Starting phenix.real_space_refine on Sat Mar 16 12:09:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qi7_18436/03_2024/8qi7_18436_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qi7_18436/03_2024/8qi7_18436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qi7_18436/03_2024/8qi7_18436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qi7_18436/03_2024/8qi7_18436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qi7_18436/03_2024/8qi7_18436_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qi7_18436/03_2024/8qi7_18436_updated.pdb" } resolution = 2.9 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= 0.001 sd= 0.045 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 64 5.16 5 C 9124 2.51 5 N 2596 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14609 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3623 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3623 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3623 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3623 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Time building chain proxies: 7.63, per 1000 atoms: 0.52 Number of scatterers: 14609 At special positions: 0 Unit cell: (124.7, 90.3, 100.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 4 15.00 O 2821 8.00 N 2596 7.00 C 9124 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: 5.34 Conformation dependent library (CDL) restraints added in 2.7 seconds 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 12 sheets defined 45.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 49 through 52 No H-bonds generated for 'chain 'A' and resid 49 through 52' Processing helix chain 'A' and resid 54 through 68 removed outlier: 3.610A pdb=" N LEU A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.794A pdb=" N ALA A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 94 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.529A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.668A pdb=" N VAL A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.888A pdb=" N ARG A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 removed outlier: 3.762A pdb=" N GLU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.635A pdb=" N ALA A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 267 through 270 Processing helix chain 'A' and resid 311 through 319 removed outlier: 3.603A pdb=" N VAL A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 343 removed outlier: 3.666A pdb=" N GLN A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 368 removed outlier: 3.506A pdb=" N ARG A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 393 through 403 removed outlier: 3.527A pdb=" N LEU A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 458 removed outlier: 3.910A pdb=" N ARG A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 469 Processing helix chain 'A' and resid 471 through 474 No H-bonds generated for 'chain 'A' and resid 471 through 474' Processing helix chain 'A' and resid 476 through 495 removed outlier: 3.510A pdb=" N LEU A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA A 495 " --> pdb=" O GLN A 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 54 through 68 removed outlier: 3.609A pdb=" N LEU D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.794A pdb=" N ALA D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 94 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.529A pdb=" N ARG D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 124 " --> pdb=" O GLN D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 removed outlier: 3.668A pdb=" N VAL D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 185 through 189 Processing helix chain 'D' and resid 206 through 216 removed outlier: 3.888A pdb=" N ARG D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 244 removed outlier: 3.762A pdb=" N GLU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 260 removed outlier: 3.635A pdb=" N ALA D 260 " --> pdb=" O SER D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 256 through 260' Processing helix chain 'D' and resid 267 through 270 Processing helix chain 'D' and resid 311 through 319 removed outlier: 3.603A pdb=" N VAL D 319 " --> pdb=" O ILE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 343 removed outlier: 3.667A pdb=" N GLN D 341 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 368 removed outlier: 3.506A pdb=" N ARG D 368 " --> pdb=" O ALA