Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 19:52:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4b_22663/08_2023/7k4b_22663_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4b_22663/08_2023/7k4b_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_22663/08_2023/7k4b_22663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4b_22663/08_2023/7k4b_22663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4b_22663/08_2023/7k4b_22663_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k4b_22663/08_2023/7k4b_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-1.21rc1-5044/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: 249 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: 249 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: 249 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: 249 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: 11.48, per 1000 atoms: 0.54 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: 8.19 Conformation dependent library (CDL) restraints added in 2.7 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: 1.95 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: 6.05 Time building geometry restraints manager: 8.77 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: 12246 29.07 - 58.15: 531 58.15 - 87.22: 73 87.22 - 116.29: 6 116.29 - 145.37: 13 Dihedral angle restraints: 12869 sinusoidal: 5749 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 12866 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: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.700 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 53.110 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.140 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.010 ------------------------------------------------------------------------------- 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 : 16.514 145.366 8261 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 % 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 *********************** 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 : 2.328 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 493 average time/residue: 0.3629 time to fit residues: 265.8789 Evaluate side-chains 331 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 320 time to evaluate : 2.315 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1909 time to fit residues: 6.7782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B 582 HIS C 118 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 217 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN C 267 GLN C 426 HIS C 582 HIS D 73 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 426 HIS D 582 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 21560 Z= 0.198 Angle : 0.663 7.086 28994 Z= 0.338 Chirality : 0.041 0.173 3166 Planarity : 0.006 0.065 3538 Dihedral : 18.228 149.688 3541 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer Outliers : 1.32 % 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: -4.20 (0.15), residues: 2412 helix: -2.56 (0.12), residues: 1376 sheet: -4.70 (0.26), residues: 76 loop : -2.77 (0.19), residues: 960 *********************** 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 384 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 356 time to evaluate : 2.304 Fit side-chains outliers start: 28 outliers final: 5 residues processed: 378 average time/residue: 0.3404 time to fit residues: 197.7999 Evaluate side-chains 296 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 291 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2822 time to fit residues: 5.6631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 181 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 235 optimal weight: 0.0980 chunk 194 optimal weight: 0.6980 chunk 216 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN A 267 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 258 HIS B 267 GLN B 572 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 252 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 370 GLN D 572 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 21560 Z= 0.239 Angle : 0.642 7.393 28994 Z= 0.320 Chirality : 0.042 0.174 3166 Planarity : 0.005 0.063 3538 Dihedral : 16.864 136.407 3541 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer Outliers : 3.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.16), residues: 2412 helix: -1.54 (0.13), residues: 1376 sheet: -4.26 (0.33), residues: 76 loop : -2.44 (0.20), residues: 960 *********************** 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 390 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 320 time to evaluate : 2.239 Fit side-chains revert: symmetry clash outliers start: 70 outliers final: 42 residues processed: 373 average time/residue: 0.3452 time to fit residues: 197.1676 Evaluate side-chains 346 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 304 time to evaluate : 2.263 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.2156 time to fit residues: 19.3451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 8.9990 chunk 164 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 0.0020 chunk 219 optimal weight: 8.9990 chunk 231 optimal weight: 4.9990 chunk 114 optimal weight: 0.4980 chunk 207 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 261 GLN A 370 GLN A 572 ASN B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN C 73 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 21560 Z= 0.141 Angle : 0.558 6.430 28994 Z= 0.280 Chirality : 0.039 0.182 3166 Planarity : 0.005 0.064 3538 Dihedral : 15.362 123.934 3541 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer Outliers : 1.51 % 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: -2.24 (0.17), residues: 2412 helix: -0.82 (0.14), residues: 1372 sheet: -4.01 (0.36), residues: 76 loop : -2.15 (0.20), residues: 964 *********************** 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 372 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 340 time to evaluate : 2.331 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 364 average time/residue: 0.3358 time to fit residues: 187.0912 Evaluate side-chains 317 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 301 time to evaluate : 2.399 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2686 time to fit residues: 10.1018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 0.5980 chunk 131 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 160 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN C 73 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3126 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= 0.261 Angle : 0.637 8.705 28994 Z= 0.311 Chirality : 0.043 0.184 3166 Planarity : 0.005 0.063 3538 Dihedral : 15.135 124.628 3541 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.17), residues: 2412 helix: -0.47 (0.14), residues: 1380 sheet: -3.81 (0.41), residues: 76 loop : -2.06 (0.21), residues: 956 *********************** 