Starting phenix.real_space_refine on Mon Dec 11 21:49:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkn_21705/12_2023/6wkn_21705_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkn_21705/12_2023/6wkn_21705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkn_21705/12_2023/6wkn_21705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkn_21705/12_2023/6wkn_21705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkn_21705/12_2023/6wkn_21705_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkn_21705/12_2023/6wkn_21705_updated.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 12636 2.51 5 N 3240 2.21 5 O 3332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 185": "OE1" <-> "OE2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A ARG 687": "NH1" <-> "NH2" Residue "A GLU 708": "OE1" <-> "OE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B GLU 561": "OE1" <-> "OE2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B GLU 599": "OE1" <-> "OE2" Residue "B GLU 614": "OE1" <-> "OE2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B ARG 687": "NH1" <-> "NH2" Residue "B GLU 708": "OE1" <-> "OE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 535": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C GLU 561": "OE1" <-> "OE2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C GLU 599": "OE1" <-> "OE2" Residue "C GLU 614": "OE1" <-> "OE2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C ARG 687": "NH1" <-> "NH2" Residue "C GLU 708": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 309": "OE1" <-> "OE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D ARG 490": "NH1" <-> "NH2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D GLU 561": "OE1" <-> "OE2" Residue "D ARG 563": "NH1" <-> "NH2" Residue "D GLU 599": "OE1" <-> "OE2" Residue "D GLU 614": "OE1" <-> "OE2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D ARG 687": "NH1" <-> "NH2" Residue "D GLU 708": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 19320 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5, 'TRP:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 99 Chain: "B" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5, 'TRP:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 99 Chain: "C" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5, 'TRP:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 99 Chain: "D" Number of atoms: 4807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4807 Classifications: {'peptide': 606} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 4 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5, 'TRP:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 99 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'LQ4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'LQ4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'LQ4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'LQ4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.17, per 1000 atoms: 0.53 Number of scatterers: 19320 At special positions: 0 Unit cell: (138.27, 138.27, 113.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3332 8.00 N 3240 7.00 C 12636 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: 7.37 Conformation dependent library (CDL) restraints added in 3.7 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 4 sheets defined 54.5% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 136 through 144 removed outlier: 3.533A pdb=" N LEU A 140 " --> pdb=" O ILE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 Processing helix chain 'A' and resid 177 through 184 Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 224 through 230 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.643A pdb=" N ALA A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.413A pdb=" N HIS A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 412 removed outlier: 3.961A pdb=" N LYS A 380 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 458 Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.716A pdb=" N LEU A 475 " --> pdb=" O TYR A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 516 removed outlier: 3.987A pdb=" N LEU A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.763A pdb=" N VAL A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 503 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A 507 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU A 512 " --> pdb=" O TRP A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 558 removed outlier: 5.517A pdb=" N ARG A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASP A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 603 removed outlier: 4.033A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 649 Processing helix chain 'A' and resid 653 through 672 Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 136 through 144 removed outlier: 3.533A pdb=" N LEU B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 Processing helix chain 'B' and resid 177 through 184 Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 224 through 230 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 261 through 281 removed outlier: 3.643A