D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 375 No H-bonds generated for 'chain 'D' and resid 373 through 375' Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.527A pdb=" N LEU D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 458 removed outlier: 3.910A pdb=" N ARG D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP D 446 " --> pdb=" O ARG D 442 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 457 " --> pdb=" O ASN D 453 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL D 458 " --> pdb=" O ILE D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 471 through 474 No H-bonds generated for 'chain 'D' and resid 471 through 474' Processing helix chain 'D' and resid 476 through 495 removed outlier: 3.509A pdb=" N LEU D 485 " --> pdb=" O ARG D 481 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG D 488 " --> pdb=" O ASN D 484 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA D 495 " --> pdb=" O GLN D 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 52 No H-bonds generated for 'chain 'B' and resid 49 through 52' Processing helix chain 'B' and resid 54 through 68 removed outlier: 3.610A pdb=" N LEU B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 removed outlier: 3.794A pdb=" N ALA B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 94 Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.529A pdb=" N ARG B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 154 removed outlier: 3.667A pdb=" N VAL B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 185 through 189 Processing helix chain 'B' and resid 206 through 216 removed outlier: 3.888A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 244 removed outlier: 3.761A pdb=" N GLU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.635A pdb=" N ALA B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 260' Processing helix chain 'B' and resid 267 through 270 Processing helix chain 'B' and resid 311 through 319 removed outlier: 3.602A pdb=" N VAL B 319 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 343 removed outlier: 3.666A pdb=" N GLN B 341 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 368 removed outlier: 3.505A pdb=" N ARG B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 393 through 403 removed outlier: 3.527A pdb=" N LEU B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 458 removed outlier: 3.910A pdb=" N ARG B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 457 " --> pdb=" O ASN B 453 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 471 through 474 No H-bonds generated for 'chain 'B' and resid 471 through 474' Processing helix chain 'B' and resid 476 through 495 removed outlier: 3.509A pdb=" N LEU B 485 " --> pdb=" O ARG B 481 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA B 495 " --> pdb=" O GLN B 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 52 No H-bonds generated for 'chain 'C' and resid 49 through 52' Processing helix chain 'C' and resid 54 through 68 removed outlier: 3.609A pdb=" N LEU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 removed outlier: 3.795A pdb=" N ALA C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 94 Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.529A pdb=" N ARG C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 124 " --> pdb=" O GLN C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 154 removed outlier: 3.667A pdb=" N VAL C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 185 through 189 Processing helix chain 'C' and resid 206 through 216 removed outlier: 3.887A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 244 removed outlier: 3.762A pdb=" N GLU C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 260 removed outlier: 3.635A pdb=" N ALA C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 256 through 260' Processing helix chain 'C' and resid 267 through 270 Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.603A pdb=" N VAL C 319 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 343 removed outlier: 3.666A pdb=" N GLN C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS C 343 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 368 removed outlier: 3.506A pdb=" N ARG C 368 " --> pdb=" O ALA C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 375 No H-bonds generated for 'chain 'C' and resid 373 through 375' Processing helix chain 'C' and resid 393 through 403 removed outlier: 3.527A pdb=" N LEU