Starting phenix.real_space_refine on Fri Mar 15 19:25:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw8_24710/03_2024/7rw8_24710.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw8_24710/03_2024/7rw8_24710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw8_24710/03_2024/7rw8_24710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw8_24710/03_2024/7rw8_24710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw8_24710/03_2024/7rw8_24710.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rw8_24710/03_2024/7rw8_24710.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 8136 2.51 5 N 2113 2.21 5 O 2263 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 176": "OD1" <-> "OD2" Residue "M ASP 218": "OD1" <-> "OD2" Residue "M TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 27": "OE1" <-> "OE2" Residue "S GLU 34": "OE1" <-> "OE2" Residue "S TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12572 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4389 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 22, 'TRANS': 575} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 17, 'ARG:plan': 15, 'ASN:plan1': 5, 'ASP:plan': 18} Unresolved non-hydrogen planarities: 232 Chain: "B" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4086 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 144} Link IDs: {'PTRANS': 26, 'TRANS': 552} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 515 Unresolved non-hydrogen angles: 618 Unresolved non-hydrogen dihedrals: 422 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 12, 'ASP:plan': 20, 'GLU:plan': 25, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 305 Chain: "M" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 2969 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain breaks: 3 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 10, 'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 133 Chain: "S" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1128 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 140} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 7.23, per 1000 atoms: 0.58 Number of scatterers: 12572 At special positions: 0 Unit cell: (97.9, 110.36, 129.94, 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 60 16.00 O 2263 8.00 N 2113 7.00 C 8136 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: 4.95 Conformation dependent library (CDL) restraints added in 2.3 seconds 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 7 sheets defined 63.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.597A pdb=" N SER A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 46 Processing helix chain 'A' and resid 51 through 69 removed outlier: 3.587A pdb=" N GLY A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.735A pdb=" N LEU A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 Processing helix chain 'A' and resid 105 through 122 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 161 through 179 Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.760A pdb=" N VAL A 183 " --> pdb=" O PRO A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 200 through 216 Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.070A pdb=" N PHE A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.646A 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: 3.864A pdb=" N SER A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 Processing helix chain 'A' and resid 342 through 357 removed outlier: 3.596A pdb=" N ARG A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 369 removed outlier: 3.975A pdb=" N HIS A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 382 through 396 Processing helix chain 'A' and resid 401 through 416 removed outlier: 3.901A pdb=" N GLU A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR A 415 " --> pdb=" O SER A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 435 removed outlier: 4.218A pdb=" N GLU A 422 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 460 through 472 removed outlier: 3.734A 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 511 No H-bonds generated for 'chain 'A' and resid 509 through 511' Processing helix chain 'A' and resid 514 through 517 Processing helix chain 'A' and resid 518 through 531 removed outlier: 4.017A pdb=" N HIS A 531 " --> pdb=" O HIS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 552 removed outlier: 3.504A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 564 removed outlier: 3.890A pdb=" N VAL A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.534A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 589 Processing helix chain 'A' and resid 591 through 599 removed outlier: 3.537A pdb=" N THR A 597 " --> pdb=" O ASP A 593 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 598 " --> pdb=" O ILE A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 23 removed outlier: 3.659A pdb=" N ASN B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 43 removed outlier: 3.960A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) 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 58 Processing helix chain 'B' and resid 62 through 80 removed outlier: 3.563A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS B 78 " --> pdb=" O MET B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 86 removed outlier: 3.527A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET B 86 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 92 removed outlier: 3.563A pdb=" N PHE B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 