 (0.25), residues: 532 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 240 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 257 average time/residue: 0.2469 time to fit residues: 89.2250 Evaluate side-chains 216 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1121 time to fit residues: 5.3277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 0.7980 chunk 126 optimal weight: 0.4980 chunk 140 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 59 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11872 Z= 0.211 Angle : 0.590 13.013 16228 Z= 0.294 Chirality : 0.041 0.304 1969 Planarity : 0.004 0.053 2071 Dihedral : 4.172 22.403 1686 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.22 % Allowed : 18.31 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1561 helix: 0.50 (0.16), residues: 987 sheet: -0.55 (0.71), residues: 54 loop : -2.27 (0.26), residues: 520 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 235 average time/residue: 0.2500 time to fit residues: 83.4904 Evaluate side-chains 209 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 195 time to evaluate : 1.457 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1289 time to fit residues: 5.0645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 67 optimal weight: 6.9990 chunk 95 optimal weight: 0.3980 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 531 HIS B 59 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 GLN M 35 ASN ** M 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11872 Z= 0.187 Angle : 0.578 9.545 16228 Z= 0.287 Chirality : 0.040 0.268 1969 Planarity : 0.003 0.042 2071 Dihedral : 4.099 21.264 1686 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.60 % Allowed : 20.09 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.22), residues: 1561 helix: 0.89 (0.17), residues: 980 sheet: -0.32 (0.72), residues: 54 loop : -2.15 (0.27), residues: 527 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 203 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 213 average time/residue: 0.2571 time to fit residues: 78.5024 Evaluate side-chains 191 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 1.415 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1102 time to fit residues: 3.3133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 112 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 GLN B 75 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 11872 Z= 0.461 Angle : 0.766 13.343 16228 Z= 0.384 Chirality : 0.046 0.314 1969 Planarity : 0.004 0.048 2071 Dihedral : 4.529 23.259 1686 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.58 % Allowed : 22.22 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1561 helix: 0.79 (0.17), residues: 973 sheet: -0.53 (0.72), residues: 54 loop : -2.16 (0.27), residues: 534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 205 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 18 residues processed: 223 average time/residue: 0.2407 time to fit residues: 77.5706 Evaluate side-chains 215 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 1.349 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1284 time to fit residues: 5.8224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.5980 chunk 135 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11872 Z= 0.208 Angle : 0.622 10.986 16228 Z= 0.310 Chirality : 0.042 0.279 1969 Planarity : 0.004 0.041 2071 Dihedral : 4.297 23.223 1686 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.33 % Allowed : 23.29 % Favored : 75.38 % 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: 0.03 (0.22), residues: 1561 helix: 1.10 (0.17), residues: 979 sheet: -0.48 (0.72), residues: 54 loop : -2.03 (0.27), residues: 528 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 207 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 216 average time/residue: 0.2492 time to fit residues: 78.5257 Evaluate side-chains 201 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 195 time to evaluate : 1.565 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1178 time to fit residues: 3.2100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 150 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11872 Z= 0.202 Angle : 0.620 14.200 16228 Z= 0.305 Chirality : 0.042 0.293 1969 Planarity : 0.004 0.042 2071 Dihedral : 4.186 20.839 1686 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.33 % Allowed : 24.36 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1561 helix: 1.15 (0.17), residues: 988 sheet: -0.42 (0.74), residues: 54 loop : -2.04 (0.27), residues: 519 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 210 average time/residue: 0.2447 time to fit residues: 74.3712 Evaluate side-chains 201 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 1.407 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1690 time to fit residues: 4.3174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 chunk 102 optimal weight: 1.9990 chunk 74 optimal weight: 0.0010 chunk 14 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 overall best weight: 1.0170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 23 ASN B 59 GLN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11872 Z= 0.244 Angle : 0.641 12.094 16228 Z= 0.316 Chirality : 0.043 0.302 1969 Planarity : 0.004 0.042 2071 Dihedral : 4.230 21.221 1686 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.16 % Allowed : 24.71 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1561 helix: 1.15 (0.17), residues: 989 sheet: -0.52 (0.73), residues: 54 loop : -2.03 (0.27), residues: 518 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 202 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 211 average time/residue: 0.2327 time to fit residues: 70.9687 Evaluate side-chains 199 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 193 time to evaluate : 1.458 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1179 time to fit residues: 3.2714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.0970 chunk 42 optimal weight: 0.1980 chunk 126 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 139 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11872 Z= 0.172 Angle : 0.610 11.788 16228 Z= 0.303 Chirality : 0.042 0.301 1969 Planarity : 0.003 0.043 2071 Dihedral : 4.136 20.146 1686 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.71 % Allowed : 25.33 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1561 helix: 1.26 (0.17), residues: 980 sheet: -0.38 (0.75), residues: 54 loop : -1.93 (0.27), residues: 527 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 209 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 211 average time/residue: 0.2244 time to fit residues: 69.3748 Evaluate side-chains 191 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 187 time to evaluate : 1.347 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1060 time to fit residues: 2.6396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 155 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 95 optimal weight: 0.0970 chunk 75 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11872 Z= 0.197 Angle : 0.641 14.781 16228 Z= 0.313 Chirality : 0.042 0.308 1969 Planarity : 0.003 0.043 2071 Dihedral : 4.131 19.494 1686 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.27 % Allowed : 25.69 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1561 helix: 1.23 (0.17), residues: 981 sheet: -0.29 (0.73), residues: 54 loop : -1.90 (0.27), residues: 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 191 time to evaluate : 1.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 193 average time/residue: 0.2326 time to fit residues: 65.8016 Evaluate side-chains 185 residues out of total 1401 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 183 time to evaluate : 1.475 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1205 time to fit residues: 2.3209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** N 192 HIS ** 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 = 0.3989 r_free = 0.3989 target = 0.157340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125637 restraints weight = 21435.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.128186 restraints weight = 14705.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130288 restraints weight = 10556.008| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11872 Z= 0.186 Angle : 0.617 11.809 16228 Z= 0.305 Chirality : 0.042 0.304 1969 Planarity : 0.003 0.043 2071 Dihedral : 4.087 20.992 1686 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.27 % Allowed : 25.87 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1561 helix: 1.29 (0.17), residues: 981 sheet: -0.26 (0.73), residues: 54 loop : -1.87 (0.27), residues: 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2388.58 seconds wall clock time: 44 minutes 18.29 seconds (2658.29 seconds total)