C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 458 removed outlier: 3.909A pdb=" N ARG C 443 " --> pdb=" O ASP C 439 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP C 446 " --> pdb=" O ARG C 442 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 457 " --> pdb=" O ASN C 453 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 458 " --> pdb=" O ILE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 471 through 474 No H-bonds generated for 'chain 'C' and resid 471 through 474' Processing helix chain 'C' and resid 476 through 495 removed outlier: 3.510A pdb=" N LEU C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA C 495 " --> pdb=" O GLN C 491 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 134 through 137 removed outlier: 3.652A pdb=" N ILE A 273 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.391A pdb=" N GLU A 191 " --> pdb=" O ILE A 161 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY A 163 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N MET A 193 " --> pdb=" O GLY A 163 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 381 through 385 removed outlier: 4.239A pdb=" N ASN A 408 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 134 through 137 removed outlier: 3.652A pdb=" N ILE D 273 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 160 through 164 removed outlier: 6.391A pdb=" N GLU D 191 " --> pdb=" O ILE D 161 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY D 163 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET D 193 " --> pdb=" O GLY D 163 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 381 through 385 removed outlier: 4.239A pdb=" N ASN D 408 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 134 through 137 removed outlier: 3.652A pdb=" N ILE B 273 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 160 through 164 removed outlier: 6.391A pdb=" N GLU B 191 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY B 163 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET B 193 " --> pdb=" O GLY B 163 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 381 through 385 removed outlier: 4.239A pdb=" N ASN B 408 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 134 through 137 removed outlier: 3.653A pdb=" N ILE C 273 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 160 through 164 removed outlier: 6.390A pdb=" N GLU C 191 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N GLY C 163 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N MET C 193 " --> pdb=" O GLY C 163 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 381 through 385 removed outlier: 4.239A pdb=" N ASN C 408 " --> pdb=" O ARG C 425 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 5.83 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: 2428 1.31 - 1.44: 3848 1.44 - 1.56: 8408 1.56 - 1.68: 4 1.68 - 1.81: 100 Bond restraints: 14788 Sorted by residual: bond pdb=" C4 LLP C 280 " pdb=" C5 LLP C 280 " ideal model delta sigma weight residual 1.455 1.354 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C4 LLP D 280 " pdb=" C5 LLP D 280 " ideal model delta sigma weight residual 1.455 1.354 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C4 LLP A 280 " pdb=" C5 LLP A 280 " ideal model delta sigma weight residual 1.455 1.354 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" C4 LLP B 280 " pdb=" C5 LLP B 280 " ideal model delta sigma weight residual 1.455 1.355 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C3 LLP D 280 " pdb=" C4 LLP D 280 " ideal model delta sigma weight residual 1.455 1.355 0.100 2.00e-02 2.50e+03 2.49e+01 ... (remaining 14783 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.05: 389 106.05 - 113.04: 7792 113.04 - 120.02: 5439 120.02 - 127.00: 6236 127.00 - 133.99: 160 Bond angle restraints: 20016 Sorted by residual: angle pdb=" CA ALA A 428 " pdb=" C ALA A 428 " pdb=" N PRO A 429 " ideal model delta sigma weight residual 118.44 125.35 -6.91 1.59e+00 3.96e-01 1.89e+01 angle pdb=" CA ALA B 428 " pdb=" C ALA B 428 " pdb=" N PRO B 429 " ideal model delta sigma weight residual 118.44 125.35 -6.91 1.59e+00 3.96e-01 1.89e+01 angle pdb=" CA ALA C 428 " pdb=" C ALA C 428 " pdb=" N PRO C 429 " ideal model delta sigma weight residual 118.44 125.34 -6.90 1.59e+00 3.96e-01 1.88e+01 angle pdb=" CA ALA D 428 " pdb=" C ALA D 428 " pdb=" N PRO D 429 " ideal model delta sigma weight residual 118.44 125.32 -6.88 1.59e+00 3.96e-01 1.87e+01 angle