Starting phenix.real_space_refine on Mon Mar 18 14:19:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4b_22663/03_2024/7k4b_22663_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4b_22663/03_2024/7k4b_22663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4b_22663/03_2024/7k4b_22663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4b_22663/03_2024/7k4b_22663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4b_22663/03_2024/7k4b_22663_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4b_22663/03_2024/7k4b_22663_neut.pdb" } resolution = 3.1 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= 0.040 sd= 0.167 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 16 5.49 5 S 160 5.16 5 C 13982 2.51 5 N 3351 2.21 5 O 3608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 75": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 492": "NH1" <-> "NH2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 594": "NH1" <-> "NH2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ARG 492": "NH1" <-> "NH2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "C ARG 25": "NH1" <-> "NH2" Residue "C ARG 26": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 263": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 350": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "C ARG 492": "NH1" <-> "NH2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 594": "NH1" <-> "NH2" Residue "C ARG 606": "NH1" <-> "NH2" Residue "C ARG 610": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "C ARG 628": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 180": "NH1" <-> "NH2" Residue "D ARG 263": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D ARG 326": "NH1" <-> "NH2" Residue "D ARG 350": "NH1" <-> "NH2" Residue "D ARG 385": "NH1" <-> "NH2" Residue "D ARG 492": "NH1" <-> "NH2" Residue "D PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 606": "NH1" <-> "NH2" Residue "D ARG 610": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21118 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4891 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 26, 'TRANS': 580} Chain breaks: 1 Chain: "B" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4891 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 26, 'TRANS': 580} Chain breaks: 1 Chain: "C" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4891 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 26, 'TRANS': 580} Chain breaks: 1 Chain: "D" Number of atoms: 4891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4891 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 26, 'TRANS': 580} Chain breaks: 1 Chain: "A" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 408 Unusual residues: {' CA': 1, 'PCW': 12, 'VUG': 2, 'Y01': 2} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-2': 2, 'PCW:plan-3': 8, 'PCW:plan-4': 9} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 442 Unusual residues: {'PCW': 12, 'VUG': 2, 'Y01': 3} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-2': 2, 'PCW:plan-3': 8, 'PCW:plan-4': 9} Unresolved non-hydrogen planarities: 94 Chain: "C" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 347 Unusual residues: {'PCW': 12, 'VUG': 1, 'Y01': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-2': 2, 'PCW:plan-3': 8, 'PCW:plan-4': 9} Unresolved non-hydrogen planarities: 94 Chain: "D" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 357 Unusual residues: {'PCW': 12, 'Y01': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 361 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 8, 'PCW:plan-2': 2, 'PCW:plan-3': 8, 'PCW:plan-4': 9} Unresolved non-hydrogen planarities: 94 Time building chain proxies: 11.74, per 1000 atoms: 0.56 Number of scatterers: 21118 At special positions: 0 Unit cell: (143.59, 143.59, 122.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 160 16.00 P 16 15.00 O 3608 8.00 N 3351 7.00 C 13982 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: 8.22 Conformation dependent library (CDL) restraints added in 3.4 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 4 sheets defined 58.6% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 29 through 46 removed outlier: 3.656A pdb=" N GLN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 66 removed outlier: 4.040A pdb=" N LYS A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 101 removed outlier: 3.765A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.851A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 107 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.620A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.751A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 removed outlier: 3.630A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.549A pdb=" N ARG A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.529A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 203' Processing helix chain 'A' and resid 210 through 222 removed outlier: 3.807A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.551A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 263 removed outlier: 3.876A pdb=" N LYS A 262 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.674A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.577A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A 306 " --> pdb=" O GLU A 303 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.680A pdb=" N SER A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 331 through 340 removed outlier: 3.502A pdb=" N LEU A 337 " --> pdb=" O GLY A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 removed outlier: 4.046A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 398 removed outlier: 3.767A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 426 through 445 removed outlier: 3.724A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 removed outlier: 3.558A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 465 Processing helix chain 'A' and resid 476 through 487 removed outlier: 3.861A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 482 " --> pdb=" O PHE A 478 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET A 485 " --> pdb=" O MET A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 removed outlier: 4.024A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 505 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 539 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.923A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 575 removed outlier: 3.514A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 removed outlier: 3.803A pdb=" N HIS A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP A 583 " --> pdb=" O GLY A 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 578 through 583' Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 593 through 608 Processing helix chain 'B' and resid 29 through 46 removed outlier: 3.656A pdb=" N GLN B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 66 removed outlier: 4.039A pdb=" N LYS B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 101 removed outlier: 3.765A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.851A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 107 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.620A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.751A