pdb=" N ALA B 265 " --> pdb=" O PRO B 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 324 through 326 No H-bonds generated for 'chain 'B' and resid 324 through 326' Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.413A pdb=" N HIS B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 412 removed outlier: 3.961A pdb=" N LYS B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 458 Processing helix chain 'B' and resid 471 through 491 removed outlier: 3.717A pdb=" N LEU B 475 " --> pdb=" O TYR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 516 removed outlier: 3.988A pdb=" N LEU B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Proline residue: B 499 - end of helix removed outlier: 3.764A pdb=" N VAL B 502 " --> pdb=" O PRO B 499 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 503 " --> pdb=" O LEU B 500 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU B 507 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 512 " --> pdb=" O TRP B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 558 removed outlier: 5.516A pdb=" N ARG B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASP B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 603 removed outlier: 4.033A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 649 Processing helix chain 'B' and resid 653 through 672 Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 136 through 144 removed outlier: 3.533A pdb=" N LEU C 140 " --> pdb=" O ILE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'C' and resid 224 through 230 Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 261 through 281 removed outlier: 3.643A pdb=" N ALA C 265 " --> pdb=" O PRO C 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 304 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 324 through 326 No H-bonds generated for 'chain 'C' and resid 324 through 326' Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.413A pdb=" N HIS C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 412 removed outlier: 3.962A pdb=" N LYS C 380 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU C 381 " --> pdb=" O PRO C 377 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 458 Processing helix chain 'C' and resid 471 through 491 removed outlier: 3.716A pdb=" N LEU C 475 " --> pdb=" O TYR C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 516 removed outlier: 3.988A pdb=" N LEU C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Proline residue: C 499 - end of helix removed outlier: 3.763A pdb=" N VAL C 502 " --> pdb=" O PRO C 499 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 503 " --> pdb=" O LEU C 500 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU C 507 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU C 512 " --> pdb=" O TRP C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 558 removed outlier: 5.517A pdb=" N ARG C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASP C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 603 removed outlier: 4.034A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 649 Processing helix chain 'C' and resid 653 through 672 Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 136 through 144 removed outlier: 3.533A pdb=" N LEU D 140 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 224 through 230 Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 261 through 281 removed outlier: 3.643A pdb=" N ALA D 265 " --> pdb=" O PRO D 261 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 304 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'D' and resid 324 through 326 No H-bonds generated for 'chain 'D' and resid 324 through 326' Processing helix chain 'D' and resid 356 through 362 Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.413A pdb=" N HIS D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 412 removed outlier: 3.960A pdb=" N LYS D 380 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 381 " --> pdb=" O PRO D 377 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 458 Processing helix chain 'D' and resid 471 through 491 removed outlier: 3.716A pdb=" N LEU D 475 " --> pdb=" O TYR D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 516 removed outlier: 3.987A pdb=" N LEU D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Proline residue: D 499 - end of helix removed outlier: 3.763A pdb=" N VAL D 502 " --> pdb=" O PRO D 499 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU D 503 " --> pdb=" O LEU D 500 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU D 507 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU D 512 " --> pdb=" O TRP D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 558 removed outlier: 5.516A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ASP D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 603 removed outlier: 4.034A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 649 Processing helix chain 'D' and resid 653 through 672 Processing sheet with id= A, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.953A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY A 692 " --> pdb=" O ASP A 700 