Starting phenix.real_space_refine on Sat Feb 17 22:00:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u88_20682/02_2024/6u88_20682_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u88_20682/02_2024/6u88_20682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u88_20682/02_2024/6u88_20682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u88_20682/02_2024/6u88_20682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u88_20682/02_2024/6u88_20682_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u88_20682/02_2024/6u88_20682_neut_updated.pdb" } resolution = 3.2 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= 0.005 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 13116 2.51 5 N 3328 2.21 5 O 3448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 86": "NH1" <-> "NH2" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ARG 197": "NH1" <-> "NH2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" 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 ARG 459": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 563": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 670": "OE1" <-> "OE2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "A GLU 724": "OE1" <-> "OE2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B GLU 262": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B ARG 317": "NH1" <-> "NH2" 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 ARG 459": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 563": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 670": "OE1" <-> "OE2" Residue "B GLU 716": "OE1" <-> "OE2" Residue "B GLU 724": "OE1" <-> "OE2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C GLU 240": "OE1" <-> "OE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C ARG 317": "NH1" <-> "NH2" 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 ARG 459": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 563": "NH1" <-> "NH2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 670": "OE1" <-> "OE2" Residue "C GLU 716": "OE1" <-> "OE2" Residue "C GLU 724": "OE1" <-> "OE2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D GLU 262": "OE1" <-> "OE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D ARG 317": "NH1" <-> "NH2" 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 ARG 459": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 563": "NH1" <-> "NH2" Residue "D ARG 591": "NH1" <-> "NH2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 670": "OE1" <-> "OE2" Residue "D GLU 716": "OE1" <-> "OE2" Residue "D GLU 724": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20004 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4978 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 589} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4978 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 589} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4978 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 589} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4978 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 589} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.74, per 1000 atoms: 0.54 Number of scatterers: 20004 At special positions: 0 Unit cell: (124.02, 124.02, 113.42, 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 3448 8.00 N 3328 7.00 C 13116 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: 7.63 Conformation dependent library (CDL) restraints added in 3.9 seconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4616 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 4 sheets defined 53.