99 through 112 removed outlier: 4.028A pdb=" N ARG B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.903A pdb=" N THR B 119 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 removed outlier: 3.589A pdb=" N LEU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 127 " --> pdb=" O CYS B 123 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 122 through 128' Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.994A pdb=" N ARG B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 170 removed outlier: 4.263A pdb=" N ALA B 170 " --> pdb=" O ARG B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 189 removed outlier: 5.346A pdb=" N ALA B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 4.388A pdb=" N ASN B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 228 removed outlier: 3.802A pdb=" N ILE B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 276 through 284 Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.930A pdb=" N LEU B 288 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 313 removed outlier: 3.756A pdb=" N LEU B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 325 removed outlier: 3.616A pdb=" N VAL B 323 " --> pdb=" O GLU B 320 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 325 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 345 removed outlier: 3.948A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.729A pdb=" N ALA B 356 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B 360 " --> pdb=" O ALA B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 384 removed outlier: 3.590A pdb=" N ALA B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE B 382 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 403 through 421 removed outlier: 3.559A pdb=" N GLU B 409 " --> pdb=" O TYR B 405 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 435 removed outlier: 3.556A pdb=" N GLU B 434 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASN B 435 " --> pdb=" O THR B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 461 through 471 removed outlier: 3.808A pdb=" N GLU B 471 " --> pdb=" O GLU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 499 through 512 Processing helix chain 'B' and resid 516 through 531 Processing helix chain 'B' and resid 533 through 542 removed outlier: 3.559A pdb=" N ALA B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 538 " --> pdb=" O PRO B 534 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 539 " --> pdb=" O VAL B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 566 Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.595A pdb=" N PHE B 581 " --> pdb=" O PRO B 578 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 36 removed outlier: 3.776A pdb=" N VAL M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 74 through 94 removed outlier: 3.534A pdb=" N VAL M 78 " --> pdb=" O ASN M 74 " (cutoff:3.500A) removed outlier: 3.527A 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 115 Processing helix chain 'M' and resid 128 through 133 removed outlier: 4.160A pdb=" N PHE M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'S' and resid 24 through 42 removed outlier: 3.512A pdb=" N VAL S 41 " --> pdb=" O ALA S 37 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG S 42 " --> pdb=" O VAL S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 96 Processing helix chain 'S' and resid 99 through 106 Processing helix chain 'S' and resid 106 through 117 Processing helix chain 'S' and resid 127 through 141 Processing sheet with id=AA1, first strand: chain 'M' and resid 14 through 19 Processing sheet with id=AA2, first strand: chain 'M' and resid 116 through 117 removed outlier: 3.530A pdb=" N ASP M 117 " --> pdb=" O TYR M 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 245 through 248 removed outlier: 5.917A pdb=" N GLU M 271 " --> pdb=" O SER M 204 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER M 204 " --> pdb=" O GLU M 271 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLU M 273 " --> pdb=" O MET M 202 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N MET M 202 " --> pdb=" O GLU M 273 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET M 275 " --> pdb=" O VAL M 200 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU M 173 " --> pdb=" O TRP M 421 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N ARG M 423 " --> pdb=" O LEU M 173 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU M 175 " --> pdb=" O ARG M 423 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE M 425 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL M 177 " --> pdb=" O ILE M 425 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ARG M 427 " --> pdb=" O VAL M 177 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU M 179 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY M 429 " --> pdb=" O GLU M 179 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL M 181 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N TYR M 431 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU M 183 " --> pdb=" O TYR M 431 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N THR M 433 " --> pdb=" O LEU M 183 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET M 185 " --> pdb=" O THR M 433 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ARG M 427 " --> pdb=" O VAL M 392 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL M 392 " --> pdb=" O ARG M 427 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY M 429 " --> pdb=" O PHE M 390 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N