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG A 702 " --> pdb=" O LYS A 690 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LYS A 690 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS A 704 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A 688 " --> pdb=" O CYS A 704 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.952A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY B 692 " --> pdb=" O ASP B 700 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG B 702 " --> pdb=" O LYS B 690 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS B 690 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS B 704 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU B 688 " --> pdb=" O CYS B 704 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.953A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY C 692 " --> pdb=" O ASP C 700 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG C 702 " --> pdb=" O LYS C 690 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS C 690 " --> pdb=" O ARG C 702 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS C 704 " --> pdb=" O LEU C 688 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU C 688 " --> pdb=" O CYS C 704 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.953A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY D 692 " --> pdb=" O ASP D 700 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ARG D 702 " --> pdb=" O LYS D 690 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS D 690 " --> pdb=" O ARG D 702 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N CYS D 704 " --> pdb=" O LEU D 688 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU D 688 " --> pdb=" O CYS D 704 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2604 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.42 Time building geometry restraints manager: 8.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2984 1.31 - 1.43: 5552 1.43 - 1.56: 11080 1.56 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 19788 Sorted by residual: bond pdb=" C13 LQ4 C 801 " pdb=" C14 LQ4 C 801 " ideal model delta sigma weight residual 1.332 1.500 -0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C13 LQ4 A 801 " pdb=" C14 LQ4 A 801 " ideal model delta sigma weight residual 1.332 1.500 -0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C13 LQ4 D 801 " pdb=" C14 LQ4 D 801 " ideal model delta sigma weight residual 1.332 1.500 -0.168 2.00e-02 2.50e+03 7.06e+01 bond pdb=" C13 LQ4 B 801 " pdb=" C14 LQ4 B 801 " ideal model delta sigma weight residual 1.332 1.499 -0.167 2.00e-02 2.50e+03 7.00e+01 bond pdb=" C15 LQ4 B 801 " pdb=" N10 LQ4 B 801 " ideal model delta sigma weight residual 1.390 1.481 -0.091 2.00e-02 2.50e+03 2.07e+01 ... (remaining 19783 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.98: 368 105.98 - 113.06: 10710 113.06 - 120.15: 7638 120.15 - 127.24: 7904 127.24 - 134.32: 248 Bond angle restraints: 26868 Sorted by residual: angle pdb=" C GLY D 204 " pdb=" N THR D 205 " pdb=" CA THR D 205 " ideal model delta sigma weight residual 122.46 127.64 -5.18 1.41e+00 5.03e-01 1.35e+01 angle pdb=" C GLY A 204 " pdb=" N THR A 205 " pdb=" CA THR A 205 " ideal model delta sigma weight residual 122.46 127.64 -5.18 1.41e+00 5.03e-01 1.35e+01 angle pdb=" C GLY B 204 " pdb=" N THR B 205 " pdb=" CA THR B 205 " ideal model delta sigma weight residual 122.46 127.64 -5.18 1.41e+00 5.03e-01 1.35e+01 angle pdb=" C GLY C 204 " pdb=" N THR C 205 " pdb=" CA THR C 205 " ideal model delta sigma weight residual 122.46 127.62 -5.16 1.41e+00 5.03e-01 1.34e+01 angle pdb=" C PHE A 467 " pdb=" N MET A 468 " pdb=" CA MET A 468 " ideal model delta sigma weight residual 121.54 128.53 -6.99 1.91e+00 2.74e-01 1.34e+01 ... (remaining 26863 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 10285 16.51 - 33.02: 907 33.02 - 49.54: 276 49.54 - 66.05: 88 66.05 - 82.56: 40 Dihedral angle restraints: 11596 sinusoidal: 4516 harmonic: 7080 Sorted by residual: dihedral pdb=" CA VAL B 532 " pdb=" C VAL B 532 " pdb=" N ILE B 533 " pdb=" CA ILE B 533 " ideal model delta harmonic sigma weight residual -180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA VAL C 532 " pdb=" C VAL C 532 " pdb=" N ILE C 533 " pdb=" CA ILE C 533 " ideal model delta harmonic sigma weight residual -180.00 -158.51 -21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA VAL A 532 " pdb=" C VAL A 532 " pdb=" N ILE A 533 " pdb=" CA ILE A 533 " ideal model delta harmonic sigma weight residual -180.00 -158.52 -21.48 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 11593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1820 0.033 - 0.065: 861 0.065 - 0.097: 273 0.097 - 0.130: 94 0.130 - 0.162: 12 Chirality restraints: 3060 Sorted by residual: chirality pdb=" CA THR D 205 " pdb=" N THR D 205 " pdb=" C THR D 205 " pdb=" CB THR D 205 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA THR C 205 " pdb=" N THR C 205 " pdb=" C THR C 205 " pdb=" CB THR C 205 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA THR B 205 " pdb=" N THR B 205 " pdb=" C THR B 205 " pdb=" CB THR B 205 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 3057 not