pdb=" N ALA B 135 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 removed outlier: 3.630A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.550A pdb=" N ARG B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.529A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 203' Processing helix chain 'B' and resid 210 through 222 removed outlier: 3.806A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.551A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 259 through 263 removed outlier: 3.877A pdb=" N LYS B 262 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 removed outlier: 3.674A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.577A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 318 removed outlier: 3.680A pdb=" N SER B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 331 through 340 removed outlier: 3.503A pdb=" N LEU B 337 " --> pdb=" O GLY B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 349 removed outlier: 4.046A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 398 removed outlier: 3.766A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 426 through 445 removed outlier: 3.724A pdb=" N TYR B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 458 removed outlier: 3.558A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 465 Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.863A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE B 482 " --> pdb=" O PHE B 478 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET B 485 " --> pdb=" O MET B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 512 removed outlier: 4.024A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 539 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.923A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 removed outlier: 3.514A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 583 removed outlier: 3.803A pdb=" N HIS B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N TRP B 583 " --> pdb=" O GLY B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 578 through 583' Processing helix chain 'B' and resid 587 through 592 Processing helix chain 'B' and resid 593 through 608 Processing helix chain 'C' and resid 29 through 46 removed outlier: 3.656A pdb=" N GLN C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C 39 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 66 removed outlier: 4.040A pdb=" N LYS C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 66 " --> pdb=" O ASN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 101 removed outlier: 3.764A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 removed outlier: 3.851A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.620A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN C 127 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.751A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 172 removed outlier: 3.630A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.549A pdb=" N ARG C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.529A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 198 through 203' Processing helix chain 'C' and resid 210 through 222 removed outlier: 3.806A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.550A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.876A pdb=" N LYS C 262 " --> pdb=" O LEU C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 removed outlier: 3.674A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 removed outlier: 3.577A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C 306 " --> pdb=" O GLU C 303 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 318 removed outlier: 3.681A pdb=" N SER C 318 " --> pdb=" O LYS C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 Processing helix chain 'C' and resid 331 through 340 removed outlier: 3.503A pdb=" N LEU C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 349 removed outlier: 4.046A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 398 removed outlier: 3.766A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 426 through 445 removed outlier: 3.724A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 458 removed outlier: 3.558A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'C' and resid 476 through 487 removed outlier: 3.861A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 482 " --> pdb=" O PHE C 478 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 512 removed outlier: 4.024A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 539 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.923A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 575 removed outlier: 3.514A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 583 removed outlier: 3.803A pdb=" N HIS C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP C 583 " --> pdb=" O GLY C 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 578 through 583' Processing helix chain 'C' and resid 587 through 592 Processing helix chain 'C' and resid 593 through 608 Processing helix chain 'D' and resid 29 through 46 removed outlier: 3.655A pdb=" N GLN D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 66 removed outlier: 4.039A pdb=" N LYS D 63 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.765A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 108 removed outlier: 3.852A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.620A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN D 127 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 removed outlier: 3.752A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.630A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.550A pdb=" N ARG D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.528A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 198 through 203' Processing helix chain 'D' and resid 210 through 222 removed outlier: 3.807A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.550A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 258 Processing helix chain 'D' and resid 259 through 263 removed outlier: 3.877A pdb=" N LYS D 262 " --> pdb=" O LEU D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.674A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 removed outlier: 3.577A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN D 306 " --> pdb=" O GLU D 303 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 318 removed outlier: 3.680A pdb=" N SER D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 331 through 340 removed outlier: 3.503A pdb=" N LEU D 337 " --> pdb=" O GLY D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 349 removed outlier: 4.046A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 398 removed outlier: 3.767A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 426 through 445 removed outlier: 3.724A pdb=" N TYR D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.558A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 465 Processing helix chain 'D' and resid 476 through 487 removed outlier: 3.862A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 482 " --> pdb=" O PHE D 478 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N MET D 485 " --> pdb=" O MET D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 512 removed outlier: 