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 96 through 102 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 136 through 145 Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 177 through 186 removed outlier: 3.736A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 249 through 255 Processing helix chain 'A' and resid 261 through 281 removed outlier: 3.700A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (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 356 through 362 Processing helix chain 'A' and resid 378 through 412 removed outlier: 5.507A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.353A 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 464 through 466 No H-bonds generated for 'chain 'A' and resid 464 through 466' Processing helix chain 'A' and resid 472 through 491 Processing helix chain 'A' and resid 495 through 518 removed outlier: 3.939A pdb=" N LEU A 498 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.508A pdb=" N VAL A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 506 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU A 512 " --> pdb=" O TRP A 509 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 559 removed outlier: 3.608A pdb=" N LYS A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 605 removed outlier: 4.274A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 650 removed outlier: 4.031A pdb=" N VAL A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 671 Processing helix chain 'B' and resid 77 through 86 Processing helix chain 'B' and resid 96 through 102 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 136 through 145 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 177 through 186 removed outlier: 3.737A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 223 through 230 Processing helix chain 'B' and resid 249 through 255 Processing helix chain 'B' and resid 261 through 281 removed outlier: 3.701A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (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 356 through 362 Processing helix chain 'B' and resid 378 through 412 removed outlier: 5.506A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.354A 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 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 472 through 491 Processing helix chain 'B' and resid 495 through 518 removed outlier: 3.939A pdb=" N LEU B 498 " --> pdb=" O GLU B 495 " (cutoff:3.500A) Proline residue: B 499 - end of helix removed outlier: 3.508A pdb=" N VAL B 502 " --> pdb=" O PRO B 499 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL B 506 " --> pdb=" O LEU B 503 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 512 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 559 removed outlier: 3.609A pdb=" N LYS B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 605 removed outlier: 4.274A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 650 removed outlier: 4.031A pdb=" N VAL B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 671 Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 96 through 102 Processing helix chain 'C' and resid 120 through 126 Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 177 through 186 removed outlier: 3.737A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'C' and resid 223 through 230 Processing helix chain 'C' and resid 249 through 255 Processing helix chain 'C' and resid 261 through 281 removed outlier: 3.700A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (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 356 through 362 Processing helix chain 'C' and resid 378 through 412 removed outlier: 5.507A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.355A 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 464 through 466 No H-bonds generated for 'chain 'C' and resid 464 through 466' Processing helix chain 'C' and resid 472 through 491 Processing helix chain 'C' and resid 495 through 518 removed outlier: 3.939A pdb=" N LEU C 498 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Proline residue: C 499 - end of helix removed outlier: 3.507A pdb=" N VAL C 502 " --> pdb=" O PRO C 499 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 506 " --> pdb=" O LEU C 503 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C 512 " --> pdb=" O TRP C 509 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 559 removed outlier: 3.609A pdb=" N LYS C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL C 532 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 605 removed outlier: 4.274A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 650 removed outlier: 4.031A pdb=" N VAL C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 