shown) Planarity restraints: 3324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C07 LQ4 B 801 " -0.053 2.00e-02 2.50e+03 2.77e-01 1.53e+03 pdb=" C08 LQ4 B 801 " -0.076 2.00e-02 2.50e+03 pdb=" C11 LQ4 B 801 " 0.273 2.00e-02 2.50e+03 pdb=" C14 LQ4 B 801 " -0.510 2.00e-02 2.50e+03 pdb=" C15 LQ4 B 801 " 0.052 2.00e-02 2.50e+03 pdb=" N10 LQ4 B 801 " 0.091 2.00e-02 2.50e+03 pdb=" O09 LQ4 B 801 " -0.230 2.00e-02 2.50e+03 pdb=" O16 LQ4 B 801 " 0.453 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 LQ4 D 801 " -0.053 2.00e-02 2.50e+03 2.77e-01 1.53e+03 pdb=" C08 LQ4 D 801 " -0.076 2.00e-02 2.50e+03 pdb=" C11 LQ4 D 801 " 0.273 2.00e-02 2.50e+03 pdb=" C14 LQ4 D 801 " -0.510 2.00e-02 2.50e+03 pdb=" C15 LQ4 D 801 " 0.052 2.00e-02 2.50e+03 pdb=" N10 LQ4 D 801 " 0.091 2.00e-02 2.50e+03 pdb=" O09 LQ4 D 801 " -0.230 2.00e-02 2.50e+03 pdb=" O16 LQ4 D 801 " 0.454 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C07 LQ4 A 801 " -0.053 2.00e-02 2.50e+03 2.77e-01 1.53e+03 pdb=" C08 LQ4 A 801 " -0.076 2.00e-02 2.50e+03 pdb=" C11 LQ4 A 801 " 0.273 2.00e-02 2.50e+03 pdb=" C14 LQ4 A 801 " -0.510 2.00e-02 2.50e+03 pdb=" C15 LQ4 A 801 " 0.052 2.00e-02 2.50e+03 pdb=" N10 LQ4 A 801 " 0.091 2.00e-02 2.50e+03 pdb=" O09 LQ4 A 801 " -0.230 2.00e-02 2.50e+03 pdb=" O16 LQ4 A 801 " 0.454 2.00e-02 2.50e+03 ... (remaining 3321 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4874 2.79 - 3.32: 17437 3.32 - 3.85: 32717 3.85 - 4.37: 37786 4.37 - 4.90: 65798 Nonbonded interactions: 158612 Sorted by model distance: nonbonded pdb=" OH TYR A 271 " pdb=" OE1 GLU A 288 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR D 271 " pdb=" OE1 GLU D 288 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR C 271 " pdb=" OE1 GLU C 288 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR B 271 " pdb=" OE1 GLU B 288 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR A 544 " pdb=" OG1 THR A 604 " model vdw 2.276 2.440 ... (remaining 158607 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.580 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 50.390 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.130 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 0.168 19788 Z= 0.425 Angle : 0.738 8.943 26868 Z= 0.392 Chirality : 0.043 0.162 3060 Planarity : 0.011 0.277 3324 Dihedral : 15.690 82.559 7020 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.53 % Allowed : 11.37 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.14), residues: 2384 helix: -1.53 (0.11), residues: 1400 sheet: -1.05 (0.61), residues: 84 loop : -2.54 (0.16), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 677 HIS 0.005 0.001 HIS B 251 PHE 0.023 0.002 PHE B 311 TYR 0.017 0.002 TYR B 343 ARG 0.003 0.001 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 448 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 33 residues processed: 524 average time/residue: 0.3192 time to fit residues: 250.7634 Evaluate side-chains 318 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 285 time to evaluate : 2.117 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1948 time to fit residues: 14.7540 ------------------------------------------------------------------------------- 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: 0.9980 chunk 181 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19788 Z= 0.153 Angle : 0.494 7.333 26868 Z= 0.252 Chirality : 0.036 0.115 3060 Planarity : 0.004 0.046 3324 Dihedral : 6.774 89.632 2668 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.48 % Allowed : 17.47 % Favored : 81.05 % 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: -1.00 (0.16), residues: 2384 helix: 0.30 (0.13), residues: 1404 sheet: -1.32 (0.59), residues: 84 loop : -2.14 (0.17), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 677 HIS 0.003 0.001 HIS D 370 PHE 0.014 0.001 PHE C 311 TYR 0.009 0.001 TYR A 98 ARG 0.003 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 298 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 312 average time/residue: 0.3063 time to fit residues: 148.1782 Evaluate side-chains 279 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 264 time to evaluate : 2.126 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1705 time to fit residues: 7.6213 ------------------------------------------------------------------------------- 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: 10.0000 chunk 181 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 0.6980 chunk 235 optimal weight: 0.0770 chunk 194 optimal weight: 8.9990 chunk 216 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 175 optimal weight: 4.9990 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19788 Z= 0.210 Angle : 0.512 6.840 26868 Z= 0.259 Chirality : 0.037 0.141 3060 Planarity : 0.004 0.035 3324 Dihedral : 6.672 86.321 2668 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.17 % Allowed : 17.52 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2384 helix: 0.94 (0.14), residues: 1392 sheet: -1.41 (0.59), residues: 84 loop : -1.58 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 509 HIS 0.007 0.001 HIS B 521 PHE 0.016 0.001 PHE D 311 