4.023A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA D 505 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 539 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.923A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 575 removed outlier: 3.514A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 578 through 583 removed outlier: 3.802A pdb=" N HIS D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP D 583 " --> pdb=" O GLY D 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 578 through 583' Processing helix chain 'D' and resid 587 through 592 Processing helix chain 'D' and resid 593 through 608 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 270 removed outlier: 6.087A pdb=" N THR A 266 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU A 277 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP A 268 " --> pdb=" O SER A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 266 through 270 removed outlier: 6.087A pdb=" N THR B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU B 277 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP B 268 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 266 through 270 removed outlier: 6.087A pdb=" N THR C 266 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU C 277 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP C 268 " --> pdb=" O SER C 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 266 through 270 removed outlier: 6.087A pdb=" N THR D 266 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU D 277 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP D 268 " --> pdb=" O SER D 275 " (cutoff:3.500A) 718 hydrogen bonds defined for protein. 2058 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: 5.83 Time building geometry restraints manager: 8.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3185 1.31 - 1.43: 5634 1.43 - 1.56: 12401 1.56 - 1.68: 68 1.68 - 1.81: 272 Bond restraints: 21560 Sorted by residual: bond pdb=" C19 PCW B 708 " pdb=" C20 PCW B 708 " ideal model delta sigma weight residual 1.333 1.548 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C19 PCW D 709 " pdb=" C20 PCW D 709 " ideal model delta sigma weight residual 1.333 1.547 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C19 PCW A 704 " pdb=" C20 PCW A 704 " ideal model delta sigma weight residual 1.333 1.547 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C19 PCW C 706 " pdb=" C20 PCW C 706 " ideal model delta sigma weight residual 1.333 1.547 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C19 PCW D 706 " pdb=" C20 PCW D 706 " ideal model delta sigma weight residual 1.333 1.545 -0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 21555 not shown) Histogram of bond angle deviations from ideal: 98.79 - 105.84: 524 105.84 - 112.89: 11485 112.89 - 119.94: 7934 119.94 - 126.99: 8741 126.99 - 134.04: 310 Bond angle restraints: 28994 Sorted by residual: angle pdb=" C19 PCW A 709 " pdb=" C20 PCW A 709 " pdb=" C21 PCW A 709 " ideal model delta sigma weight residual 127.82 110.02 17.80 3.00e+00 1.11e-01 3.52e+01 angle pdb=" C19 PCW D 714 " pdb=" C20 PCW D 714 " pdb=" C21 PCW D 714 " ideal model delta sigma weight residual 127.82 110.25 17.57 3.00e+00 1.11e-01 3.43e+01 angle pdb=" C THR A 360 " pdb=" N SER A 361 " pdb=" CA SER A 361 " ideal model delta sigma weight residual 122.29 130.86 -8.57 1.48e+00 4.57e-01 3.35e+01 angle pdb=" C THR D 360 " pdb=" N SER D 361 " pdb=" CA SER D 361 " ideal model delta sigma weight residual 122.29 130.82 -8.53 1.48e+00 4.57e-01 3.32e+01 angle pdb=" C THR B 360 " pdb=" N SER B 361 " pdb=" CA SER B 361 " ideal model delta sigma weight residual 122.29 130.79 -8.50 1.48e+00 4.57e-01 3.30e+01 ... (remaining 28989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.07: 12817 29.07 - 58.15: 621 58.15 - 87.22: 114 87.22 - 116.29: 8 116.29 - 145.37: 13 Dihedral angle restraints: 13573 sinusoidal: 6453 harmonic: 7120 Sorted by residual: dihedral pdb=" CA ASN A 129 " pdb=" C ASN A 129 " pdb=" N MET A 130 " pdb=" CA MET A 130 " ideal model delta harmonic sigma weight residual 180.00 149.05 30.95 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA ASN B 129 " pdb=" C ASN B 129 " pdb=" N MET B 130 " pdb=" CA MET B 130 " ideal model delta harmonic sigma weight residual 180.00 149.08 30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA ASN C 129 " pdb=" C ASN C 129 " pdb=" N MET C 130 " pdb=" CA MET C 130 " ideal model delta harmonic sigma weight residual 180.00 149.10 30.90 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 13570 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2829 0.101 - 0.201: 297 0.201 - 0.302: 25 0.302 - 0.402: 11 0.402 - 0.503: 4 Chirality restraints: 3166 Sorted by residual: chirality pdb=" CG LEU A 367 " pdb=" CB LEU A 367 " pdb=" CD1 LEU A 367 " pdb=" CD2 LEU A 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" CG LEU D 367 " pdb=" CB LEU D 367 " pdb=" CD1 LEU D 367 " pdb=" CD2 LEU D 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.28e+00 chirality pdb=" CG LEU C 367 " pdb=" CB LEU C 367 " pdb=" CD1 LEU C 367 " pdb=" CD2 LEU C 367 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.24e+00 ... (remaining 3163 not shown) Planarity restraints: 3538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW B 703 " 0.147 2.00e-02 2.50e+03 1.34e-01 1.80e+02 pdb=" C19 PCW B 703 " -0.174 2.00e-02 2.50e+03 pdb=" C20 PCW B 703 " -0.086 2.00e-02 2.50e+03 pdb=" C21 PCW B 703 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW C 702 " -0.145 2.00e-02 2.50e+03 1.32e-01 1.75e+02 pdb=" C19 PCW C 702 " 0.171 2.00e-02 2.50e+03 pdb=" C20 PCW C 702 " 0.086 2.00e-02 2.50e+03 pdb=" C21 PCW C 702 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW A 716 " 0.145 2.00e-02 2.50e+03 1.32e-01 1.74e+02 pdb=" C19 PCW A 716 " -0.171 2.00e-02 2.50e+03 pdb=" C20 PCW A 716 " -0.085 2.00e-02 2.50e+03 pdb=" C21 PCW A 716 " 0.111 2.00e-02 2.50e+03 ... (remaining 3535 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5690 2.81 - 3.33: 17769 3.33 - 3.85: 32652 3.85 - 4.38: 41664 4.38 - 4.90: 69820 Nonbonded interactions: 167595 Sorted by model distance: nonbonded pdb=" OG SER D 506 " pdb=" OH TYR D 526 " model vdw 2.287 2.440 nonbonded pdb=" OG SER B 506 " pdb=" OH TYR B 526 " model vdw 2.287 2.440 nonbonded pdb=" OG SER C 506 " pdb=" OH TYR C 526 " model vdw 2.287 2.440 nonbonded pdb=" OG SER A 506 " pdb=" OH TYR A 526 " model vdw 2.288 2.440 nonbonded pdb=" NH1 ARG B 632 " pdb=" OD1 ASP C 34 " model vdw 2.328 2.520 ... (remaining 167590 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 638 or (resid 708 through 709 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ )) or (resid 710 and (name C15 or name C16 or name C17 or name C18 or name C19)) \ )) selection = (chain 'B' and (resid 22 through 638 or (resid 708 through 709 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ )) or (resid 710 and (name C15 or name C16 or name C17 or name C18 or name C19)) \ )) selection = (chain 'C' and (resid 22 through 638 or resid 708 through 709 or (resid 710 and \ (name C15 or name C16 or name C17 or name C18 or name C19)))) selection = (chain 'D' and (resid 22 through 638 or (resid 708 through 709 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ )) or (resid 710 and (name C15 or