671 Processing helix chain 'D' and resid 77 through 86 Processing helix chain 'D' and resid 96 through 102 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 136 through 145 Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 177 through 186 removed outlier: 3.737A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 223 through 230 Processing helix chain 'D' and resid 249 through 255 Processing helix chain 'D' and resid 261 through 281 removed outlier: 3.701A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (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 356 through 362 Processing helix chain 'D' and resid 378 through 412 removed outlier: 5.507A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.354A 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 464 through 466 No H-bonds generated for 'chain 'D' and resid 464 through 466' Processing helix chain 'D' and resid 472 through 491 Processing helix chain 'D' and resid 495 through 518 removed outlier: 3.939A pdb=" N LEU D 498 " --> pdb=" O GLU D 495 " (cutoff:3.500A) Proline residue: D 499 - end of helix removed outlier: 3.507A pdb=" N VAL D 502 " --> pdb=" O PRO D 499 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 506 " --> pdb=" O LEU D 503 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU D 512 " --> pdb=" O TRP D 509 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 559 removed outlier: 3.608A pdb=" N LYS D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA D 554 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 593 through 605 removed outlier: 4.274A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 650 removed outlier: 4.030A pdb=" N VAL D 649 " --> pdb=" O MET D 645 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) Processing helix chain 'D' and resid 657 through 671 Processing sheet with id= A, first strand: chain 'A' and resid 687 through 691 removed outlier: 3.773A pdb=" N TRP A 333 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP A 344 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS A 329 " --> pdb=" O ASP A 344 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 687 through 691 removed outlier: 3.773A pdb=" N TRP B 333 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP B 344 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS B 329 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 687 through 691 removed outlier: 3.773A pdb=" N TRP C 333 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP C 344 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS C 329 " --> pdb=" O ASP C 344 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 687 through 691 removed outlier: 3.773A pdb=" N TRP D 333 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASP D 344 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS D 329 " --> pdb=" O ASP D 344 " (cutoff:3.500A) 900 hydrogen bonds defined for protein. 2532 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.29 Time building geometry restraints manager: 8.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6127 1.34 - 1.46: 5154 1.46 - 1.59: 9059 1.59 - 1.71: 0 1.71 - 1.83: 172 Bond restraints: 20512 Sorted by residual: bond pdb=" C04 P0T C1001 " pdb=" C08 P0T C1001 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C04 P0T D1001 " pdb=" C08 P0T D1001 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C04 P0T A1001 " pdb=" C08 P0T A1001 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" C04 P0T B1001 " pdb=" C08 P0T B1001 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C15 P0T A1001 " pdb=" C18 P0T A1001 " ideal model delta sigma weight residual 1.503 1.552 -0.049 2.00e-02 2.50e+03 6.04e+00 ... (remaining 20507 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.24: 496 106.24 - 113.28: 10904 113.28 - 120.32: 8615 120.32 - 127.36: 7529 127.36 - 134.40: 272 Bond angle restraints: 27816 Sorted by residual: angle pdb=" N TYR A 634 " pdb=" CA TYR A 634 " pdb=" C TYR A 634 " ideal model delta sigma weight residual 111.14 106.84 4.30 1.08e+00 8.57e-01 1.58e+01 angle pdb=" N TYR C 634 " pdb=" CA TYR C 634 " pdb=" C TYR C 634 " ideal model delta sigma weight residual 111.14 