PHE M 390 " --> pdb=" O GLY M 429 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR M 431 " --> pdb=" O MET M 388 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU M 391 " --> pdb=" O LYS M 319 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LYS M 319 " --> pdb=" O GLU M 391 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU M 316 " --> pdb=" O ALA M 359 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA M 359 " --> pdb=" O LEU M 316 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N GLN M 318 " --> pdb=" O ARG M 357 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ARG M 357 " --> pdb=" O GLN M 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 253 through 254 Processing sheet with id=AA5, first strand: chain 'M' and resid 287 through 294 removed outlier: 3.524A pdb=" N GLY M 332 " --> pdb=" O GLU M 371 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 14 through 19 removed outlier: 6.531A pdb=" N THR S 14 " --> pdb=" O ASN S 9 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN S 9 " --> pdb=" O THR S 14 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS S 70 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ILE S 5 " --> pdb=" O CYS S 68 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N CYS S 68 " --> pdb=" O ILE S 5 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE S 7 " --> pdb=" O TYR S 66 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR S 66 " --> pdb=" O ILE S 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 118 through 119 794 hydrogen bonds defined for protein. 2325 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 5.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4064 1.34 - 1.46: 1943 1.46 - 1.57: 6713 1.57 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 12808 Sorted by residual: bond pdb=" CG1 ILE A 17 " pdb=" CD1 ILE A 17 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.57e+00 bond pdb=" CB CYS A 171 " pdb=" SG CYS A 171 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CB VAL A 483 " pdb=" CG1 VAL A 483 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CB VAL B 298 " pdb=" CG1 VAL B 298 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CB MET S 117 " pdb=" CG MET S 117 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 9.81e-01 ... (remaining 12803 not shown) Histogram of bond angle deviations from ideal: 97.51 - 104.82: 184 104.82 - 112.14: 6795 112.14 - 119.45: 3986 119.45 - 126.77: 6414 126.77 - 134.08: 130 Bond angle restraints: 17509 Sorted by residual: angle pdb=" N ASN B 179 " pdb=" CA ASN B 179 " pdb=" C ASN B 179 " ideal model delta sigma weight residual 113.18 105.78 7.40 1.33e+00 5.65e-01 3.10e+01 angle pdb=" CA GLU A 601 " pdb=" C GLU A 601 " pdb=" O GLU A 601 " ideal model delta sigma weight residual 120.51 113.88 6.63 1.43e+00 4.89e-01 2.15e+01 angle pdb=" CA GLU A 601 " pdb=" C GLU A 601 " pdb=" N MET A 602 " ideal model delta sigma weight residual 116.84 123.58 -6.74 1.71e+00 3.42e-01 1.56e+01 angle pdb=" N HIS A 493 " pdb=" CA HIS A 493 " pdb=" C HIS A 493 " ideal model delta sigma weight residual 108.34 113.09 -4.75 1.31e+00 5.83e-01 1.32e+01 angle pdb=" C GLU A 600 " pdb=" N GLU A 601 " pdb=" CA GLU A 601 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 ... (remaining 17504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7048 18.00 - 35.99: 513 35.99 - 53.99: 83 53.99 - 71.99: 15 71.99 - 89.98: 10 Dihedral angle restraints: 7669 sinusoidal: 2595 harmonic: 5074 Sorted by residual: dihedral pdb=" CA HIS A 493 " pdb=" C HIS A 493 " pdb=" N GLU A 494 " pdb=" CA GLU A 494 " ideal model delta harmonic sigma weight residual 180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA TRP A 462 " pdb=" C TRP A 462 " pdb=" N TYR A 463 " pdb=" CA TYR A 463 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LEU B 248 " pdb=" C LEU B 248 " pdb=" N SER B 249 " pdb=" CA SER B 249 " ideal model delta harmonic sigma weight residual -180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 7666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1400 0.034 - 0.069: 577 0.069 - 0.103: 140 0.103 - 0.137: 45 0.137 - 0.172: 8 Chirality restraints: 2170 Sorted by residual: chirality pdb=" CG LEU B 68 " pdb=" CB LEU B 68 " pdb=" CD1 LEU B 68 " pdb=" CD2 LEU B 68 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.02e-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 2.38 0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2167 not shown) Planarity restraints: 2207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 179 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO A 180 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 64 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.63e+00 pdb=" C GLU B 64 " -0.037 2.00e-02 2.50e+03 pdb=" O GLU B 64 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 65 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 97 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO B 98 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " 0.029 5.00e-02 4.00e+02 ... (remaining 2204 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 75 2.63 - 3.20: 11575 3.20 - 3.77: 18770 3.77 - 4.33: 24370 4.33 - 4.90: 41725 Nonbonded interactions: 96515 Sorted by model distance: nonbonded pdb=" O ILE A 511 " pdb=" OG SER A 517 " model vdw 2.069 2.440 nonbonded pdb=" OE1 GLU B 297 " pdb=" OH TYR M 83 " model vdw 2.095 2.440 nonbonded pdb=" OD2 ASP A 444 " pdb=" OH TYR A 478 " model vdw 2.199 2.440 nonbonded pdb=" O VAL A 300 " pdb=" OG SER A 303 " model vdw 2.233 2.440 nonbonded pdb=" O LEU A 244 " pdb=" OG1 THR A 248 " model vdw 2.233 2.440 ... (remaining 96510 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: 2.000 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: 10.090 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 36.250 Find NCS groups from input model: 0.520 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 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 : 0.004 0.049 12808 Z= 0.258 Angle : 0.581 7.401 17509 Z= 0.321 Chirality : 0.041 0.172 2170 Planarity : 0.004 0.055 2207 Dihedral : 13.413 89.982 4361 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.99 (0.20), residues: 1696 helix: 1.59 (0.17), residues: 981 sheet: 1.03 (0.37), residues: 183 loop : -1.26 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 462 HIS 0.004 0.001 HIS A 70 PHE 0.019 0.002 PHE S 49 TYR 0.028 0.002 TYR B 70 ARG 0.003 0.000 ARG B 419 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.524 Fit side-chains REVERT: S 29 GLN cc_start: 0.6340 (mm-40) cc_final: 0.5580 (mm-40) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.2272 time to fit residues: 38.9960 Evaluate side-chains 74 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 98 optimal weight: 0.8980 chunk 153 optimal weight: 4.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 307 ASN M 49 ASN M 334 GLN M 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12808 Z= 0.265 Angle : 0.536 9.651 17509 Z= 0.280 Chirality : 0.040 0.149 2170 Planarity : 0.004 0.042 2207 Dihedral : 3.995 24.950 1823 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.73 % Allowed : 5.53 % Favored : 93.73 % 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: 1.26 (0.21), residues: 1696 helix: 1.78 (0.17), residues: 993 sheet: 1.15 (0.39), residues: 183 loop : -1.16 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 462 HIS 0.009 0.001 HIS A 200 PHE 0.014 0.001 PHE M 32 TYR 0.027 0.001 TYR A 247 ARG 0.004 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 1.461 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 84 average time/residue: 0.1753 time to fit residues: 25.3131 Evaluate side-chains 78 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 22 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 166 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 152 optimal weight: 0.3980 chunk 52 optimal weight: 0.7980 chunk 123 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12808 Z= 0.139 Angle : 0.474 12.213 17509 Z= 0.244 Chirality : 0.038 0.143 2170 Planarity : 0.003 0.035 2207 Dihedral : 3.779 23.734 1823 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.98 % Allowed : 7.65 % Favored : 91.38 % 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: 1.58 (0.21), residues: 1696 helix: 2.07 (0.17), residues: 988 sheet: 1.15 (0.38), residues: 183 loop : -1.03 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.005 0.001 HIS A 200 PHE 0.014 0.001 PHE M 105 TYR 0.015 0.001 TYR B 70 ARG 0.002 0.000 ARG S 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 1.489 Fit side-chains REVERT: A 418 TYR cc_start: 0.5280 (m-10) cc_final: 0.5042 (m-10) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 0.1876 time to fit residues: 27.5525 Evaluate side-chains 79 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 72 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain S residue 75 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12808 Z= 0.151 Angle : 0.459 11.831 17509 Z= 0.238 Chirality : 0.038 0.139 2170 Planarity : 0.003 0.035 2207 Dihedral : 3.665 23.093 1823 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.98 % Allowed : 8.87 % Favored : 90.15 % 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: 1.73 (0.21), residues: 1696 helix: 2.20 (0.17), residues: 993 sheet: 1.17 (0.38), residues: 184 loop : -0.98 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 462 HIS 0.004 0.001 HIS A 200 PHE 0.010 0.001 PHE M 105 TYR 0.019 0.001 TYR M 277 ARG 0.002 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.456 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 83 average time/residue: 0.1844 time to fit residues: 25.8488 Evaluate side-chains 82 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain S residue 75 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 67 optimal weight: 0.1980 chunk 139 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12808 Z= 0.146 Angle : 0.459 11.814 17509 Z= 0.235 Chirality : 0.038 0.140 2170 Planarity : 0.003 0.034 2207 Dihedral : 3.585 22.221 1823 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.38 % Allowed : 9.52 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.21), residues: 1696 helix: 2.30 (0.17), residues: 994 sheet: 1.17 (0.38), residues: 184 loop : -0.94 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 462 HIS 0.004 0.001 HIS A 200 PHE 0.010 0.001 PHE M 93 TYR 0.011 0.001 TYR M 277 ARG 0.002 0.000 ARG S 60 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 1.525 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 88 average time/residue: 0.1747 time to fit residues: 26.2663 Evaluate side-chains 82 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain S residue 75 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12808 Z= 0.166 Angle : 0.467 14.358 17509 Z= 0.238 Chirality : 0.038 0.142 2170 Planarity : 0.003 0.035 2207 Dihedral : 3.566 22.105 1823 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.30 % Allowed : 10.01 % Favored : 88.69 % 