name C16 or name C17 or name C18 or name C19)) \ )) } 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 individual isotropic 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: 0.010 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: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.790 Check model and map are aligned: 0.280 Set scattering table: 0.210 Process input model: 52.950 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.110 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 : 0.013 0.215 21560 Z= 0.807 Angle : 1.534 17.801 28994 Z= 0.697 Chirality : 0.067 0.503 3166 Planarity : 0.011 0.134 3538 Dihedral : 17.365 145.366 8965 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.91 % Favored : 91.00 % Rotamer: Outliers : 0.95 % Allowed : 5.62 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -6.09 (0.11), residues: 2412 helix: -4.21 (0.07), residues: 1364 sheet: -5.03 (0.19), residues: 84 loop : -3.42 (0.17), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 593 HIS 0.009 0.002 HIS B 582 PHE 0.024 0.003 PHE B 169 TYR 0.030 0.003 TYR A 547 ARG 0.011 0.001 ARG C 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 480 time to evaluate : 2.285 Fit side-chains REVERT: A 51 LEU cc_start: 0.8078 (tt) cc_final: 0.7796 (tp) REVERT: A 78 MET cc_start: 0.8288 (mmt) cc_final: 0.8018 (mmt) REVERT: A 90 ASP cc_start: 0.7995 (p0) cc_final: 0.7632 (m-30) REVERT: A 130 MET cc_start: 0.6181 (mmm) cc_final: 0.5605 (mmm) REVERT: A 174 ASN cc_start: 0.7626 (t0) cc_final: 0.7344 (t0) REVERT: A 211 PHE cc_start: 0.8673 (m-10) cc_final: 0.8391 (m-10) REVERT: A 306 GLN cc_start: 0.8389 (mt0) cc_final: 0.7831 (mm-40) REVERT: A 324 TYR cc_start: 0.8349 (m-10) cc_final: 0.8145 (m-80) REVERT: A 378 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7779 (pmm) REVERT: A 381 LYS cc_start: 0.7903 (mmtm) cc_final: 0.7082 (mtmm) REVERT: A 495 TRP cc_start: 0.9102 (m100) cc_final: 0.8845 (m100) REVERT: B 51 LEU cc_start: 0.8186 (tt) cc_final: 0.7924 (tp) REVERT: B 78 MET cc_start: 0.8369 (mmt) cc_final: 0.8121 (mmt) REVERT: B 90 ASP cc_start: 0.8036 (p0) cc_final: 0.7653 (m-30) REVERT: B 174 ASN cc_start: 0.7699 (t0) cc_final: 0.7241 (t0) REVERT: B 222 TYR cc_start: 0.8293 (m-80) cc_final: 0.8011 (m-80) REVERT: B 306 GLN cc_start: 0.8390 (mt0) cc_final: 0.7870 (mm-40) REVERT: B 315 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7745 (mt-10) REVERT: B 322 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8165 (mtpp) REVERT: B 381 LYS cc_start: 0.7960 (mmtm) cc_final: 0.7147 (mtmm) REVERT: B 481 MET cc_start: 0.7935 (ptt) cc_final: 0.7494 (ptt) REVERT: B 495 TRP cc_start: 0.9108 (m100) cc_final: 0.8870 (m100) REVERT: C 45 TRP cc_start: 0.7872 (m-10) cc_final: 0.7641 (m-10) REVERT: C 51 LEU cc_start: 0.8172 (tt) cc_final: 0.7938 (tp) REVERT: C 78 MET cc_start: 0.8442 (mmt) cc_final: 0.8201 (mmt) REVERT: C 90 ASP cc_start: 0.8087 (p0) cc_final: 0.7698 (m-30) REVERT: C 174 ASN cc_start: 0.7769 (t0) cc_final: 0.7567 (t0) REVERT: C 222 TYR cc_start: 0.8363 (m-80) cc_final: 0.8061 (m-80) REVERT: C 306 GLN cc_start: 0.8367 (mt0) cc_final: 0.7836 (mm-40) REVERT: C 315 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7736 (mt-10) REVERT: C 381 LYS cc_start: 0.7896 (mmtm) cc_final: 0.7036 (ttpp) REVERT: C 481 MET cc_start: 0.7895 (ptt) cc_final: 0.7659 (ptt) REVERT: C 495 TRP cc_start: 0.9123 (m100) cc_final: 0.8892 (m100) REVERT: D 51 LEU cc_start: 0.8174 (tt) cc_final: 0.7969 (tp) REVERT: D 73 HIS cc_start: 0.7860 (m90) cc_final: 0.7605 (m-70) REVERT: D 90 ASP cc_start: 0.7951 (p0) cc_final: 0.7683 (m-30) REVERT: D 107 PHE cc_start: 0.8397 (m-80) cc_final: 0.8179 (m-80) REVERT: D 222 TYR cc_start: 0.8430 (m-80) cc_final: 0.7702 (m-80) REVERT: D 306 GLN cc_start: 0.8338 (mt0) cc_final: 0.7865 (mm-40) REVERT: D 315 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7830 (mt-10) REVERT: D 481 MET cc_start: 0.7908 (ptt) cc_final: 0.7697 (ptt) outliers start: 20 outliers final: 11 residues processed: 493 average time/residue: 0.3542 time to fit residues: 259.8930 Evaluate side-chains 353 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 341 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 165 HIS A 201 HIS A 206 GLN A 217 ASN A 252 ASN A 261 GLN A 267 GLN A 426 HIS A 582 HIS B 118 GLN B 165 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 217 ASN B 252 ASN B 261 GLN B 267 GLN B 426 HIS C 118 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 217 ASN C 252 ASN C 261 GLN C 267 GLN C 426 HIS D 118 GLN D 165 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN D 217 ASN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 267 GLN D 290 GLN D 370 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21560 Z= 0.194 Angle : 0.679 7.408 28994 Z= 0.342 Chirality : 0.041 0.169 3166 Planarity : 0.006 0.063 3538 Dihedral : 18.295 146.120 4273 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.65 % Allowed : 11.11 % Favored : 87.24 % 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: -4.24 (0.15), residues: 2412 helix: -2.59 (0.11), residues: 1380 sheet: -4.71 (0.26), residues: 76 loop : -2.78 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 593 HIS 0.003 0.001 HIS B 201 PHE 0.029 0.002 PHE C 531 TYR 0.013 0.001 TYR B 467 ARG 0.006 0.001 ARG B 628 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 363 time to evaluate : 2.255 Fit side-chains REVERT: A 90 ASP cc_start: 0.8060 (p0) cc_final: 0.7198 (m-30) REVERT: A 130 MET cc_start: 0.5699 (mmm) cc_final: 0.5334 (mmm) REVERT: A 222 TYR cc_start: 0.8398 (m-80) cc_final: 0.8085 (m-80) REVERT: A 230 GLN cc_start: 0.7877 (pm20) cc_final: 0.7600 (pt0) REVERT: A 260 MET cc_start: 0.8186 (tpt) cc_final: 0.7972 (tpt) REVERT: A 306 GLN cc_start: 0.8321 (mt0) cc_final: 0.7812 (mm-40) REVERT: A 338 LEU cc_start: 0.8428 (tt) cc_final: 0.8083 (mp) REVERT: A 381 LYS cc_start: 0.7262 (mmtm) cc_final: 0.6538 (mtmm) REVERT: A 495 TRP cc_start: 0.9176 (m100) cc_final: 0.8926 (m100) REVERT: B 90 ASP cc_start: 0.8069 (p0) cc_final: 0.7214 (m-30) REVERT: B 130 MET cc_start: 0.5804 (mmm) cc_final: 0.5283 (mmm) REVERT: B 230 GLN cc_start: 0.7850 (pm20) cc_final: 0.7582 (pt0) REVERT: B 306 GLN cc_start: 0.8276 (mt0) cc_final: 0.7810 (mm-40) REVERT: B 315 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7660 (mt-10) REVERT: B 322 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8119 (mtpp) REVERT: B 338 LEU cc_start: 0.8443 (tt) cc_final: 0.8129 (mp) REVERT: B 381 LYS cc_start: 0.7396 (mmtm) cc_final: 0.6649 (mtmm) REVERT: B 481 MET cc_start: 0.7849 (ptt) cc_final: 0.7612 (ptt) REVERT: B 485 MET cc_start: 0.7919 (mtm) cc_final: 0.7678 (mtt) REVERT: B 495 TRP cc_start: 0.9158 (m100) cc_final: 0.8911 (m100) REVERT: C 90 ASP cc_start: 0.8070 (p0) cc_final: 0.7200 (m-30) REVERT: C 130 MET cc_start: 0.5889 (mmm) cc_final: 0.5361 (mmm) REVERT: C 230 GLN cc_start: 0.7788 (pm20) cc_final: 0.7535 (pt0) REVERT: C 306 GLN cc_start: 0.8253 (mt0) cc_final: 0.7795 (mm-40) REVERT: C 315 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7659 (mt-10) REVERT: C 338 LEU cc_start: 0.8438 (tt) cc_final: 0.8143 (mp) REVERT: C 381 LYS cc_start: 0.7367 (mmtm) cc_final: 0.6621 (mtmm) REVERT: C 481 MET cc_start: 0.7900 (ptt) cc_final: 0.7571 (ptt) REVERT: D 73 HIS cc_start: 