106.85 4.29 1.08e+00 8.57e-01 1.58e+01 angle pdb=" N TYR B 634 " pdb=" CA TYR B 634 " pdb=" C TYR B 634 " ideal model delta sigma weight residual 111.14 106.85 4.29 1.08e+00 8.57e-01 1.58e+01 angle pdb=" N TYR D 634 " pdb=" CA TYR D 634 " pdb=" C TYR D 634 " ideal model delta sigma weight residual 111.14 106.85 4.29 1.08e+00 8.57e-01 1.58e+01 angle pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C08 P0T A1001 " ideal model delta sigma weight residual 111.12 120.59 -9.47 3.00e+00 1.11e-01 9.96e+00 ... (remaining 27811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.24: 10818 20.24 - 40.47: 1066 40.47 - 60.71: 156 60.71 - 80.94: 36 80.94 - 101.18: 12 Dihedral angle restraints: 12088 sinusoidal: 4944 harmonic: 7144 Sorted by residual: dihedral pdb=" CA VAL C 652 " pdb=" C VAL C 652 " pdb=" N ALA C 653 " pdb=" CA ALA C 653 " ideal model delta harmonic sigma weight residual -180.00 -151.74 -28.26 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA VAL D 652 " pdb=" C VAL D 652 " pdb=" N ALA D 653 " pdb=" CA ALA D 653 " ideal model delta harmonic sigma weight residual -180.00 -151.78 -28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA VAL B 652 " pdb=" C VAL B 652 " pdb=" N ALA B 653 " pdb=" CA ALA B 653 " ideal model delta harmonic sigma weight residual -180.00 -151.81 -28.19 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 12085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2047 0.053 - 0.105: 861 0.105 - 0.158: 140 0.158 - 0.210: 53 0.210 - 0.263: 15 Chirality restraints: 3116 Sorted by residual: chirality pdb=" CB VAL B 652 " pdb=" CA VAL B 652 " pdb=" CG1 VAL B 652 " pdb=" CG2 VAL B 652 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL A 652 " pdb=" CA VAL A 652 " pdb=" CG1 VAL A 652 " pdb=" CG2 VAL A 652 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL C 652 " pdb=" CA VAL C 652 " pdb=" CG1 VAL C 652 " pdb=" CG2 VAL C 652 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3113 not shown) Planarity restraints: 3428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 725 " 0.063 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO A 726 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 726 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 726 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 725 " -0.063 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO C 726 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO C 726 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 726 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 725 " -0.063 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO B 726 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 726 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 726 " -0.051 5.00e-02 4.00e+02 ... (remaining 3425 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 6591 2.84 - 3.36: 17608 3.36 - 3.87: 34304 3.87 - 4.39: 38799 4.39 - 4.90: 66572 Nonbonded interactions: 163874 Sorted by model distance: nonbonded pdb=" O SER B 466 " pdb=" OG SER B 470 " model vdw 2.328 2.440 nonbonded pdb=" O SER C 466 " pdb=" OG SER C 470 " model vdw 2.329 2.440 nonbonded pdb=" O SER D 466 " pdb=" OG SER D 470 " model vdw 2.329 2.440 nonbonded pdb=" O SER A 466 " pdb=" OG SER A 470 " model vdw 2.329 2.440 nonbonded pdb=" O SER D 470 " pdb=" OG SER D 470 " model vdw 2.333 2.440 ... (remaining 163869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 6.460 Check model and map are aligned: 0.330 Set scattering table: 0.200 Process input model: 53.350 Find NCS groups from input model: 1.240 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: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.009 0.084 20512 Z= 0.577 Angle : 1.052 10.385 27816 Z= 0.553 Chirality : 0.059 0.263 3116 Planarity : 0.009 0.095 3428 Dihedral : 16.098 101.178 7472 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.74 % Allowed : 10.70 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.11), residues: 2412 helix: -3.13 (0.08), residues: 1456 sheet: -3.31 (0.36), residues: 124 loop : -3.12 (0.14), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 454 HIS 0.011 0.002 HIS B 251 PHE 