pdb=" CA GLY A 427 " pdb=" C GLY A 427 " pdb=" O GLY A 427 " ideal model delta sigma weight residual 121.19 117.38 3.81 9.10e-01 1.21e+00 1.75e+01 ... (remaining 20011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 8742 21.45 - 42.91: 210 42.91 - 64.36: 16 64.36 - 85.81: 12 85.81 - 107.26: 4 Dihedral angle restraints: 8984 sinusoidal: 3656 harmonic: 5328 Sorted by residual: dihedral pdb=" CG LLP D 280 " pdb=" CD LLP D 280 " pdb=" CE LLP D 280 " pdb=" NZ LLP D 280 " ideal model delta sinusoidal sigma weight residual 119.81 -132.93 -107.26 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" CG LLP C 280 " pdb=" CD LLP C 280 " pdb=" CE LLP C 280 " pdb=" NZ LLP C 280 " ideal model delta sinusoidal sigma weight residual 119.81 -132.95 -107.24 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" CG LLP A 280 " pdb=" CD LLP A 280 " pdb=" CE LLP A 280 " pdb=" NZ LLP A 280 " ideal model delta sinusoidal sigma weight residual 119.81 -132.96 -107.23 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 8981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1730 0.045 - 0.091: 345 0.091 - 0.136: 107 0.136 - 0.181: 4 0.181 - 0.226: 10 Chirality restraints: 2196 Sorted by residual: chirality pdb=" CA PRO A 429 " pdb=" N PRO A 429 " pdb=" C PRO A 429 " pdb=" CB PRO A 429 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PRO B 429 " pdb=" N PRO B 429 " pdb=" C PRO B 429 " pdb=" CB PRO B 429 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA PRO C 429 " pdb=" N PRO C 429 " pdb=" C PRO C 429 " pdb=" CB PRO C 429 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2193 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 167 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" C PRO D 167 " 0.044 2.00e-02 2.50e+03 pdb=" O PRO D 167 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP D 168 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 167 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C PRO A 167 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO A 167 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 168 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 167 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C PRO C 167 " 0.044 2.00e-02 2.50e+03 pdb=" O PRO C 167 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP C 168 " -0.015 2.00e-02 2.50e+03 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4001 2.80 - 3.32: 12175 3.32 - 3.85: 21178 3.85 - 4.37: 28021 4.37 - 4.90: 48310 Nonbonded interactions: 113685 Sorted by model distance: nonbonded pdb=" OG SER C 142 " pdb=" OP1 LLP C 280 " model vdw 2.275 2.440 nonbonded pdb=" OG SER D 142 " pdb=" OP1 LLP D 280 " model vdw 2.275 2.440 nonbonded pdb=" OG SER B 142 " pdb=" OP1 LLP B 280 " model vdw 2.275 2.440 nonbonded pdb=" OG SER A 142 " pdb=" OP1 LLP A 280 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR D 96 " pdb=" OP3 LLP C 280 " model vdw 2.387 2.440 ... (remaining 113680 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.470 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.940 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 14788 Z= 0.429 Angle : 0.604 8.082 20016 Z= 0.344 Chirality : 0.043 0.226 2196 Planarity : 0.004 0.039 2632 Dihedral : 9.924 107.265 5560 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.35 % Favored : 93.44 % Rotamer: Outliers : 0.79 % Allowed : 2.63 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.16), residues: 1828 helix: -4.06 (0.09), residues: 700 sheet: -1.40 (0.35), residues: 188 loop : -1.41 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 134 HIS 0.002 0.001 HIS B 279 PHE 0.008 0.001 PHE C 216 TYR 0.010 0.001 TYR A 195 ARG 0.002 0.000 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.799 Fit side-chains REVERT: A 128 ASP cc_start: 0.8421 (t0) cc_final: 0.7972 (t0) REVERT: D 128 ASP cc_start: 0.8442 (t0) cc_final: 0.8010 (t0) REVERT: D 307 ILE cc_start: 0.7256 (OUTLIER) cc_final: 0.7050 (pt) REVERT: B 128 ASP cc_start: 0.8444 (t0) cc_final: 0.8025 (t0) REVERT: B 307 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.7091 (pt) REVERT: C 128 ASP cc_start: 0.8452 (t0) cc_final: 0.8027 (t0) REVERT: C 307 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.6993 (pt) REVERT: C 475 ASP cc_start: 0.7353 (t0) cc_final: 0.7152 (t70) outliers start: 12 outliers final: 4 residues processed: 181 average time/residue: 1.6938 time to fit residues: 330.1068 Evaluate side-chains 108 