0.7785 (m90) cc_final: 0.7569 (m-70) REVERT: D 90 ASP cc_start: 0.7918 (p0) cc_final: 0.7342 (m-30) REVERT: D 222 TYR cc_start: 0.8366 (m-80) cc_final: 0.7980 (m-80) REVERT: D 230 GLN cc_start: 0.7942 (pm20) cc_final: 0.7655 (pt0) REVERT: D 306 GLN cc_start: 0.8250 (mt0) cc_final: 0.7777 (mm-40) REVERT: D 315 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7698 (mt-10) REVERT: D 451 VAL cc_start: 0.8286 (p) cc_final: 0.8024 (t) REVERT: D 518 GLU cc_start: 0.7926 (tp30) cc_final: 0.7699 (mm-30) outliers start: 35 outliers final: 15 residues processed: 388 average time/residue: 0.3346 time to fit residues: 197.8922 Evaluate side-chains 324 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 309 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 519 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 0.0570 chunk 60 optimal weight: 20.0000 chunk 218 optimal weight: 0.4980 chunk 235 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 74 optimal weight: 0.0670 chunk 175 optimal weight: 0.0000 overall best weight: 0.3040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN A 258 HIS A 267 GLN A 370 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 258 HIS B 267 GLN B 370 GLN B 572 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 258 HIS D 118 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 258 HIS D 261 GLN D 572 ASN D 582 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21560 Z= 0.137 Angle : 0.584 7.520 28994 Z= 0.294 Chirality : 0.039 0.157 3166 Planarity : 0.005 0.063 3538 Dihedral : 16.161 132.827 4273 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.07 % Allowed : 11.39 % Favored : 85.54 % 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: -3.02 (0.16), residues: 2412 helix: -1.45 (0.13), residues: 1364 sheet: -4.23 (0.32), residues: 76 loop : -2.51 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 495 HIS 0.003 0.001 HIS D 165 PHE 0.011 0.001 PHE B 531 TYR 0.010 0.001 TYR B 467 ARG 0.007 0.000 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 359 time to evaluate : 2.406 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7920 (p0) cc_final: 0.7172 (m-30) REVERT: A 130 MET cc_start: 0.4871 (mmm) cc_final: 0.4642 (mmm) REVERT: A 222 TYR cc_start: 0.8149 (m-80) cc_final: 0.7780 (m-80) REVERT: A 230 GLN cc_start: 0.7888 (pm20) cc_final: 0.7589 (pt0) REVERT: A 306 GLN cc_start: 0.8214 (mt0) cc_final: 0.7697 (mm-40) REVERT: A 378 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8170 (pmm) REVERT: B 90 ASP cc_start: 0.7954 (p0) cc_final: 0.7200 (m-30) REVERT: B 130 MET cc_start: 0.4929 (mmm) cc_final: 0.4689 (mmm) REVERT: B 222 TYR cc_start: 0.8171 (m-80) cc_final: 0.7880 (m-80) REVERT: B 230 GLN cc_start: 0.7823 (pm20) cc_final: 0.7529 (pt0) REVERT: B 306 GLN cc_start: 0.8226 (mt0) cc_final: 0.7745 (mm-40) REVERT: B 315 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7662 (mt-10) REVERT: B 378 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8085 (pmm) REVERT: B 448 SER cc_start: 0.8840 (t) cc_final: 0.8209 (m) REVERT: B 464 ASN cc_start: 0.8205 (m-40) cc_final: 0.7955 (m-40) REVERT: B 485 MET cc_start: 0.7835 (mtm) cc_final: 0.7632 (mtt) REVERT: C 90 ASP cc_start: 0.7962 (p0) cc_final: 0.7206 (m-30) REVERT: C 130 MET cc_start: 0.4985 (mmm) cc_final: 0.4717 (mmm) REVERT: C 222 TYR cc_start: 0.8253 (m-80) cc_final: 0.7913 (m-80) REVERT: C 230 GLN cc_start: 0.7723 (pm20) cc_final: 0.7458 (pt0) REVERT: C 306 GLN cc_start: 0.8197 (mt0) cc_final: 0.7707 (mm-40) REVERT: C 315 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7659 (mt-10) REVERT: C 338 LEU cc_start: 0.8259 (tt) cc_final: 0.8051 (mp) REVERT: C 381 LYS cc_start: 0.7291 (mmtm) cc_final: 0.6559 (mtmm) REVERT: D 90 ASP cc_start: 0.7884 (p0) cc_final: 0.7400 (m-30) REVERT: D 96 MET cc_start: 0.8457 (mmt) cc_final: 0.8256 (mmt) REVERT: D 130 MET cc_start: 0.5121 (mmm) cc_final: 0.4622 (tpt) REVERT: D 222 TYR cc_start: 0.8312 (m-80) cc_final: 0.8028 (m-80) REVERT: D 230 GLN cc_start: 0.7895 (pm20) cc_final: 0.7626 (pt0) REVERT: D 252 ASN cc_start: 0.8782 (t160) cc_final: 0.8528 (t0) REVERT: D 306 GLN cc_start: 0.8165 (mt0) cc_final: 0.7744 (mm-40) REVERT: D 518 GLU cc_start: 0.7882 (tp30) cc_final: 0.7647 (mm-30) REVERT: D 594 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6937 (mpp-170) outliers start: 65 outliers final: 41 residues processed: 401 average time/residue: 0.3314 time to fit residues: 204.4718 Evaluate side-chains 359 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 316 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 448 SER Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 448 SER Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 582 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 0.0010 chunk 164 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 104 optimal weight: 0.3980 chunk 146 optimal weight: 20.0000 chunk 219 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 207 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 ASN B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN B 582 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 572 ASN C 582 HIS D 73 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN D 267 GLN D 572 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21560 Z= 0.130 Angle : 0.553 7.100 28994 Z= 0.278 Chirality : 0.039 0.180 3166 Planarity : 0.005 0.064 3538 Dihedral : 15.414 126.637 4273 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.26 % Allowed : 13.04 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.17), residues: 2412 helix: -0.77 (0.14), residues: 1364 sheet: -4.07 (0.35), residues: 76 loop : -2.36 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP C 495 HIS 0.023 0.001 HIS D 582 PHE 0.009 0.001 PHE B 211 TYR 0.015 0.001 TYR B 324 ARG 0.004 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 316 time to evaluate : 2.124 Fit side-chains REVERT: A 90 ASP cc_start: 0.7903 (p0) cc_final: 0.7308 (m-30) REVERT: A 130 MET cc_start: 0.4474 (mmm) cc_final: 0.4111 (tpt) REVERT: A 222 TYR cc_start: 0.8057 (m-80) cc_final: 0.7623 (m-80) REVERT: A 230 GLN cc_start: 0.7918 (pm20) cc_final: 0.7626 (pt0) REVERT: A 306 GLN cc_start: 0.8204 (mt0) cc_final: 0.7703 (mm-40) REVERT: B 90 ASP cc_start: 0.7923 (p0) cc_final: 0.7346 (m-30) REVERT: B 130 MET cc_start: 0.4586 (mmm) cc_final: 0.4213 (tpt) REVERT: B 222 TYR cc_start: 0.8127 (m-80) cc_final: 0.7716 (m-80) REVERT: B 230 GLN cc_start: 0.7873 (pm20) cc_final: 0.7656 (pt0) REVERT: B 306 GLN cc_start: 0.8158 (mt0) cc_final: 0.7714 (mm-40) REVERT: B 315 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7568 (mt-10) REVERT: B 378 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.8067 (pmm) REVERT: B 448 SER cc_start: 0.8760 (t) cc_final: 0.8161 (m) REVERT: B 464 ASN cc_start: 0.8139 (m-40) cc_final: 0.7903 (m-40) REVERT: C 90 ASP cc_start: 0.7932 (p0) cc_final: 0.7339 (m-30) REVERT: C 130 MET cc_start: 0.4600 (mmm) cc_final: 0.4185 (tpt) REVERT: C 222 TYR cc_start: 0.8219 (m-80) cc_final: 0.7758 (m-80) REVERT: C 230 GLN cc_start: 0.7812 (pm20) cc_final: 0.7581 (pt0) REVERT: C 306 GLN cc_start: 0.8133 (mt0) cc_final: 0.7688 (mm-40) REVERT: C 315 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7615 (mt-10) REVERT: C 338 LEU cc_start: 0.8233 (tt) cc_final: 0.7941 (mp) REVERT: C 378 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.8029 (pmm) REVERT: C 464 ASN cc_start: 0.8144 (m-40) cc_final: 0.7887 (m-40) REVERT: D 90 ASP cc_start: 0.7877 (p0) cc_final: 0.7438 (m-30) REVERT: D 96 MET cc_start: 0.8409 (mmt) cc_final: 0.8157 (mmt) REVERT: D 130 MET cc_start: 0.4809 (mmm) cc_final: 0.4316 (tpt) REVERT: D 140 ARG cc_start: 0.7565 (ptp90) cc_final: 0.7270 (mtm-85) REVERT: D 306 GLN cc_start: 0.8143 (mt0) cc_final: 0.7744 (mm-40) REVERT: D 315 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7653 (mt-10) REVERT: D 518 GLU cc_start: 0.7843 (tp30) cc_final: 0.7608 (mm-30) outliers start: 69 outliers final: 48 residues processed: 365 average time/residue: 0.3169 time to fit residues: 178.9647 Evaluate side-chains 353 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 303 time to evaluate : 2.