Starting phenix.real_space_refine on Sun Mar 17 23:13:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkn_21705/03_2024/6wkn_21705_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkn_21705/03_2024/6wkn_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_21705/03_2024/6wkn_21705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkn_21705/03_2024/6wkn_21705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkn_21705/03_2024/6wkn_21705_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wkn_21705/03_2024/6wkn_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.23, 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: 7.33 Conformation dependent library (CDL) restraints added in 3.5 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: 3.43 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: 4.58 Time building geometry restraints manager: 8.00 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: 0.670 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: 0.020 Extract box with map and model: 4.510 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 49.170 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.000 ------------------------------------------------------------------------------- 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 : 2.130 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: A 183 LEU cc_start: 0.8800 (tp) cc_final: 0.8495 (mt) REVERT: A 243 ASP cc_start: 0.8515 (p0) cc_final: 0.8034 (p0) REVERT: A 269 HIS cc_start: 0.6808 (m90) cc_final: 0.6553 (m90) REVERT: A 277 MET cc_start: 0.8038 (ttm) cc_final: 0.7732 (ttp) REVERT: A 453 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8483 (mt) REVERT: A 468 MET cc_start: 0.6470 (mtp) cc_final: 0.6211 (mtm) REVERT: A 474 ILE cc_start: 0.8552 (pt) cc_final: 0.8236 (mt) REVERT: A 599 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7761 (tp30) REVERT: A 631 LEU cc_start: 0.8740 (tt) cc_final: 0.8489 (tt) REVERT: A 638 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 685 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: B 183 LEU cc_start: 0.8821 (tp) cc_final: 0.8513 (mt) REVERT: B 243 ASP cc_start: 0.8513 (p0) cc_final: 0.8024 (p0) REVERT: B 269 HIS cc_start: 0.6772 (m90) cc_final: 0.6528 (m90) REVERT: B 277 MET cc_start: 0.8017 (ttm) cc_final: 0.7710 (ttp) REVERT: B 453 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8495 (mt) REVERT: B 474 ILE cc_start: 0.8564 (pt) cc_final: 0.8293 (mt) REVERT: B 599 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7751 (tp30) REVERT: B 631 LEU cc_start: 0.8745 (tt) cc_final: 0.8491 (tt) REVERT: B 638 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.7921 (mp) REVERT: B 685 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: C 183 LEU cc_start: 0.8798 (tp) cc_final: 0.8485 (mt) REVERT: C 243 ASP cc_start: 0.8524 (p0) cc_final: 0.8041 (p0) REVERT: C 269 HIS cc_start: 0.6774 (m90) cc_final: 0.6519 (m90) REVERT: C 277 MET cc_start: 0.8035 (ttm) cc_final: 0.7721 (ttp) REVERT: C 453 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8479 (mt) REVERT: C 468 MET cc_start: 0.6465 (mtp) cc_final: 0.6199 (mtm) REVERT: C 474 ILE cc_start: 0.8579 (pt) cc_final: 0.8299 (mt) REVERT: C 599 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7778 (tp30) REVERT: C 631 LEU cc_start: 0.8746 (tt) cc_final: 0.8492 (tt) REVERT: C 638 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.7979 (mp) REVERT: C 685 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: D 183 LEU cc_start: 0.8783 (tp) cc_final: 0.8476 (mt) REVERT: D 243 ASP cc_start: 0.8535 (p0) cc_final: 0.8044 (p0) REVERT: D 269 HIS cc_start: 0.6785 (m90) cc_final: 0.6528 (m90) REVERT: D 277 MET cc_start: 0.8032 (ttm) cc_final: 0.7727 (ttp) REVERT: D 453 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8474 (mt) REVERT: D 474 ILE cc_start: 0.8577 (pt) cc_final: 0.8309 (mt) REVERT: D 599 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7801 (tp30) REVERT: D 631 LEU cc_start: 0.8752 (tt) cc_final: 0.8494 (tt) REVERT: D 638 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.7927 (mp) REVERT: D 685 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.6683 (mp0) outliers start: 92 outliers final: 33 residues processed: 524 average time/residue: 0.3204 time to fit residues: 250.5338 Evaluate side-chains 337 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 288 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 685 GLU Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 685 GLU Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 599 GLU Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 685 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 0.0980 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 217 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7791 moved from start: 0.1837 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= 0.153 Angle : 0.482 6.394 26868 Z= 0.248 Chirality : 0.036 0.126 3060 Planarity : 0.004 0.047 3324 Dihedral : 8.888 89.197 2762 