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 376 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 316 time to evaluate : 2.213 Fit side-chains outliers start: 60 outliers final: 21 residues processed: 362 average time/residue: 0.3417 time to fit residues: 189.0431 Evaluate side-chains 322 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 301 time to evaluate : 2.053 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1932 time to fit residues: 10.4922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 0.0170 chunk 57 optimal weight: 0.8980 chunk 232 optimal weight: 1.9990 chunk 192 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 572 ASN C 73 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 21560 Z= 0.152 Angle : 0.558 7.382 28994 Z= 0.275 Chirality : 0.040 0.174 3166 Planarity : 0.004 0.065 3538 Dihedral : 13.954 124.595 3541 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.18), residues: 2412 helix: -0.01 (0.15), residues: 1368 sheet: -3.72 (0.41), residues: 76 loop : -1.95 (0.20), residues: 968 *********************** 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 351 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 325 time to evaluate : 2.374 Fit side-chains outliers start: 26 outliers final: 13 residues processed: 339 average time/residue: 0.3550 time to fit residues: 183.7352 Evaluate side-chains 315 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 302 time to evaluate : 2.276 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2316 time to fit residues: 8.4051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 169 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 231 optimal weight: 0.2980 chunk 144 optimal weight: 0.0980 chunk 141 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN C 73 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 21560 Z= 0.179 Angle : 0.563 6.623 28994 Z= 0.277 Chirality : 0.041 0.181 3166 Planarity : 0.004 0.063 3538 Dihedral : 13.318 124.519 3541 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.18), residues: 2412 helix: 0.18 (0.15), residues: 1380 sheet: -3.68 (0.41), residues: 76 loop : -1.87 (0.21), residues: 956 *********************** 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 339 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 313 time to evaluate : 2.279 Fit side-chains outliers start: 26 outliers final: 16 residues processed: 335 average time/residue: 0.3619 time to fit residues: 184.6517 Evaluate side-chains 310 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 294 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2046 time to fit residues: 9.3359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 0.0020 chunk 69 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN C 73 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 21560 Z= 0.202 Angle : 0.576 7.471 28994 Z= 0.285 Chirality : 0.041 0.190 3166 Planarity : 0.004 0.064 3538 Dihedral : 13.023 124.735 3541 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.18), residues: 2412 helix: 0.25 (0.15), residues: 1380 sheet: -3.65 (0.42), residues: 76 loop : -1.80 (0.21), residues: 956 *********************** 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 318 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 308 time to evaluate : 2.349 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 317 average time/residue: 0.3563 time to fit residues: 171.1134 Evaluate side-chains 298 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 295 time to evaluate : 2.242 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1867 time to fit residues: 4.1320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 0.8980 chunk 221 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 215 optimal weight: 0.0370 chunk 129 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 214 optimal weight: 5.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 546 ASN ** D 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3681 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= 0.155 Angle : 0.556 7.401 28994 Z= 0.275 Chirality : 0.040 0.170 3166 Planarity : 0.004 0.064 3538 Dihedral : 12.656 124.526 3541 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 0.52 % 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: -0.84 (0.18), residues: 2412 helix: 0.43 (0.15), residues: 1380 sheet: -3.67 (0.41), residues: 76 loop : -1.73 (0.21), residues: 956 *********************** 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 320 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 309 time to evaluate : 2.280 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 316 average time/residue: 0.3508 time to fit residues: 168.2165 Evaluate side-chains 301 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 297 time to evaluate : 2.194 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1863 time to fit residues: 4.5034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 220 optimal weight: 0.8980 chunk 190 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 21560 Z= 0.236 Angle : 0.595 7.431 28994 Z= 0.293 Chirality : 0.042 0.182 3166 Planarity : 0.004 0.063 3538 Dihedral : 12.763 124.756 3541 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 0.28 % 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: -0.87 (0.18), residues: 2412 helix: 0.39 (0.15), residues: 1376 sheet: -3.60 (0.42), residues: 76 loop : -1.73 (0.21), residues: 960 ********************** 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 311 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 305 time to evaluate : 2.329 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 308 average time/residue: 0.3638 time to fit residues: 170.8506 Evaluate side-chains 300 residues out of total 2116 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 296 time to evaluate : 2.277 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2544 time to fit residues: 5.1188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.6980 chunk 202 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 175 optimal weight: 0.0670 chunk 28 optimal weight: 0.0670 chunk 52 optimal weight: 0.6980 chunk 190 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 195 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.158524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.127730 restraints weight = 24545.742| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.64 r_work: 0.3252 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 21560 Z= 0.129 Angle : 0.536 8.006 28994 Z= 0.267 Chirality : 0.039 0.163 3166 Planarity : 0.004 0.065 3538 Dihedral : 12.102 124.163 3541 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer Outliers : 0.28 % 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: -0.56 (0.18), residues: 2412 helix: 0.66 (0.15), residues: 1384 sheet: -3.62 (0.40), residues: 76 loop : -1.62 (0.21), residues: 952 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4866.14 seconds wall clock time: 90 minutes 54.15 seconds (5454.15 seconds total)