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 262 LYS Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 208 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 370 GLN B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 596 GLN C 73 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 596 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21560 Z= 0.281 Angle : 0.629 7.462 28994 Z= 0.313 Chirality : 0.043 0.185 3166 Planarity : 0.005 0.062 3538 Dihedral : 15.494 121.264 4273 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.88 % Allowed : 13.89 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 2412 helix: -0.50 (0.14), residues: 1364 sheet: -3.89 (0.38), residues: 76 loop : -2.25 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 583 HIS 0.024 0.001 HIS C 582 PHE 0.015 0.002 PHE D 211 TYR 0.017 0.002 TYR A 324 ARG 0.004 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 307 time to evaluate : 2.260 Fit side-chains revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7873 (p0) cc_final: 0.7328 (m-30) REVERT: A 130 MET cc_start: 0.4869 (mmm) cc_final: 0.4517 (mmm) REVERT: A 230 GLN cc_start: 0.7875 (pm20) cc_final: 0.7577 (pt0) REVERT: A 306 GLN cc_start: 0.8229 (mt0) cc_final: 0.7691 (mm-40) REVERT: A 356 THR cc_start: 0.7570 (p) cc_final: 0.6993 (t) REVERT: A 502 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7941 (mt) REVERT: B 90 ASP cc_start: 0.7905 (p0) cc_final: 0.7377 (m-30) REVERT: B 130 MET cc_start: 0.5039 (mmm) cc_final: 0.4671 (mmm) REVERT: B 230 GLN cc_start: 0.7851 (pm20) cc_final: 0.7609 (pt0) REVERT: B 306 GLN cc_start: 0.8199 (mt0) cc_final: 0.7705 (mm-40) REVERT: B 315 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7567 (mt-10) REVERT: B 502 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8022 (mt) REVERT: C 90 ASP cc_start: 0.7911 (p0) cc_final: 0.7372 (m-30) REVERT: C 130 MET cc_start: 0.5168 (mmm) cc_final: 0.4781 (mmm) REVERT: C 306 GLN cc_start: 0.8184 (mt0) cc_final: 0.7690 (mm-40) REVERT: C 315 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7583 (mt-10) REVERT: C 338 LEU cc_start: 0.8421 (tt) cc_final: 0.8075 (mp) REVERT: C 502 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8050 (mt) REVERT: D 90 ASP cc_start: 0.7884 (p0) cc_final: 0.7466 (m-30) REVERT: D 130 MET cc_start: 0.5124 (mmm) cc_final: 0.4687 (tpt) REVERT: D 140 ARG cc_start: 0.7597 (ptp90) cc_final: 0.7321 (mtm-85) REVERT: D 306 GLN cc_start: 0.8181 (mt0) cc_final: 0.7733 (mm-40) REVERT: D 502 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8042 (mt) REVERT: D 518 GLU cc_start: 0.7972 (tp30) cc_final: 0.7713 (mm-30) outliers start: 82 outliers final: 65 residues processed: 371 average time/residue: 0.3397 time to fit residues: 193.0221 Evaluate side-chains 367 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 298 time to evaluate : 2.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 502 LEU Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.0060 chunk 208 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 192 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN A 370 GLN B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 582 HIS C 73 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 582 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21560 Z= 0.159 Angle : 0.565 7.507 28994 Z= 0.281 Chirality : 0.040 0.179 3166 Planarity : 0.004 0.064 3538 Dihedral : 14.873 114.860 4273 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.25 % Allowed : 13.23 % Favored : 82.51 % 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: -1.63 (0.17), residues: 2412 helix: -0.18 (0.15), residues: 1372 sheet: -3.88 (0.39), residues: 76 loop : -2.11 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 495 HIS 0.015 0.001 HIS D 582 PHE 0.012 0.001 PHE D 211 TYR 0.015 0.001 TYR A 324 ARG 0.003 0.000 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 304 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7899 (p0) cc_final: 0.7385 (m-30) REVERT: A 96 MET cc_start: 0.8412 (mmt) cc_final: 0.8117 (mmt) REVERT: A 130 MET cc_start: 0.4767 (mmm) cc_final: 0.4459 (tpt) REVERT: A 230 GLN cc_start: 0.7831 (pm20) cc_final: 0.7559 (pt0) REVERT: A 306 GLN cc_start: 0.8169 (mt0) cc_final: 0.7619 (mm-40) REVERT: A 356 THR cc_start: 0.7422 (p) cc_final: 0.6904 (t) REVERT: A 594 ARG cc_start: 0.7145 (mtt90) cc_final: 0.6893 (mpp-170) REVERT: B 90 ASP cc_start: 0.7908 (p0) cc_final: 0.7405 (m-30) REVERT: B 130 MET cc_start: 0.4887 (mmm) cc_final: 0.4597 (tpt) REVERT: B 140 ARG cc_start: 0.7551 (ptp90) cc_final: 0.7202 (mtm-85) REVERT: B 230 GLN cc_start: 0.7850 (pm20) cc_final: 0.7613 (pt0) REVERT: B 306 GLN cc_start: 0.8168 (mt0) cc_final: 0.7662 (mm-40) REVERT: B 502 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8060 (mt) REVERT: B 594 ARG cc_start: 0.7090 (mtt90) cc_final: 0.6888 (mpp-170) REVERT: C 90 ASP cc_start: 0.7927 (p0) cc_final: 0.7405 (m-30) REVERT: C 130 MET cc_start: 0.4886 (mmm) cc_final: 0.4567 (tpt) REVERT: C 140 ARG cc_start: 0.7652 (ptp90) cc_final: 0.7291 (mtm-85) REVERT: C 306 GLN cc_start: 0.8143 (mt0) cc_final: 0.7644 (mm-40) REVERT: C 338 LEU cc_start: 0.8337 (tt) cc_final: 0.8095 (mp) REVERT: C 594 ARG cc_start: 0.7073 (mtt90) cc_final: 0.6863 (mpp-170) REVERT: D 90 ASP cc_start: 0.7853 (p0) cc_final: 0.7457 (m-30) REVERT: D 130 MET cc_start: 0.4837 (mmm) cc_final: 0.4409 (tpt) REVERT: D 140 ARG cc_start: 0.7571 (ptp90) cc_final: 0.7296 (mtm-85) REVERT: D 306 GLN cc_start: 0.8154 (mt0) cc_final: 0.7707 (mm-40) REVERT: D 315 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7643 (mt-10) REVERT: D 518 GLU cc_start: 0.7936 (tp30) cc_final: 0.7665 (mm-30) outliers start: 90 outliers final: 67 residues processed: 372 average time/residue: 0.3280 time to fit residues: 187.1612 Evaluate side-chains 366 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 298 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 177 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 4.9990 chunk 26 optimal weight: 30.0000 chunk 132 optimal weight: 0.0270 chunk 169 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 0.3980 chunk 129 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 144 optimal weight: 0.0060 chunk 141 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.4254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 582 HIS C 73 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 582 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21560 Z= 0.131 Angle : 0.548 7.982 28994 Z= 0.272 Chirality : 0.039 0.164 3166 Planarity : 0.004 0.063 3538 Dihedral : 14.303 107.312 4270 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.59 % Allowed : 13.80 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.18), residues: 2412 helix: 0.14 (0.15), residues: 1368 sheet: -3.88 (0.40), residues: 76 loop : -2.01 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 593 HIS 0.007 0.001 HIS C 582 PHE 0.007 0.001 PHE D 211 TYR 0.012 0.001 TYR A 324 ARG 0.003 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 314 time to evaluate : 2.