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.49 % Allowed : 16.04 % Favored : 80.46 % 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: -0.97 (0.16), residues: 2384 helix: 0.31 (0.13), residues: 1404 sheet: -1.17 (0.59), residues: 84 loop : -2.12 (0.17), residues: 896 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 0.015 0.001 PHE C 311 TYR 0.009 0.001 TYR D 98 ARG 0.003 0.000 ARG D 371 *********************** 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 367 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 296 time to evaluate : 2.188 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: A 277 MET cc_start: 0.7800 (ttm) cc_final: 0.7551 (ttp) REVERT: A 368 ASN cc_start: 0.8039 (p0) cc_final: 0.7791 (p0) REVERT: A 453 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8454 (mt) REVERT: A 631 LEU cc_start: 0.8629 (tt) cc_final: 0.8164 (mp) REVERT: A 638 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7877 (mp) REVERT: A 677 TRP cc_start: 0.7771 (OUTLIER) cc_final: 0.6747 (p-90) REVERT: B 277 MET cc_start: 0.7806 (ttm) cc_final: 0.7557 (ttp) REVERT: B 368 ASN cc_start: 0.8063 (p0) cc_final: 0.7808 (p0) REVERT: B 453 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8470 (mt) REVERT: B 631 LEU cc_start: 0.8623 (tt) cc_final: 0.8132 (mp) REVERT: B 677 TRP cc_start: 0.7809 (OUTLIER) cc_final: 0.6832 (p-90) REVERT: C 277 MET cc_start: 0.7792 (ttm) cc_final: 0.7556 (ttp) REVERT: C 368 ASN cc_start: 0.8051 (p0) cc_final: 0.7802 (p0) REVERT: C 453 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8458 (mt) REVERT: C 631 LEU cc_start: 0.8633 (tt) cc_final: 0.8162 (mp) REVERT: C 638 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7848 (mp) REVERT: C 677 TRP cc_start: 0.7796 (OUTLIER) cc_final: 0.6803 (p-90) REVERT: D 243 ASP cc_start: 0.8028 (p0) cc_final: 0.7807 (p0) REVERT: D 277 MET cc_start: 0.7798 (ttm) cc_final: 0.7552 (ttp) REVERT: D 368 ASN cc_start: 0.8067 (p0) cc_final: 0.7813 (p0) REVERT: D 453 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8453 (mt) REVERT: D 631 LEU cc_start: 0.8638 (tt) cc_final: 0.8180 (mp) REVERT: D 638 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7891 (mp) REVERT: D 677 TRP cc_start: 0.7814 (OUTLIER) cc_final: 0.6835 (p-90) outliers start: 71 outliers final: 42 residues processed: 342 average time/residue: 0.2951 time to fit residues: 156.9941 Evaluate side-chains 300 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 247 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 469 ASP Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 469 ASP Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 594 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 638 LEU Chi-restraints excluded: chain D residue 677 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.2980 chunk 67 optimal weight: 7.9990 chunk 181 optimal weight: 0.0670 chunk 148 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 216 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.8520 ------------------------------------------------------------------------------- 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 200 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2223 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= 0.139 Angle : 0.462 7.345 26868 Z= 0.233 Chirality : 0.035 0.165 3060 Planarity : 0.004 0.035 3324 Dihedral : 7.738 89.136 2710 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.76 % Allowed : 17.67 % Favored : 79.58 % 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: 0.09 (0.17), residues: 2384 helix: 1.16 (0.14), residues: 1388 sheet: -1.04 (0.60), residues: 84 loop : -1.58 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 677 HIS 0.002 0.001 HIS D 370 PHE 0.013 0.001 PHE D 311 TYR 0.014 0.001 TYR A 98 ARG 0.005 0.000 ARG B 684 *********************** 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 321 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 265 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7693 (tpp80) cc_final: 0.7452 (tpp80) REVERT: A 243 ASP cc_start: 0.8348 (p0) cc_final: 0.7960 (p0) REVERT: A 368 ASN cc_start: 0.7974 (p0) cc_final: 0.7769 (p0) REVERT: A 453 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8354 (mt) REVERT: A 631 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8136 (mp) REVERT: A 677 TRP cc_start: 0.7800 (OUTLIER) cc_final: 0.6742 (p-90) REVERT: B 243 ASP cc_start: 0.8358 (p0) cc_final: 0.8009 (p0) REVERT: B 368 ASN cc_start: 0.8020 (p0) cc_final: 0.7812 (p0) REVERT: B 453 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8410 (mt) REVERT: B 631 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8129 (mp) REVERT: B 677 TRP cc_start: 0.7782 (OUTLIER) cc_final: 0.6789 (p-90) REVERT: C 243 ASP cc_start: 0.8361 (p0) cc_final: 0.8011 (p0) REVERT: C 368 ASN cc_start: 0.7981 (p0) cc_final: 0.7773 (p0) REVERT: C 453 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8375 (mt) REVERT: C 631 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8149 (mp) REVERT: C 677 TRP cc_start: 0.7793 (OUTLIER) cc_final: 0.6804 (p-90) REVERT: D 193 ARG cc_start: 0.7767 (tpp80) cc_final: 0.7500 (tpp80) REVERT: D 243 ASP cc_start: 0.8001 (p0) cc_final: 0.7727 (p0) REVERT: D 453 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8397 (mt) REVERT: D 631 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8163 (mp) REVERT: D 677 TRP cc_start: 0.7791 (OUTLIER) cc_final: 0.6813 (p-90) outliers start: 56 outliers final: 30 residues processed: 308 average time/residue: 0.2887 time to fit residues: 139.1281 Evaluate side-chains 292 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 250 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 677 TRP 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: 0.8980 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 207 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 191 HIS ** 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: 0.7776 moved from start: 0.2496 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= 0.140 Angle : 0.451 7.750 26868 Z= 0.231 Chirality : 0.036 0.166 3060 Planarity : 0.003 0.041 3324 Dihedral : 7.423 89.317 2700 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.85 % Allowed : 18.45 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2384 helix: 1.56 (0.14), residues: 1392 sheet: -1.07 (0.50), residues: 120 loop : -1.36 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 677 HIS 0.002 0.001 HIS D 251 PHE 0.013 0.001 PHE A 311 TYR 0.014 0.001 TYR B 98 ARG 0.003 0.000 ARG C 684 *********************** 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 328 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 270 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7459 (tpp80) REVERT: A 243 ASP cc_start: 0.8343 (p0) cc_final: 0.7954 (p0) REVERT: A 453 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8393 (mt) REVERT: A 631 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8135 (mp) REVERT: A 677 TRP cc_start: 0.7799 (OUTLIER) cc_final: 0.6816 (p-90) REVERT: B 243 ASP cc_start: 0.8350 (p0) cc_final: 0.7979 (p0) REVERT: B 453 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8417 (mt) REVERT: B 631 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8133 (mp) REVERT: B 677 TRP cc_start: 0.7794 (OUTLIER) cc_final: 0.6836 (p-90) REVERT: C 193 ARG cc_start: 0.7740 (tpp80) cc_final: 0.7528 (tpp80) REVERT: C 243 ASP cc_start: 0.8358 (p0) cc_final: 0.7969 (p0) REVERT: C 453 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8397 (mt) REVERT: C 631 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8130 (mp) REVERT: C 677 TRP cc_start: 0.7791 (OUTLIER) cc_final: 0.6856 (p-90) REVERT: D 453 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8409 (mt) REVERT: D 631 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8153 (mp) REVERT: D 640 MET cc_start: 0.7525 (ttp) cc_final: 0.7306 (ttp) REVERT: D 677 TRP cc_start: 0.7786 (OUTLIER) cc_final: 0.6863 (p-90) outliers start: 58 outliers final: 37 residues processed: 317 average time/residue: 0.3163 time to fit residues: 156.8053 Evaluate side-chains 299 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 250 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 160 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 GLN B 294 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19788 Z= 0.253 Angle : 0.535 6.564 26868 Z= 0.273 Chirality : 0.038 0.138 3060 Planarity : 0.004 0.062 3324 Dihedral : 7.493 86.054 2696 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.53 % Allowed : 18.70 % Favored : 76.77 % 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: 0.21 (0.17), residues: 2384 helix: 1.22 (0.14), residues: 1444 sheet: -1.06 (0.51), residues: 112 loop : -1.65 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 677 HIS 0.005 0.001 HIS A 370 PHE 0.017 0.001 PHE B 311 TYR 0.020 0.002 TYR D 447 ARG 0.009 0.001 ARG A 539 *********************** 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 375 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 283 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.8587 (p0) cc_final: 0.8157 (p0) REVERT: A 453 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8482 (mt) REVERT: A 631 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8153 (mp) REVERT: A 677 TRP cc_start: 0.7898 (OUTLIER) cc_final: 0.7050 (p-90) REVERT: B 243 ASP cc_start: 0.8585 (p0) cc_final: 0.8174 (p0) REVERT: B 453 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8483 (mt) REVERT: B 631 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8171 (mp) REVERT: B 638 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7849 (mp) REVERT: B 677 TRP cc_start: 0.7878 (OUTLIER) cc_final: 0.7060 (p-90) REVERT: C 243 ASP cc_start: 0.8591 (p0) cc_final: 0.8169 (p0) REVERT: C 453 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8476 (mt) REVERT: C 631 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8166 (mp) REVERT: C 677 TRP cc_start: 0.7878 (OUTLIER) cc_final: 0.7061 (p-90) REVERT: D 453 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8492 (mt) REVERT: D 631 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8183 (mp) REVERT: D 677 TRP cc_start: 0.7870 (OUTLIER) cc_final: 0.7059 (p-90) outliers start: 92 outliers final: 61 residues processed: 349 average time/residue: 0.2754 time to fit residues: 151.7398 Evaluate side-chains 334 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 260 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 222 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 222 GLN Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** C 363 HIS ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19788 Z= 0.288 Angle : 0.564 6.817 26868 Z= 0.289 Chirality : 0.039 0.137 3060 Planarity : 0.004 0.047 3324 Dihedral : 7.577 86.239 2696 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.48 % Allowed : 20.18 % Favored : 75.34 % 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: 0.14 (0.17), residues: 2384 helix: 1.14 (0.14), residues: 1440 sheet: -0.74 (0.64), residues: 84 loop : -1.64 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 677 HIS 0.005 0.001 HIS C 370 PHE 0.016 0.002 PHE A 311 TYR 0.020 0.002 TYR A 343 ARG 0.006 0.001 ARG A 539 *********************** 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 360 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 269 time to evaluate : 2.159 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.8578 (p0) cc_final: 0.8226 (p0) REVERT: A 453 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8508 (mt) REVERT: A 631 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8143 (mp) REVERT: A 677 TRP cc_start: 0.7934 (OUTLIER) cc_final: 0.7199 (p-90) REVERT: B 243 ASP cc_start: 0.8589 (p0) cc_final: 0.8225 (p0) REVERT: B 453 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8527 (mt) REVERT: B 631 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8184 (mp) REVERT: B 638 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7718 (mp) REVERT: B 677 TRP cc_start: 0.7926 (OUTLIER) cc_final: 0.7200 (p-90) REVERT: C 243 ASP cc_start: 0.8585 (p0) cc_final: 0.8234 (p0) REVERT: C 453 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8503 (mt) REVERT: C 631 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8170 (mp) REVERT: C 638 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.7949 (mp) REVERT: C 677 TRP cc_start: 0.7936 (OUTLIER) cc_final: 0.7217 (p-90) REVERT: D 453 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8518 (mt) REVERT: D 631 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8186 (mp) REVERT: D 677 TRP cc_start: 0.7925 (OUTLIER) cc_final: 0.7209 (p-90) outliers start: 91 outliers final: 64 residues processed: 334 average time/residue: 0.2768 time to fit residues: 146.7419 Evaluate side-chains 333 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 255 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 638 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 TRP Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 195 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 231 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7808 moved from start: 0.2937 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= 0.145 Angle : 0.479 6.458 26868 Z= 0.242 Chirality : 0.036 0.133 3060 Planarity : 0.004 0.050 3324 Dihedral : 7.454 89.393 2696 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.40 % Allowed : 20.87 % Favored : 75.74 % 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: 0.73 (0.17), residues: 2384 helix: 1.61 (0.14), residues: 1416 sheet: -0.93 (0.52), residues: 112 loop : -1.24 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 223 HIS 0.002 0.001 HIS B 413 PHE 0.012 0.001 PHE C 311 TYR 0.018 0.001 TYR B 447 ARG 0.005 0.000 ARG A 539 *********************** 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 341 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 272 time to evaluate : 2.137 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.8318 (p0) cc_final: 0.7910 (p0) REVERT: A 453 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8409 (mt) REVERT: A 631 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8151 (mp) REVERT: A 677 TRP cc_start: 0.7844 (OUTLIER) cc_final: 0.6994 (p-90) REVERT: B 243 ASP cc_start: 0.8325 (p0) cc_final: 0.7934 (p0) REVERT: B 296 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8183 (mt) REVERT: B 453 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8424 (mt) REVERT: B 631 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8144 (mp) REVERT: B 677 TRP cc_start: 0.7835 (OUTLIER) cc_final: 0.6999 (p-90) REVERT: C 243 ASP cc_start: 0.8322 (p0) cc_final: 0.7909 (p0) REVERT: C 296 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8175 (mt) REVERT: C 453 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8424 (mt) REVERT: C 631 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8132 (mp) REVERT: C 677 TRP cc_start: 0.7836 (OUTLIER) cc_final: 0.6995 (p-90) REVERT: D 243 ASP cc_start: 0.8385 (p0) cc_final: 0.8125 (p0) REVERT: D 453 