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain D residue 254 HIS Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain B residue 254 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 254 HIS Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14788 Z= 0.172 Angle : 0.568 7.835 20016 Z= 0.293 Chirality : 0.040 0.152 2196 Planarity : 0.005 0.051 2632 Dihedral : 9.445 97.296 2114 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.11 % Allowed : 6.84 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.22 (0.17), residues: 1828 helix: -1.47 (0.16), residues: 760 sheet: -0.79 (0.35), residues: 196 loop : -1.53 (0.19), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 57 HIS 0.002 0.001 HIS D 247 PHE 0.006 0.001 PHE A 291 TYR 0.011 0.001 TYR A 195 ARG 0.006 0.000 ARG D 486 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 1.738 Fit side-chains REVERT: A 128 ASP cc_start: 0.8457 (t0) cc_final: 0.8015 (t0) REVERT: A 308 PRO cc_start: 0.8984 (Cg_endo) cc_final: 0.8783 (Cg_exo) REVERT: A 457 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7516 (mm-30) REVERT: D 128 ASP cc_start: 0.8477 (t0) cc_final: 0.8049 (t0) REVERT: D 307 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6961 (pt) REVERT: D 308 PRO cc_start: 0.8966 (Cg_endo) cc_final: 0.8685 (Cg_exo) REVERT: D 457 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7515 (mm-30) REVERT: B 128 ASP cc_start: 0.8482 (t0) cc_final: 0.8059 (t0) REVERT: B 200 LYS cc_start: 0.8893 (mptp) cc_final: 0.8477 (mptt) REVERT: B 307 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.7001 (pt) REVERT: B 308 PRO cc_start: 0.8985 (Cg_endo) cc_final: 0.8697 (Cg_exo) REVERT: B 457 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7541 (mm-30) REVERT: C 128 ASP cc_start: 0.8493 (t0) cc_final: 0.8045 (t0) REVERT: C 200 LYS cc_start: 0.8854 (mptp) cc_final: 0.8468 (mptt) REVERT: C 307 ILE cc_start: 0.7198 (OUTLIER) cc_final: 0.6920 (pt) REVERT: C 308 PRO cc_start: 0.8959 (Cg_endo) cc_final: 0.8644 (Cg_exo) REVERT: C 359 ARG cc_start: 0.6742 (mtt-85) cc_final: 0.6528 (mtt-85) REVERT: C 475 ASP cc_start: 0.7486 (t0) cc_final: 0.7282 (t70) outliers start: 32 outliers final: 4 residues processed: 133 average time/residue: 1.2684 time to fit residues: 186.1930 Evaluate side-chains 107 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain D residue 254 HIS Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain B residue 254 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 254 HIS Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 139 optimal weight: 0.0270 chunk 113 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14788 Z= 0.206 Angle : 0.564 8.898 20016 Z= 0.281 Chirality : 0.041 0.149 2196 Planarity : 0.004 0.053 2632 Dihedral : 7.729 77.369 2114 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.12 % Allowed : 7.76 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.49 (0.18), residues: 1828 helix: -0.52 (0.17), residues: 792 sheet: 0.05 (0.36), residues: 188 loop : -1.65 (0.20), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 57 HIS 0.004 0.001 HIS A 330 PHE 0.010 0.001 PHE D 311 TYR 0.014 0.002 TYR C 195 ARG 0.006 0.000 ARG A 486 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.611 Fit side-chains REVERT: A 128 ASP cc_start: 0.8466 (t0) cc_final: 0.8032 (t0) REVERT: A 308 PRO cc_start: 0.8970 (Cg_endo) cc_final: 0.8758 (Cg_exo) REVERT: A 457 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7654 (mm-30) REVERT: D 128 ASP cc_start: 0.8477 (t0) cc_final: 0.8054 (t0) REVERT: D 457 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7655 (mm-30) REVERT: B 128 ASP cc_start: 0.8485 (t0) cc_final: 0.8042 (t0) REVERT: B 200 LYS cc_start: 0.8884 (mptp) cc_final: 0.8482 (mptt) REVERT: B 457 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7683 (mm-30) REVERT: C 128 ASP cc_start: 0.8508 (t0) cc_final: 0.8062 (t0) REVERT: C 200 LYS cc_start: 0.8837 (mptp) cc_final: 0.8490 (mppt) outliers start: 17 outliers final: 9 residues processed: 113 average time/residue: 1.3029 time to fit residues: 162.5589 Evaluate side-chains 96 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain D residue 254 HIS Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain B residue 254 HIS Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 254 HIS Chi-restraints excluded: chain C residue 439 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 167 optimal weight: 0.6980 chunk 