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7872 (p0) cc_final: 0.7410 (m-30) REVERT: A 130 MET cc_start: 0.4574 (mmm) cc_final: 0.4276 (tpt) REVERT: A 140 ARG cc_start: 0.7508 (ptp90) cc_final: 0.7169 (mtm-85) REVERT: A 306 GLN cc_start: 0.8129 (mt0) cc_final: 0.7595 (mm-40) REVERT: A 474 MET cc_start: 0.7383 (tmm) cc_final: 0.6474 (tpp) REVERT: B 90 ASP cc_start: 0.7863 (p0) cc_final: 0.7432 (m-30) REVERT: B 130 MET cc_start: 0.4649 (mmm) cc_final: 0.4303 (tpt) REVERT: B 140 ARG cc_start: 0.7528 (ptp90) cc_final: 0.7186 (mtm-85) REVERT: B 306 GLN cc_start: 0.8141 (mt0) cc_final: 0.7651 (mm-40) REVERT: B 315 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7626 (mt-10) REVERT: B 474 MET cc_start: 0.7432 (tmm) cc_final: 0.6526 (tpp) REVERT: B 502 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8045 (mt) REVERT: C 90 ASP cc_start: 0.7873 (p0) cc_final: 0.7421 (m-30) REVERT: C 130 MET cc_start: 0.4660 (mmm) cc_final: 0.4324 (tpt) REVERT: C 140 ARG cc_start: 0.7656 (ptp90) cc_final: 0.7304 (mtm-85) REVERT: C 174 ASN cc_start: 0.7737 (t0) cc_final: 0.7524 (t0) REVERT: C 222 TYR cc_start: 0.8360 (m-80) cc_final: 0.7815 (m-80) REVERT: C 306 GLN cc_start: 0.8106 (mt0) cc_final: 0.7635 (mm-40) REVERT: C 338 LEU cc_start: 0.8319 (tt) cc_final: 0.7933 (mp) REVERT: C 502 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8057 (mt) REVERT: D 90 ASP cc_start: 0.7862 (p0) cc_final: 0.7536 (m-30) REVERT: D 130 MET cc_start: 0.4620 (mmm) cc_final: 0.4339 (tpt) REVERT: D 140 ARG cc_start: 0.7573 (ptp90) cc_final: 0.7328 (mtm-85) REVERT: D 174 ASN cc_start: 0.7681 (t0) cc_final: 0.7442 (t0) REVERT: D 306 GLN cc_start: 0.8087 (mt0) cc_final: 0.7652 (mm-40) REVERT: D 518 GLU cc_start: 0.7889 (tp30) cc_final: 0.7618 (mm-30) outliers start: 76 outliers final: 60 residues processed: 367 average time/residue: 0.2709 time to fit residues: 153.3982 Evaluate side-chains 361 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 299 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 324 TYR Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 0.0770 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 181 optimal weight: 0.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 261 GLN A 370 GLN B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS C 73 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 370 GLN C 582 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21560 Z= 0.152 Angle : 0.555 7.988 28994 Z= 0.275 Chirality : 0.040 0.168 3166 Planarity : 0.004 0.063 3538 Dihedral : 14.042 101.596 4270 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.45 % Allowed : 13.94 % Favored : 82.61 % 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: -1.09 (0.18), residues: 2412 helix: 0.28 (0.15), residues: 1372 sheet: -3.86 (0.40), residues: 76 loop : -1.90 (0.21), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 495 HIS 0.007 0.001 HIS D 582 PHE 0.007 0.001 PHE C 537 TYR 0.012 0.001 TYR B 324 ARG 0.004 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 304 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7849 (p0) cc_final: 0.7452 (m-30) REVERT: A 130 MET cc_start: 0.4662 (mmm) cc_final: 0.4425 (tpt) REVERT: A 140 ARG cc_start: 0.7493 (ptp90) cc_final: 0.7154 (mtm-85) REVERT: A 306 GLN cc_start: 0.8114 (mt0) cc_final: 0.7584 (mm-40) REVERT: A 474 MET cc_start: 0.7349 (tmm) cc_final: 0.6445 (tpp) REVERT: B 90 ASP cc_start: 0.7864 (p0) cc_final: 0.7486 (m-30) REVERT: B 130 MET cc_start: 0.4753 (mmm) cc_final: 0.4507 (tpt) REVERT: B 140 ARG cc_start: 0.7579 (ptp90) cc_final: 0.7227 (mtm-85) REVERT: B 306 GLN cc_start: 0.8128 (mt0) cc_final: 0.7666 (mm-40) REVERT: B 315 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 474 MET cc_start: 0.7404 (tmm) cc_final: 0.6511 (tpp) REVERT: B 502 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8065 (mt) REVERT: C 57 ASP cc_start: 0.7660 (t70) cc_final: 0.7273 (t70) REVERT: C 90 ASP cc_start: 0.7859 (p0) cc_final: 0.7442 (m-30) REVERT: C 130 MET cc_start: 0.4734 (mmm) cc_final: 0.4390 (tpt) REVERT: C 140 ARG cc_start: 0.7632 (ptp90) cc_final: 0.7277 (mtm-85) REVERT: C 306 GLN cc_start: 0.8087 (mt0) cc_final: 0.7621 (mm-40) REVERT: C 338 LEU cc_start: 0.8329 (tt) cc_final: 0.7926 (mp) REVERT: C 502 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8065 (mt) REVERT: D 90 ASP cc_start: 0.7848 (p0) cc_final: 0.7530 (m-30) REVERT: D 130 MET cc_start: 0.4679 (mmm) cc_final: 0.4452 (tpt) REVERT: D 140 ARG cc_start: 0.7579 (ptp90) cc_final: 0.7353 (mtm-85) REVERT: D 174 ASN cc_start: 0.7709 (t0) cc_final: 0.7503 (t0) REVERT: D 260 MET cc_start: 0.8003 (tpt) cc_final: 0.7782 (mmt) REVERT: D 306 GLN cc_start: 0.8075 (mt0) cc_final: 0.7645 (mm-40) REVERT: D 474 MET cc_start: 0.7314 (tmm) cc_final: 0.6599 (tpp) REVERT: D 518 GLU cc_start: 0.7894 (tp30) cc_final: 0.7618 (mm-30) outliers start: 73 outliers final: 63 residues processed: 360 average time/residue: 0.3548 time to fit residues: 198.3142 Evaluate side-chains 363 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 298 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 215 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 169 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 203 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 261 GLN A 370 GLN B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS C 73 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21560 Z= 0.195 Angle : 0.573 8.522 28994 Z= 0.283 Chirality : 0.041 0.173 3166 Planarity : 0.004 0.063 3538 Dihedral : 13.954 95.237 4270 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.36 % Allowed : 14.51 % Favored : 82.14 % 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: -1.04 (0.18), residues: 2412 helix: 0.34 (0.15), residues: 1368 sheet: -3.83 (0.40), residues: 76 loop : -1.91 (0.21), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 583 HIS 0.004 0.001 HIS D 582 PHE 0.014 0.001 PHE B 211 TYR 0.011 0.001 TYR B 324 ARG 0.004 0.000 ARG A 628 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 309 time to evaluate : 2.