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8439 (mt) REVERT: D 631 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8173 (mp) REVERT: D 677 TRP cc_start: 0.7838 (OUTLIER) cc_final: 0.7001 (p-90) outliers start: 69 outliers final: 46 residues processed: 315 average time/residue: 0.2698 time to fit residues: 134.8985 Evaluate side-chains 329 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 269 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 296 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.7904 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19788 Z= 0.327 Angle : 0.586 7.540 26868 Z= 0.296 Chirality : 0.040 0.136 3060 Planarity : 0.004 0.049 3324 Dihedral : 7.535 85.056 2696 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.84 % Allowed : 20.67 % Favored : 75.49 % 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: 0.26 (0.17), residues: 2384 helix: 1.24 (0.14), residues: 1440 sheet: -0.77 (0.63), residues: 84 loop : -1.57 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 677 HIS 0.006 0.001 HIS D 370 PHE 0.017 0.002 PHE C 311 TYR 0.023 0.002 TYR A 343 ARG 0.005 0.001 ARG A 539 *********************** 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 344 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 266 time to evaluate : 2.126 Fit side-chains REVERT: A 243 ASP cc_start: 0.8613 (p0) cc_final: 0.8274 (p0) REVERT: A 453 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8535 (mt) REVERT: A 631 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8136 (mp) REVERT: A 677 TRP cc_start: 0.7975 (OUTLIER) cc_final: 0.7318 (p-90) REVERT: B 243 ASP cc_start: 0.8623 (p0) cc_final: 0.8291 (p0) REVERT: B 453 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8521 (mt) REVERT: B 631 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8148 (mp) REVERT: B 677 TRP cc_start: 0.7968 (OUTLIER) cc_final: 0.7241 (p-90) REVERT: C 243 ASP cc_start: 0.8610 (p0) cc_final: 0.8253 (p0) REVERT: C 453 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8529 (mt) REVERT: C 631 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8180 (mp) REVERT: C 677 TRP cc_start: 0.7980 (OUTLIER) cc_final: 0.7254 (p-90) REVERT: D 453 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8526 (mt) REVERT: D 631 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8163 (mp) REVERT: D 677 TRP cc_start: 0.7967 (OUTLIER) cc_final: 0.7249 (p-90) outliers start: 78 outliers final: 61 residues processed: 315 average time/residue: 0.2707 time to fit residues: 136.1487 Evaluate side-chains 328 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 255 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 650 ASN Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 650 ASN Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 TRP Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 4.9990 chunk 221 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 129 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 235 GLN ** 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** D 294 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19788 Z= 0.177 Angle : 0.497 7.431 26868 Z= 0.252 Chirality : 0.037 0.132 3060 Planarity : 0.004 0.051 3324 Dihedral : 7.463 88.692 2696 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.89 % Allowed : 20.82 % Favored : 75.30 % 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: 0.74 (0.17), residues: 2384 helix: 1.58 (0.14), residues: 1420 sheet: -0.69 (0.62), residues: 84 loop : -1.22 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 677 HIS 0.003 0.001 HIS B 370 PHE 0.012 0.001 PHE B 311 TYR 0.017 0.001 TYR C 447 ARG 0.004 0.000 ARG D 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 355 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 276 time to evaluate : 2.186 Fit side-chains REVERT: A 243 ASP cc_start: 0.8439 (p0) cc_final: 0.8033 (p0) REVERT: A 453 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8475 (mt) REVERT: A 631 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8158 (mp) REVERT: A 677 TRP cc_start: 0.7911 (OUTLIER) cc_final: 0.6957 (p-90) REVERT: B 243 ASP cc_start: 0.8442 (p0) cc_final: 0.8043 (p0) REVERT: B 453 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8475 (mt) REVERT: B 631 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8149 (mp) REVERT: B 677 TRP cc_start: 0.7886 (OUTLIER) cc_final: 0.6947 (p-90) REVERT: C 243 ASP cc_start: 0.8418 (p0) cc_final: 0.8033 (p0) REVERT: C 296 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8206 (mt) REVERT: C 453 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8469 (mt) REVERT: C 631 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8197 (mp) REVERT: C 677 TRP cc_start: 0.7896 (OUTLIER) cc_final: 0.6968 (p-90) REVERT: D 243 ASP cc_start: 0.8464 (p0) cc_final: 0.8180 (p0) REVERT: D 453 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8482 (mt) REVERT: D 631 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8183 (mp) REVERT: D 677 TRP cc_start: 0.7895 (OUTLIER) cc_final: 0.6962 (p-90) outliers