TYR 0.014 0.001 TYR D 98 ARG 0.004 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 286 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 324 average time/residue: 0.3036 time to fit residues: 152.8299 Evaluate side-chains 270 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 248 time to evaluate : 1.964 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1703 time to fit residues: 9.9412 ------------------------------------------------------------------------------- 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: 10.0000 chunk 164 optimal weight: 4.9990 chunk 113 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 104 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 0.9980 chunk 231 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19788 Z= 0.145 Angle : 0.470 7.242 26868 Z= 0.237 Chirality : 0.036 0.157 3060 Planarity : 0.003 0.031 3324 Dihedral : 6.688 89.050 2668 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.28 % Allowed : 18.65 % Favored : 80.07 % 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: 0.39 (0.17), residues: 2384 helix: 1.46 (0.14), residues: 1388 sheet: -1.23 (0.58), residues: 84 loop : -1.53 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 223 HIS 0.002 0.001 HIS D 251 PHE 0.013 0.001 PHE D 311 TYR 0.011 0.001 TYR C 98 ARG 0.003 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 284 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 302 average time/residue: 0.2880 time to fit residues: 138.2887 Evaluate side-chains 277 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 263 time to evaluate : 2.308 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1848 time to fit residues: 8.3005 ------------------------------------------------------------------------------- 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: 0.9980 chunk 131 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 197 optimal weight: 9.9990 chunk 160 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 208 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 GLN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19788 Z= 0.303 Angle : 0.562 6.311 26868 Z= 0.287 Chirality : 0.039 0.144 3060 Planarity : 0.004 0.042 3324 Dihedral : 6.760 85.386 2668 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.90 % Allowed : 19.64 % Favored : 77.46 % 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: -0.01 (0.17), residues: 2384 helix: 1.09 (0.14), residues: 1436 sheet: -1.24 (0.60), residues: 84 loop : -1.77 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 677 HIS 0.010 0.001 HIS D 521 PHE 0.017 0.002 PHE A 311 TYR 0.020 0.002 TYR D 447 ARG 0.004 0.001 ARG A 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 261 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 44 residues processed: 300 average time/residue: 0.2982 time to fit residues: 143.3142 Evaluate side-chains 291 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 247 time to evaluate : 2.376 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.1793 time to fit residues: 17.9965 ------------------------------------------------------------------------------- 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: 4.9990 chunk 208 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 136 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 192 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 HIS ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 HIS ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19788 Z= 0.189 Angle : 0.503 6.956 26868 Z= 0.256 Chirality : 0.037 0.141 3060 Planarity : 0.004 0.048 3324 Dihedral : 6.769 87.899 2668 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.84 % Allowed : 20.67 % Favored : 78.49 % 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: 0.49 (0.17), residues: 2384 helix: 1.43 (0.14), residues: 1416 sheet: -1.12 (0.51), residues: 120 loop : -1.36 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 223 HIS 0.003 0.001 HIS D 370 PHE 0.014 0.001 PHE D 311 TYR 0.018 0.001 TYR C 447 ARG 0.003 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 283 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 293 average time/residue: 0.2958 time to fit residues: 137.2506 Evaluate side-chains 281 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 270 time to evaluate : 2.230 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1636 time to fit residues: 6.6562 ------------------------------------------------------------------------------- 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: 7.9990 chunk 26 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 195 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19788 Z= 0.198 Angle : 0.508 6.783 26868 Z= 0.258 Chirality : 0.037 0.137 3060 Planarity : 0.004 0.050 3324 Dihedral : 6.765 87.309 2668 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.69 % Allowed : 21.90 % Favored : 77.41 % 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: 0.59 (0.17), residues: 2384 helix: 1.49 (0.14), residues: 1424 sheet: -1.14 (0.61), residues: 84 loop : -1.30 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 223 HIS 0.006 0.001 HIS D 521 PHE 0.013 0.001 PHE A 311 TYR 0.018 0.001 TYR C 447 ARG 0.004 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 280 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 289 average time/residue: 0.3089 time to fit residues: 139.4474 Evaluate side-chains 274 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 267 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1763 time to fit residues: 5.4056 ------------------------------------------------------------------------------- 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: 2.