177 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14788 Z= 0.249 Angle : 0.601 8.840 20016 Z= 0.300 Chirality : 0.043 0.152 2196 Planarity : 0.005 0.059 2632 Dihedral : 7.114 73.594 2108 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.05 % Allowed : 8.16 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.33 (0.19), residues: 1828 helix: -0.25 (0.18), residues: 820 sheet: 0.33 (0.37), residues: 188 loop : -1.81 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 134 HIS 0.004 0.001 HIS C 330 PHE 0.011 0.002 PHE C 291 TYR 0.016 0.002 TYR B 195 ARG 0.003 0.000 ARG C 359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 1.630 Fit side-chains REVERT: A 128 ASP cc_start: 0.8428 (t0) cc_final: 0.7981 (t0) REVERT: A 308 PRO cc_start: 0.8921 (Cg_endo) cc_final: 0.8657 (Cg_exo) REVERT: D 128 ASP cc_start: 0.8438 (t0) cc_final: 0.7998 (t0) REVERT: B 128 ASP cc_start: 0.8447 (t0) cc_final: 0.8010 (t0) REVERT: B 200 LYS cc_start: 0.8876 (mptp) cc_final: 0.8546 (mppt) REVERT: C 128 ASP cc_start: 0.8457 (t0) cc_final: 0.8022 (t0) REVERT: C 200 LYS cc_start: 0.8836 (mptp) cc_final: 0.8462 (mptt) outliers start: 16 outliers final: 15 residues processed: 97 average time/residue: 1.2510 time to fit residues: 134.5433 Evaluate side-chains 99 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 254 HIS Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 254 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 254 HIS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 439 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.5980 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14788 Z= 0.192 Angle : 0.545 7.306 20016 Z= 0.273 Chirality : 0.041 0.144 2196 Planarity : 0.004 0.051 2632 Dihedral : 6.721 67.069 2108 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.99 % Allowed : 9.41 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.91 (0.19), residues: 1828 helix: 0.25 (0.18), residues: 804 sheet: 0.37 (0.39), residues: 192 loop : -1.71 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 57 HIS 0.003 0.001 HIS C 330 PHE 0.008 0.001 PHE A 291 TYR 0.012 0.001 TYR B 195 ARG 0.003 0.000 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 1.702 Fit side-chains REVERT: A 128 ASP cc_start: 0.8413 (t0) cc_final: 0.7979 (t0) REVERT: A 308 PRO cc_start: 0.8924 (Cg_endo) cc_final: 0.8647 (Cg_exo) REVERT: D 128 ASP cc_start: 0.8422 (t0) cc_final: 0.7994 (t0) REVERT: D 308 PRO cc_start: 0.8922 (Cg_endo) cc_final: 0.8618 (Cg_exo) REVERT: B 128 ASP cc_start: 0.8429 (t0) cc_final: 0.8002 (t0) REVERT: B 200 LYS cc_start: 0.8863 (mptp) cc_final: 0.8538 (mppt) REVERT: B 308 PRO cc_start: 0.8938 (Cg_endo) cc_final: 0.8635 (Cg_exo) REVERT: C 128 ASP cc_start: 0.8439 (t0) cc_final: 0.8018 (t0) REVERT: C 200 LYS cc_start: 0.8858 (mptp) cc_final: 0.8567 (mppt) outliers start: 15 outliers final: 8 residues processed: 98 average time/residue: 1.3514 time to fit residues: 145.9724 Evaluate side-chains 95 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 439 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 8.9990 chunk 160 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14788 Z= 0.246 Angle : 0.587 7.557 20016 Z= 0.293 Chirality : 0.042 0.150 2196 Planarity : 0.005 0.057 2632 Dihedral : 6.538 72.515 2100 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.45 % Allowed : 9.61 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.88 (0.19), residues: 1828 helix: 0.33 (0.18), residues: 804 sheet: 0.43 (0.40), residues: 192 loop : -1.77 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 134 HIS 0.004 0.001 HIS C 270 PHE 0.010 0.002 PHE C 291 TYR 0.015 0.002 TYR B 195 ARG 0.003 0.000 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 89 time to evaluate : 1.507 Fit side-chains REVERT: A 60 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8576 (mp) REVERT: A 128 ASP cc_start: 0.8404 (t0) cc_final: 0.7956 (t0) REVERT: A 308 PRO cc_start: 0.8902 (Cg_endo) cc_final: 0.8610 (Cg_exo) REVERT: A 503 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: D 60 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8582 (mp) REVERT: D 128 ASP cc_start: 0.8412 (t0) cc_final: 0.7966 (t0) REVERT: D 308 PRO cc_start: 0.8898 (Cg_endo) cc_final: 0.8593 (Cg_exo) REVERT: D 498 MET cc_start: 0.8508 (tpp) cc_final: 0.8148 (ttp) REVERT: D 503 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: B 60 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8629 (mp) REVERT: B 128 ASP cc_start: 0.8418 (t0) cc_final: 0.7977 (t0) REVERT: B 200 LYS cc_start: 0.8869 (mptp) cc_final: 0.8533 (mppt) REVERT: B 308 PRO cc_start: 0.8916 (Cg_endo) cc_final: 0.8611 (Cg_exo) REVERT: B 503 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: C 60 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8588 (mp) REVERT: C 128 ASP cc_start: 0.8423 (t0) cc_final: 0.7990 (t0) REVERT: C 200 LYS cc_start: 0.8871 (mptp) cc_final: 0.8565 (mppt) REVERT: C 503 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7589 (pm20) outliers start: 22 outliers final: 10 residues processed: 111 average time/residue: 1.3773 time to fit residues: 167.7764 Evaluate side-chains 107 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain D residue 503 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain B residue 503 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 503 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 0.0870 chunk 20 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 100 optimal weight: 0.0770 chunk 149 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 108 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14788 Z= 0.121 Angle : 0.480 7.009 20016 Z= 0.241 Chirality : 0.038 0.133 2196 Planarity : 0.004 0.048 2632 Dihedral : 6.001 61.148 2100 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.99 % Allowed : 10.39 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.21 (0.20), residues: 1828 helix: 1.06 (0.19), residues: 784 sheet: 0.35 (0.41), residues: 200 loop : -1.45 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 57 HIS 0.002 0.001 HIS B 171 PHE 0.006 0.001 PHE D 441 TYR 0.008 0.001 TYR D 106 ARG 0.003 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.754 Fit side-chains REVERT: A 128 ASP cc_start: 0.8448 (t0) cc_final: 0.8012 (t0) REVERT: A 308 PRO cc_start: 0.8924 (Cg_endo) cc_final: 0.8646 (Cg_exo) REVERT: A 498 MET cc_start: 0.8439 (tpp) cc_final: 0.8091 (ttp) REVERT: D 128 ASP cc_start: 0.8452 (t0) cc_final: 0.8020 (t0) REVERT: D 308 PRO cc_start: 0.8919 (Cg_endo) cc_final: 0.8630 (Cg_exo) REVERT: D 498 MET cc_start: 0.8403 (tpp) cc_final: 0.8153 (ttp) REVERT: B 128 ASP cc_start: 0.8457 (t0) cc_final: 0.8028 (t0) REVERT: B 200 LYS cc_start: 0.8857 (mptp) cc_final: 0.8542 (mppt) REVERT: B 308 PRO cc_start: 0.8936 (Cg_endo) cc_final: 0.8647 (Cg_exo) REVERT: B 498 MET cc_start: 0.8464 (tpp) cc_final: 0.8104 (ttp) REVERT: C 128 ASP cc_start: 0.8432 (t0) cc_final: 0.8005 (t0) REVERT: C 200 LYS cc_start: 0.8840 (mptp) cc_final: 0.8574 (mppt) REVERT: C 308 PRO cc_start: 0.8912 (Cg_endo) cc_final: 0.8614 (Cg_exo) outliers start: 15 outliers final: 0 residues processed: 121 average time/residue: 1.3408 time to fit residues: 179.1424 Evaluate side-chains 102 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.0010 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14788 Z= 0.147 Angle : 0.497 7.189 20016 Z= 0.249 Chirality : 0.039 0.132 2196 Planarity : 0.004 0.048 2632 Dihedral : 5.928 60.677 2100 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.79 % Allowed : 10.66 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.20), residues: 1828 helix: 1.34 (0.19), residues: 784 sheet: 0.45 (0.41), residues: 200 loop : -1.40 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 57 HIS 0.002 0.001 HIS A 270 PHE 0.007 0.001 PHE C 291 TYR 0.010 0.001 TYR B 195 ARG 0.003 0.000 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.669 Fit side-chains REVERT: A 128 ASP cc_start: 0.8436 (t0) cc_final: 0.8003 (t0) REVERT: A 308 PRO cc_start: 0.8908 (Cg_endo) cc_final: 0.8650 (Cg_exo) REVERT: A 498 MET cc_start: 0.8462 (tpp) cc_final: 0.8118 (ttp) REVERT: D 128 ASP cc_start: 0.8417 (t0) cc_final: 0.7983 (t0) REVERT: D 308 PRO cc_start: 0.8902 (Cg_endo) cc_final: 0.8639 (Cg_exo) REVERT: D 498 MET cc_start: 0.8435 (tpp) cc_final: 0.8111 (ttp) REVERT: B 128 ASP cc_start: 0.8446 (t0) cc_final: 0.8024 (t0) REVERT: B 200 LYS cc_start: 0.8848 (mptp) cc_final: 0.8536 (mppt) REVERT: B 308 PRO cc_start: 0.8919 (Cg_endo) cc_final: 0.8657 (Cg_exo) REVERT: B 498 MET cc_start: 0.8486 (tpp) cc_final: 0.8129 (ttp) REVERT: C 128 ASP cc_start: 0.8418 (t0) cc_final: 0.7978 (t0) REVERT: C 200 LYS cc_start: 0.8860 (mptp) cc_final: 0.8581 (mppt) REVERT: C 308 PRO cc_start: 0.8895 (Cg_endo) cc_final: 0.8620 (Cg_exo) outliers start: 12 outliers final: 0 residues processed: 112 average time/residue: 1.3533 