start: 79 outliers final: 62 residues processed: 321 average time/residue: 0.2738 time to fit residues: 141.6056 Evaluate side-chains 340 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 265 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 359 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 TRP Chi-restraints excluded: chain D residue 691 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 6.9990 chunk 227 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 108 optimal weight: 0.5980 chunk 158 optimal weight: 0.9980 chunk 239 optimal weight: 9.9990 chunk 220 optimal weight: 0.8980 chunk 190 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 147 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19788 Z= 0.145 Angle : 0.473 7.108 26868 Z= 0.238 Chirality : 0.036 0.130 3060 Planarity : 0.004 0.051 3324 Dihedral : 7.317 89.784 2696 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.35 % Allowed : 21.56 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.17), residues: 2384 helix: 1.85 (0.14), residues: 1420 sheet: -0.71 (0.62), residues: 84 loop : -1.13 (0.19), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 677 HIS 0.002 0.001 HIS D 251 PHE 0.010 0.001 PHE C 311 TYR 0.017 0.001 TYR C 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 337 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 269 time to evaluate : 2.314 Fit side-chains REVERT: A 243 ASP cc_start: 0.8254 (p0) cc_final: 0.7851 (p0) REVERT: A 453 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8423 (mt) REVERT: A 631 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8134 (mp) REVERT: A 677 TRP cc_start: 0.7869 (OUTLIER) cc_final: 0.7047 (p-90) REVERT: B 243 ASP cc_start: 0.8264 (p0) cc_final: 0.7838 (p0) REVERT: B 453 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8420 (mt) REVERT: B 631 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8086 (mp) REVERT: B 677 TRP cc_start: 0.7869 (OUTLIER) cc_final: 0.7036 (p-90) REVERT: C 243 ASP cc_start: 0.8251 (p0) cc_final: 0.7835 (p0) REVERT: C 296 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8118 (mt) REVERT: C 453 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8421 (mt) REVERT: C 631 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8156 (mp) REVERT: C 642 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7573 (pt) REVERT: C 677 TRP cc_start: 0.7870 (OUTLIER) cc_final: 0.7045 (p-90) REVERT: D 243 ASP cc_start: 0.8276 (p0) cc_final: 0.7988 (p0) REVERT: D 453 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8432 (mt) REVERT: D 631 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8166 (mp) REVERT: D 677 TRP cc_start: 0.7867 (OUTLIER) cc_final: 0.7039 (p-90) outliers start: 68 outliers final: 51 residues processed: 312 average time/residue: 0.2644 time to fit residues: 132.6961 Evaluate side-chains 320 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 255 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 494 THR Chi-restraints excluded: chain A residue 521 HIS Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 677 TRP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 145 ASP Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 521 HIS Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 TRP Chi-restraints excluded: chain B residue 691 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 340 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 521 HIS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 642 ILE Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 677 TRP Chi-restraints excluded: chain C residue 691 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 404 MET Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 494 THR Chi-restraints excluded: chain D residue 521 HIS Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 677 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 35 optimal weight: 10.0000 overall best weight: 0.8920 ------------------------------------------------------------------------------- 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** B 363 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.160137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.140234 restraints weight = 24908.691| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.62 r_work: 0.3560 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19788 Z= 0.148 Angle : 0.478 7.544 26868 Z= 0.239 Chirality : 0.036 0.130 3060 Planarity : 0.004 0.051 3324 Dihedral : 7.238 89.980 2696 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.35 % Allowed : 21.46 % Favored : 75.20 % 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: 1.19 (0.17), residues: 2384 helix: 2.02 (0.14), residues: 1396 sheet: -0.72 (0.61), residues: 84 loop : -1.07 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 677 HIS 0.002 0.001 HIS C 251 PHE 0.011 0.001 PHE A 311 TYR 0.018 0.001 TYR C 98 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: 3847.24 seconds wall clock time: 70 minutes 34.30 seconds (4234.30 seconds total)