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 157 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19788 Z= 0.195 Angle : 0.498 6.485 26868 Z= 0.252 Chirality : 0.037 0.135 3060 Planarity : 0.004 0.051 3324 Dihedral : 6.782 87.541 2668 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.49 % Allowed : 21.95 % Favored : 77.56 % 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: 0.71 (0.17), residues: 2384 helix: 1.56 (0.14), residues: 1424 sheet: -1.15 (0.61), residues: 84 loop : -1.21 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 677 HIS 0.003 0.001 HIS A 370 PHE 0.013 0.001 PHE B 311 TYR 0.018 0.001 TYR B 447 ARG 0.004 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 278 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 283 average time/residue: 0.2970 time to fit residues: 133.8637 Evaluate side-chains 272 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 267 time to evaluate : 2.355 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1885 time to fit residues: 4.7252 ------------------------------------------------------------------------------- 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: 0.0370 chunk 221 optimal weight: 0.6980 chunk 202 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19788 Z= 0.161 Angle : 0.478 6.641 26868 Z= 0.241 Chirality : 0.036 0.132 3060 Planarity : 0.004 0.052 3324 Dihedral : 6.789 88.769 2668 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.30 % Allowed : 22.74 % Favored : 76.97 % 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: 0.89 (0.17), residues: 2384 helix: 1.72 (0.14), residues: 1424 sheet: -1.16 (0.60), residues: 84 loop : -1.15 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 660 HIS 0.005 0.001 HIS D 521 PHE 0.011 0.001 PHE A 311 TYR 0.018 0.001 TYR B 447 ARG 0.004 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 277 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 279 average time/residue: 0.2906 time to fit residues: 128.3957 Evaluate side-chains 268 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 264 time to evaluate : 1.905 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1744 time to fit residues: 4.1088 ------------------------------------------------------------------------------- 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: 0.9980 chunk 227 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 239 optimal weight: 0.0370 chunk 220 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19788 Z= 0.134 Angle : 0.464 6.682 26868 Z= 0.233 Chirality : 0.035 0.130 3060 Planarity : 0.003 0.052 3324 Dihedral : 6.794 89.968 2668 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.05 % Allowed : 22.74 % Favored : 77.21 % 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: 1.17 (0.18), residues: 2384 helix: 1.96 (0.14), residues: 1420 sheet: -0.98 (0.51), residues: 120 loop : -1.04 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 660 HIS 0.002 0.001 HIS C 438 PHE 0.010 0.001 PHE A 311 TYR 0.018 0.001 TYR B 447 ARG 0.004 0.000 ARG D 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 2.277 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.2953 time to fit residues: 126.7832 Evaluate side-chains 261 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 2.132 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8343 ------------------------------------------------------------------------------- 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: 0.8980 chunk 202 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 24 optimal weight: 0.0770 chunk 35 optimal weight: 9.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.160114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.140643 restraints weight = 25182.564| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.55 r_work: 0.3568 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19788 Z= 0.136 Angle : 0.465 6.454 26868 Z= 0.233 Chirality : 0.036 0.130 3060 Planarity : 0.003 0.052 3324 Dihedral : 6.484 89.496 2668 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.05 % Allowed : 23.03 % Favored : 76.92 % 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: 1.34 (0.18), residues: 2384 helix: 2.14 (0.14), residues: 1396 sheet: -0.99 (0.51), residues: 120 loop : -0.95 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 660 HIS 0.006 0.001 HIS D 521 PHE 0.010 0.001 PHE A 311 TYR 0.018 0.001 TYR B 447 ARG 0.004 0.000 ARG D 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3867.28 seconds wall clock time: 71 minutes 28.66 seconds (4288.66 seconds total)