time to fit residues: 166.7801 Evaluate side-chains 102 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 71 optimal weight: 0.0770 chunk 129 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 164 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14788 Z= 0.149 Angle : 0.496 7.056 20016 Z= 0.248 Chirality : 0.039 0.132 2196 Planarity : 0.004 0.049 2632 Dihedral : 5.923 61.039 2100 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.86 % Allowed : 10.53 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.21 (0.20), residues: 1828 helix: 1.55 (0.19), residues: 784 sheet: 0.47 (0.41), residues: 200 loop : -1.36 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 57 HIS 0.002 0.001 HIS D 270 PHE 0.007 0.001 PHE D 291 TYR 0.010 0.001 TYR D 195 ARG 0.003 0.000 ARG D 359 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.662 Fit side-chains REVERT: A 128 ASP cc_start: 0.8405 (t0) cc_final: 0.7978 (t0) REVERT: A 308 PRO cc_start: 0.8912 (Cg_endo) cc_final: 0.8657 (Cg_exo) REVERT: A 498 MET cc_start: 0.8427 (tpp) cc_final: 0.8102 (ttp) REVERT: D 128 ASP cc_start: 0.8405 (t0) cc_final: 0.7982 (t0) REVERT: D 308 PRO cc_start: 0.8906 (Cg_endo) cc_final: 0.8650 (Cg_exo) REVERT: D 498 MET cc_start: 0.8417 (tpp) cc_final: 0.8095 (ttp) REVERT: B 128 ASP cc_start: 0.8418 (t0) cc_final: 0.7998 (t0) REVERT: B 200 LYS cc_start: 0.8840 (mptp) cc_final: 0.8531 (mppt) REVERT: B 308 PRO cc_start: 0.8922 (Cg_endo) cc_final: 0.8666 (Cg_exo) REVERT: B 498 MET cc_start: 0.8454 (tpp) cc_final: 0.8115 (ttp) REVERT: C 128 ASP cc_start: 0.8426 (t0) cc_final: 0.7988 (t0) REVERT: C 200 LYS cc_start: 0.8864 (mptp) cc_final: 0.8590 (mppt) REVERT: C 308 PRO cc_start: 0.8901 (Cg_endo) cc_final: 0.8639 (Cg_exo) outliers start: 13 outliers final: 0 residues processed: 110 average time/residue: 1.3826 time to fit residues: 167.0796 Evaluate side-chains 94 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 115 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14788 Z= 0.140 Angle : 0.485 7.147 20016 Z= 0.242 Chirality : 0.039 0.134 2196 Planarity : 0.004 0.047 2632 Dihedral : 5.807 59.005 2100 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.39 (0.20), residues: 1828 helix: 1.76 (0.19), residues: 784 sheet: 0.53 (0.41), residues: 200 loop : -1.31 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 57 HIS 0.002 0.001 HIS D 270 PHE 0.006 0.001 PHE D 441 TYR 0.009 0.001 TYR D 195 ARG 0.003 0.000 ARG A 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 1.639 Fit side-chains REVERT: A 128 ASP cc_start: 0.8364 (t0) cc_final: 0.7941 (t0) REVERT: A 308 PRO cc_start: 0.8913 (Cg_endo) cc_final: 0.8670 (Cg_exo) REVERT: A 498 MET cc_start: 0.8380 (tpp) cc_final: 0.8085 (ttp) REVERT: D 128 ASP cc_start: 0.8403 (t0) cc_final: 0.7986 (t0) REVERT: D 308 PRO cc_start: 0.8915 (Cg_endo) cc_final: 0.8661 (Cg_exo) REVERT: D 498 MET cc_start: 0.8392 (tpp) cc_final: 0.8091 (ttp) REVERT: B 128 ASP cc_start: 0.8379 (t0) cc_final: 0.7980 (t0) REVERT: B 200 LYS cc_start: 0.8828 (mptp) cc_final: 0.8524 (mppt) REVERT: B 308 PRO cc_start: 0.8931 (Cg_endo) cc_final: 0.8676 (Cg_exo) REVERT: B 498 MET cc_start: 0.8405 (tpp) cc_final: 0.8100 (ttp) REVERT: C 128 ASP cc_start: 0.8407 (t0) cc_final: 0.7983 (t0) REVERT: C 200 LYS cc_start: 0.8860 (mptp) cc_final: 0.8592 (mppt) REVERT: C 308 PRO cc_start: 0.8905 (Cg_endo) cc_final: 0.8655 (Cg_exo) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 1.4740 time to fit residues: 159.5834 Evaluate side-chains 100 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.131479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112387 restraints weight = 16625.979| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.81 r_work: 0.3027 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14788 Z= 0.131 Angle : 0.475 6.893 20016 Z= 0.237 Chirality : 0.038 0.127 2196 Planarity : 0.004 0.047 2632 Dihedral : 5.714 57.174 2100 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.07 % Allowed : 11.25 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.57 (0.20), residues: 1828 helix: 1.96 (0.19), residues: 784 sheet: 0.57 (0.41), residues: 200 loop : -1.26 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 57 HIS 0.002 0.001 HIS A 270 PHE 0.006 0.001 PHE D 441 TYR 0.008 0.001 TYR B 106 ARG 0.003 0.000 ARG D 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3765.08 seconds wall clock time: 67 minutes 55.99 seconds (4075.99 seconds total)