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: 1.95 (0.21), residues: 1696 helix: 2.40 (0.17), residues: 995 sheet: 1.15 (0.38), residues: 184 loop : -0.92 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 462 HIS 0.003 0.001 HIS A 200 PHE 0.009 0.001 PHE M 93 TYR 0.009 0.001 TYR M 8 ARG 0.002 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.515 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 86 average time/residue: 0.1740 time to fit residues: 25.4815 Evaluate side-chains 83 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 0.0270 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12808 Z= 0.144 Angle : 0.458 13.254 17509 Z= 0.236 Chirality : 0.038 0.141 2170 Planarity : 0.003 0.034 2207 Dihedral : 3.524 22.037 1823 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.30 % Allowed : 10.25 % Favored : 88.45 % 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: 1696 helix: 2.46 (0.17), residues: 996 sheet: 1.16 (0.38), residues: 184 loop : -0.86 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 462 HIS 0.003 0.001 HIS A 200 PHE 0.009 0.001 PHE M 93 TYR 0.008 0.001 TYR M 8 ARG 0.002 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 1.525 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 89 average time/residue: 0.1729 time to fit residues: 26.6386 Evaluate side-chains 86 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 68 CYS Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 128 optimal weight: 9.9990 chunk 148 optimal weight: 0.6980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12808 Z= 0.159 Angle : 0.466 13.711 17509 Z= 0.239 Chirality : 0.038 0.139 2170 Planarity : 0.003 0.035 2207 Dihedral : 3.520 22.314 1823 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.06 % Allowed : 10.90 % Favored : 88.04 % 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: 2.10 (0.21), residues: 1696 helix: 2.51 (0.17), residues: 996 sheet: 1.20 (0.38), residues: 184 loop : -0.84 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 462 HIS 0.003 0.001 HIS A 200 PHE 0.009 0.001 PHE M 56 TYR 0.009 0.001 TYR M 8 ARG 0.002 0.000 ARG A 388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.630 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 88 average time/residue: 0.1735 time to fit residues: 26.5817 Evaluate side-chains 87 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 75 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 0.0000 chunk 143 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12808 Z= 0.128 Angle : 0.461 13.281 17509 Z= 0.235 Chirality : 0.038 0.145 2170 Planarity : 0.003 0.036 2207 Dihedral : 3.447 22.306 1823 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.14 % Allowed : 11.07 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.21), residues: 1696 helix: 2.55 (0.17), residues: 996 sheet: 1.27 (0.38), residues: 182 loop : -0.80 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 462 HIS 0.003 0.001 HIS A 200 PHE 0.009 0.001 PHE M 93 TYR 0.007 0.001 TYR M 8 ARG 0.001 0.000 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 1.591 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 91 average time/residue: 0.1808 time to fit residues: 28.2052 Evaluate side-chains 88 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 0.0470 chunk 111 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12808 Z= 0.143 Angle : 0.475 13.923 17509 Z= 0.238 Chirality : 0.038 0.146 2170 Planarity : 0.003 0.036 2207 Dihedral : 3.433 22.581 1823 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.06 % Allowed : 11.15 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.21), residues: 1696 helix: 2.57 (0.17), residues: 995 sheet: 1.21 (0.38), residues: 184 loop : -0.74 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 462 HIS 0.003 0.001 HIS A 70 PHE 0.009 0.001 PHE M 56 TYR 0.009 0.001 TYR B 405 ARG 0.001 0.000 ARG A 341 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3392 Ramachandran restraints generated. 1696 Oldfield, 0 Emsley, 1696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 1.565 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 86 average time/residue: 0.1802 time to fit residues: 26.3156 Evaluate side-chains 89 residues out of total 1527 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain M residue 435 CYS Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 40 THR Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain S residue 115 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.1980 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.064430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.047512 restraints weight = 56214.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.049259 restraints weight = 30646.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.050451 restraints weight = 20979.584| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12808 Z= 0.192 Angle : 0.487 13.866 17509 Z= 0.246 Chirality : 0.038 0.141 2170 Planarity : 0.003 0.037 2207 Dihedral : 3.474 22.578 1823 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.06 % Allowed : 11.15 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.21), residues: 1696 helix: 2.59 (0.17), residues: 994 sheet: 1.15 (0.38), residues: 183 loop : -0.74 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 462 HIS 0.003 0.001 HIS A 70 PHE 0.027 0.001 PHE M 174 TYR 0.009 0.001 TYR M 8 ARG 0.002 0.000 ARG M 423 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2054.09 seconds wall clock time: 38 minutes 9.97 seconds (2289.97 seconds total)