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.7843 (p0) cc_final: 0.7452 (m-30) REVERT: A 130 MET cc_start: 0.4687 (mmm) cc_final: 0.4380 (tpt) REVERT: A 140 ARG cc_start: 0.7516 (ptp90) cc_final: 0.7195 (mtm-85) REVERT: A 306 GLN cc_start: 0.8091 (mt0) cc_final: 0.7571 (mm-40) REVERT: A 474 MET cc_start: 0.7362 (tmm) cc_final: 0.6468 (tpp) REVERT: B 57 ASP cc_start: 0.7633 (t70) cc_final: 0.7247 (t70) REVERT: B 90 ASP cc_start: 0.7855 (p0) cc_final: 0.7496 (m-30) REVERT: B 130 MET cc_start: 0.4781 (mmm) cc_final: 0.4501 (tpt) REVERT: B 140 ARG cc_start: 0.7614 (ptp90) cc_final: 0.7302 (mtm-85) REVERT: B 282 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7741 (mt-10) REVERT: B 306 GLN cc_start: 0.8099 (mt0) cc_final: 0.7642 (mm-40) REVERT: B 315 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7618 (mt-10) REVERT: B 356 THR cc_start: 0.7218 (p) cc_final: 0.6720 (t) REVERT: B 502 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8067 (mt) REVERT: C 57 ASP cc_start: 0.7651 (t70) cc_final: 0.7254 (t70) REVERT: C 90 ASP cc_start: 0.7875 (p0) cc_final: 0.7536 (m-30) REVERT: C 130 MET cc_start: 0.4743 (mmm) cc_final: 0.4382 (mmm) REVERT: C 140 ARG cc_start: 0.7666 (ptp90) cc_final: 0.7343 (mtm-85) REVERT: C 306 GLN cc_start: 0.8096 (mt0) cc_final: 0.7627 (mm-40) REVERT: C 338 LEU cc_start: 0.8333 (tt) cc_final: 0.7889 (mp) REVERT: C 474 MET cc_start: 0.7434 (tmm) cc_final: 0.6608 (tpp) REVERT: C 502 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8070 (mt) REVERT: D 90 ASP cc_start: 0.7825 (p0) cc_final: 0.7533 (m-30) REVERT: D 130 MET cc_start: 0.4754 (mmm) cc_final: 0.4488 (tpt) REVERT: D 140 ARG cc_start: 0.7602 (ptp90) cc_final: 0.7385 (mtm-85) REVERT: D 174 ASN cc_start: 0.7706 (t0) cc_final: 0.7439 (t0) REVERT: D 306 GLN cc_start: 0.8086 (mt0) cc_final: 0.7637 (mm-40) REVERT: D 474 MET cc_start: 0.7366 (tmm) cc_final: 0.6616 (tpp) REVERT: D 518 GLU cc_start: 0.7936 (tp30) cc_final: 0.7656 (mm-30) outliers start: 71 outliers final: 64 residues processed: 363 average time/residue: 0.3089 time to fit residues: 174.3063 Evaluate side-chains 371 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 305 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 575 ILE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.0770 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 0.0040 chunk 158 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 220 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 overall best weight: 0.5350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 261 GLN B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 582 HIS C 73 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21560 Z= 0.132 Angle : 0.552 10.095 28994 Z= 0.273 Chirality : 0.040 0.161 3166 Planarity : 0.004 0.064 3538 Dihedral : 13.528 89.224 4270 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.93 % Allowed : 15.12 % Favored : 81.95 % 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: -0.82 (0.18), residues: 2412 helix: 0.51 (0.15), residues: 1376 sheet: -3.89 (0.40), residues: 76 loop : -1.79 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 583 HIS 0.007 0.001 HIS B 582 PHE 0.011 0.001 PHE C 211 TYR 0.012 0.001 TYR A 324 ARG 0.004 0.000 ARG A 628 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 315 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASP cc_start: 0.7644 (t70) cc_final: 0.7154 (t70) REVERT: A 90 ASP cc_start: 0.7800 (p0) cc_final: 0.7460 (m-30) REVERT: A 130 MET cc_start: 0.4625 (mmm) cc_final: 0.4412 (tpt) REVERT: A 140 ARG cc_start: 0.7558 (ptp90) cc_final: 0.7241 (mtm-85) REVERT: A 306 GLN cc_start: 0.8042 (mt0) cc_final: 0.7527 (mm-40) REVERT: A 474 MET cc_start: 0.7348 (tmm) cc_final: 0.6322 (tpp) REVERT: A 481 MET cc_start: 0.7861 (ptt) cc_final: 0.7602 (ptt) REVERT: A 485 MET cc_start: 0.7964 (mtp) cc_final: 0.7601 (mtt) REVERT: B 57 ASP cc_start: 0.7586 (t70) cc_final: 0.7212 (t70) REVERT: B 90 ASP cc_start: 0.7864 (p0) cc_final: 0.7524 (m-30) REVERT: B 130 MET cc_start: 0.4723 (mmm) cc_final: 0.4522 (tpt) REVERT: B 140 ARG cc_start: 0.7603 (ptp90) cc_final: 0.7289 (mtm-85) REVERT: B 306 GLN cc_start: 0.8023 (mt0) cc_final: 0.7547 (mm-40) REVERT: B 356 THR cc_start: 0.7275 (p) cc_final: 0.6813 (t) REVERT: B 474 MET cc_start: 0.7354 (tmm) cc_final: 0.6515 (tpp) REVERT: C 57 ASP cc_start: 0.7598 (t70) cc_final: 0.7214 (t70) REVERT: C 90 ASP cc_start: 0.7845 (p0) cc_final: 0.7502 (m-30) REVERT: C 140 ARG cc_start: 0.7670 (ptp90) cc_final: 0.7356 (mtm-85) REVERT: C 222 TYR cc_start: 0.8337 (m-80) cc_final: 0.7824 (m-80) REVERT: C 306 GLN cc_start: 0.8037 (mt0) cc_final: 0.7566 (mm-40) REVERT: C 315 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7616 (mt-10) REVERT: C 338 LEU cc_start: 0.8315 (tt) cc_final: 0.7892 (mp) REVERT: C 474 MET cc_start: 0.7400 (tmm) cc_final: 0.6447 (tpp) REVERT: C 502 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.8086 (mt) REVERT: D 90 ASP cc_start: 0.7727 (p0) cc_final: 0.7508 (m-30) REVERT: D 140 ARG cc_start: 0.7614 (ptp90) cc_final: 0.7370 (mtm-85) REVERT: D 174 ASN cc_start: 0.7667 (t0) cc_final: 0.7415 (t0) REVERT: D 222 TYR cc_start: 0.8237 (m-80) cc_final: 0.7796 (m-80) REVERT: D 306 GLN cc_start: 0.8014 (mt0) cc_final: 0.7557 (mm-40) REVERT: D 474 MET cc_start: 0.7259 (tmm) cc_final: 0.6406 (tpp) REVERT: D 518 GLU cc_start: 0.7909 (tp30) cc_final: 0.7614 (mm-30) outliers start: 62 outliers final: 57 residues processed: 360 average time/residue: 0.3153 time to fit residues: 175.8820 Evaluate side-chains 365 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 307 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 324 TYR Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 494 CYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 582 HIS Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 367 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 440 MET Chi-restraints excluded: chain B residue 494 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 582 HIS Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 440 MET Chi-restraints excluded: chain C residue 494 CYS Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 523 PHE Chi-restraints excluded: chain C residue 582 HIS Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 440 MET Chi-restraints excluded: chain D residue 494 CYS Chi-restraints excluded: chain D residue 519 GLU Chi-restraints excluded: chain D residue 523 PHE Chi-restraints excluded: chain D residue 575 ILE Chi-restraints excluded: chain D residue 582 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.9990 chunk 202 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 175 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 190 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS A 261 GLN B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS C 73 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.157560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.126037 restraints weight = 24655.554| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.66 r_work: 0.3251 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21560 Z= 0.137 Angle : 0.546 7.971 28994 Z= 0.270 Chirality : 0.040 0.162 3166 Planarity : 0.004 0.064 3538 Dihedral : 13.177 88.376 4270 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.93 % Allowed : 15.36 % Favored : 81.71 % 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: -0.70 (0.18), residues: 2412 helix: 0.61 (0.15), residues: 1376 sheet: -3.90 (0.39), residues: 76 loop : -1.76 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 583 HIS 0.006 0.001 HIS B 582 PHE 0.009 0.001 PHE B 211 TYR 0.012 0.001 TYR A 324 ARG 0.004 0.000 ARG A 628 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5059.78 seconds wall clock time: 92 minutes 49.04 seconds (5569.04 seconds total)