0.021 0.003 PHE A 209 TYR 0.017 0.003 TYR C 228 ARG 0.008 0.001 ARG D 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 359 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 GLN cc_start: 0.7791 (tp40) cc_final: 0.7509 (tt0) REVERT: A 591 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7711 (mmt-90) REVERT: A 595 ASP cc_start: 0.7405 (m-30) cc_final: 0.6976 (t0) REVERT: A 632 LEU cc_start: 0.8830 (mt) cc_final: 0.8531 (mt) REVERT: A 634 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: B 148 ASN cc_start: 0.6492 (p0) cc_final: 0.6260 (p0) REVERT: B 383 GLN cc_start: 0.7765 (tp40) cc_final: 0.7479 (tt0) REVERT: B 405 PHE cc_start: 0.7520 (t80) cc_final: 0.7290 (m-10) REVERT: B 591 ARG cc_start: 0.8135 (ptm160) cc_final: 0.7699 (mmt-90) REVERT: B 595 ASP cc_start: 0.7428 (m-30) cc_final: 0.6966 (t0) REVERT: B 617 ARG cc_start: 0.7719 (ttt180) cc_final: 0.7511 (ttt180) REVERT: B 632 LEU cc_start: 0.8839 (mt) cc_final: 0.8540 (mt) REVERT: B 634 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: C 148 ASN cc_start: 0.6514 (p0) cc_final: 0.6264 (p0) REVERT: C 383 GLN cc_start: 0.7757 (tp40) cc_final: 0.7465 (tt0) REVERT: C 405 PHE cc_start: 0.7523 (t80) cc_final: 0.7290 (m-10) REVERT: C 481 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8810 (mp) REVERT: C 591 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7700 (mmt-90) REVERT: C 595 ASP cc_start: 0.7425 (m-30) cc_final: 0.6967 (t0) REVERT: C 617 ARG cc_start: 0.7717 (ttt180) cc_final: 0.7512 (ttt180) REVERT: C 632 LEU cc_start: 0.8835 (mt) cc_final: 0.8536 (mt) REVERT: C 634 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: D 148 ASN cc_start: 0.6512 (p0) cc_final: 0.6282 (p0) REVERT: D 383 GLN cc_start: 0.7750 (tp40) cc_final: 0.7462 (tt0) REVERT: D 405 PHE cc_start: 0.7526 (t80) cc_final: 0.7286 (m-10) REVERT: D 481 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8812 (mp) REVERT: D 591 ARG cc_start: 0.8126 (ptm160) cc_final: 0.7715 (mmt-90) REVERT: D 595 ASP cc_start: 0.7376 (m-30) cc_final: 0.7016 (t0) REVERT: D 617 ARG cc_start: 0.7725 (ttt180) cc_final: 0.7515 (ttt180) REVERT: D 632 LEU cc_start: 0.8837 (mt) cc_final: 0.8540 (mt) REVERT: D 634 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7605 (m-80) outliers start: 16 outliers final: 4 residues processed: 367 average time/residue: 0.3780 time to fit residues: 200.3071 Evaluate side-chains 267 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 257 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 154 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN A 263 ASN A 414 GLN A 487 GLN B 127 ASN B 154 ASN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 263 ASN B 414 GLN B 487 GLN C 127 ASN C 154 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN C 263 ASN C 414 GLN C 487 GLN D 127 ASN D 154 ASN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 263 ASN D 414 GLN D 487 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20512 Z= 0.156 Angle : 0.493 5.798 27816 Z= 0.249 Chirality : 0.037 0.184 3116 Planarity : 0.005 0.076 3428 Dihedral : 8.420 59.967 2776 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.61 % Allowed : 13.51 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -2.08 (0.15), residues: 2412 helix: -0.51 (0.13), residues: 1404 sheet: -2.90 (0.39), residues: 124 loop : -2.50 (0.17), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 454 HIS 0.003 0.001 HIS D 313 PHE 0.019 0.001 PHE B 540 TYR 0.010 0.001 TYR A 629 ARG 0.003 0.000 ARG C 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 297 time to evaluate : 2.247 Fit side-chains revert: symmetry clash REVERT: A 111 TYR cc_start: 0.7729 (m-80) cc_final: 0.7352 (m-80) REVERT: A 205 THR cc_start: 0.8974 (t) cc_final: 0.8695 (m) REVERT: A 277 MET cc_start: 0.8540 (tpp) cc_final: 0.8045 (mmt) REVERT: A 383 GLN cc_start: 0.7709 (tp40) cc_final: 0.7306 (mt0) REVERT: A 473 GLU cc_start: 0.7806 (mp0) cc_final: 0.7568 (mp0) REVERT: A 591 ARG cc_start: 0.8087 (ptm160) cc_final: 0.7715 (mmm160) REVERT: A 595 ASP cc_start: 0.7191 (m-30) cc_final: 0.6873 (t0) REVERT: A 617 ARG cc_start: 0.7689 (ttt180) cc_final: 0.7368 (ttt180) REVERT: A 634 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7759 (m-80) REVERT: B 111 TYR cc_start: 0.7789 (m-80) cc_final: 0.7401 (m-80) REVERT: B 205 THR cc_start: 0.8958 (t) cc_final: 0.8693 (m) REVERT: B 277 MET cc_start: 0.8525 (tpp) cc_final: 0.8055 (mmt) REVERT: B 383 GLN cc_start: 0.7723 (tp40) cc_final: 0.7322 (mt0) REVERT: B 473 GLU cc_start: 0.7825 (mp0) cc_final: 0.7580 (mp0) REVERT: B 591 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7707 (mmm160) REVERT: B 595 ASP cc_start: 0.7140 (m-30) cc_final: 0.6795 (t0) REVERT: B 617 ARG cc_start: 0.7693 (ttt180) cc_final: 0.7388 (ttt180) REVERT: B 634 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7692 (m-80) REVERT: C 205 THR cc_start: 0.8975 (t) cc_final: 0.8694 (m) REVERT: C 277 MET cc_start: 0.8529 (tpp) cc_final: 0.8053 (mmt) REVERT: C 383 GLN cc_start: 0.7704 (tp40) cc_final: 0.7301 (mt0) REVERT: C 473 GLU cc_start: 0.7822 (mp0) cc_final: 0.7581 (mp0) REVERT: C 591 ARG cc_start: 0.8085 (ptm160) cc_final: 0.7702 (mmm160) REVERT: C 595 ASP cc_start: 0.7138 (m-30) cc_final: 0.6791 (t0) REVERT: C 617 ARG cc_start: 0.7696 (ttt180) cc_final: 0.7373 (ttt180) REVERT: C 634 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7735 (m-80) REVERT: D 205 THR cc_start: 0.8966 (t) cc_final: 0.8681 (m) REVERT: D 277 MET cc_start: 0.8538 (tpp) cc_final: 0.8070 (mmt) REVERT: D 383 GLN cc_start: 0.7705 (tp40) cc_final: 0.7323 (mt0) REVERT: D 473 GLU cc_start: 0.7827 (mp0) cc_final: 0.7572 (mp0) REVERT: D 591 ARG cc_start: 0.8100 (ptm160) cc_final: 0.7678 (mmm160) REVERT: D 595 ASP cc_start: 0.7134 (m-30) cc_final: 0.6794 (t0) REVERT: D 634 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7727 (m-80) outliers start: 35 outliers final: 12 residues processed: 317 average time/residue: 0.3405 time to fit residues: 161.3308 Evaluate side-chains 272 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 256 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 4.9990 chunk 68 optimal weight: 0.5980 chunk 184 optimal weight: 7.9990 chunk 150 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 239 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** C 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** D 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20512 Z= 0.310 Angle : 0.573 6.541 27816 Z= 0.283 Chirality : 0.040 0.159 3116 Planarity : 0.005 0.068 3428 Dihedral : 7.963 56.720 2772 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.49 % Allowed : 14.07 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -1.31 (0.16), residues: 2412 helix: 0.11 (0.13), residues: 1432 sheet: -2.64 (0.43), residues: 124 loop : -2.21 (0.18), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 677 HIS 0.005 0.001 HIS D 169 PHE 0.015 0.001 PHE B 540 TYR 0.015 0.002 TYR B 208 ARG 0.003 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 274 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6411 (mmtm) cc_final: 0.5814 (mtmt) REVERT: A 111 TYR cc_start: 0.7777 (m-80) cc_final: 0.7361 (m-80) REVERT: A 205 THR cc_start: 0.9006 (t) cc_final: 0.8765 (m) REVERT: A 375 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8267 (pp) REVERT: A 591 ARG cc_start: 0.8141 (ptm160) cc_final: 0.7648 (mmt-90) REVERT: A 595 ASP cc_start: 0.7353 (m-30) cc_final: 0.6994 (t0) REVERT: A 634 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: B 104 LYS cc_start: 0.6407 (mmtm) cc_final: 0.5798 (mtmt) REVERT: B 111 TYR cc_start: 0.7826 (m-80) cc_final: 0.7368 (m-80) REVERT: B 205 THR cc_start: 0.9014 (t) cc_final: 0.8777 (m) REVERT: B 375 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8256 (pp) REVERT: B 473 GLU cc_start: 0.7819 (mp0) cc_final: 0.7573 (mp0) REVERT: B 591 ARG cc_start: 0.8151 (ptm160) cc_final: 0.7680 (mmt-90) REVERT: B 595 ASP cc_start: 0.7357 (m-30) cc_final: 0.6992 (t0) REVERT: B 634 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: C 104 LYS cc_start: 0.6412 (mmtm) cc_final: 0.5802 (mtmt) REVERT: C 111 TYR cc_start: 0.7723 (m-80) cc_final: 0.7322 (m-80) REVERT: C 205 THR cc_start: 0.9004 (t) cc_final: 0.8763 (m) REVERT: C 375 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8259 (pp) REVERT: C 591 ARG cc_start: 0.8140 (ptm160) cc_final: 0.7646 (mmt-90) REVERT: C 595 ASP cc_start: 0.7361 (m-30) cc_final: 0.6995 (t0) REVERT: C 634 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: D 104 LYS cc_start: 0.6411 (mmtm) cc_final: 0.5804 (mtmt) REVERT: D 111 TYR cc_start: 0.7722 (m-80) cc_final: 0.7324 (m-80) REVERT: D 205 THR cc_start: 0.9012 (t) cc_final: 0.8774 (m) REVERT: D 375 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8195 (pp) REVERT: D 591 ARG cc_start: 0.8143 (ptm160) cc_final: 0.7679 (mmt-90) REVERT: D 595 ASP cc_start: 0.7357 (m-30) cc_final: 0.6991 (t0) REVERT: D 634 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7664 (m-80) outliers start: 54 outliers final: 37 residues processed: 320 average time/residue: 0.3190 time to fit residues: 156.2853 Evaluate side-chains 300 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 255 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Chi-restraints excluded: chain D residue 721 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 115 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 222 optimal weight: 0.9990 chunk 235 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 247 ASN B 186 ASN B 247 ASN C 186 ASN C 247 ASN D 186 ASN D 247 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20512 Z= 0.160 Angle : 0.495 5.807 27816 Z= 0.242 Chirality : 0.037 0.136 3116 Planarity : 0.004 0.061 3428 Dihedral : 7.791 59.742 2772 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.08 % Allowed : 15.22 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.17), residues: 2412 helix: 0.69 (0.14), residues: 1432 sheet: -2.52 (0.44), residues: 124 loop : -1.82 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 454 HIS 0.004 0.001 HIS B 251 PHE 0.012 0.001 PHE B 540 TYR 0.009 0.001 TYR A 629 ARG 0.003 0.000 ARG B 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 297 time to evaluate : 2.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6283 (mmtm) cc_final: 0.5757 (mtmt) REVERT: A 205 THR cc_start: 0.9003 (t) cc_final: 0.8767 (m) REVERT: A 375 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8234 (pp) REVERT: A 473 GLU cc_start: 0.7768 (mp0) cc_final: 0.7546 (mp0) REVERT: A 591 ARG cc_start: 0.8091 (ptm160) cc_final: 0.7631 (mmm160) REVERT: A 595 ASP cc_start: 0.7347 (m-30) cc_final: 0.6973 (t0) REVERT: A 634 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: B 104 LYS cc_start: 0.6240 (mmtm) cc_final: 0.5750 (mtmt) REVERT: B 205 THR cc_start: 0.9006 (t) cc_final: 0.8767 (m) REVERT: B 255 MET cc_start: 0.7886 (mmt) cc_final: 0.7403 (mmt) REVERT: B 375 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8230 (pp) REVERT: B 473 GLU cc_start: 0.7758 (mp0) cc_final: 0.7511 (mp0) REVERT: B 591 ARG cc_start: 0.8090 (ptm160) cc_final: 0.7634 (mmm160) REVERT: B 595 ASP cc_start: 0.7354 (m-30) cc_final: 0.6975 (t0) REVERT: B 634 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.7549 (m-80) REVERT: B 640 MET cc_start: 0.7887 (tmm) cc_final: 0.7361 (ttp) REVERT: C 104 LYS cc_start: 0.6309 (mmtm) cc_final: 0.5705 (mttt) REVERT: C 205 THR cc_start: 0.8993 (t) cc_final: 0.8751 (m) REVERT: C 255 MET cc_start: 0.7876 (mmt) cc_final: 0.7397 (mmt) REVERT: C 375 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8230 (pp) REVERT: C 473 GLU cc_start: 0.7759 (mp0) cc_final: 0.7519 (mp0) REVERT: C 591 ARG cc_start: 0.8090 (ptm160) cc_final: 0.7633 (mmm160) REVERT: C 595 ASP cc_start: 0.7357 (m-30) cc_final: 0.6973 (t0) REVERT: C 634 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: C 640 MET cc_start: 0.7884 (tmm) cc_final: 0.7374 (ttp) REVERT: D 104 LYS cc_start: 0.6305 (mmtm) cc_final: 0.5706 (mttt) REVERT: D 205 THR cc_start: 0.9003 (t) cc_final: 0.8762 (m) REVERT: D 255 MET cc_start: 0.7879 (mmt) cc_final: 0.7401 (mmt) REVERT: D 375 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8144 (pp) REVERT: D 473 GLU cc_start: 0.7759 (mp0) cc_final: 0.7513 (mp0) REVERT: D 591 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7636 (mmm160) REVERT: D 595 ASP cc_start: 0.7352 (m-30) cc_final: 0.6970 (t0) REVERT: D 634 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7569 (m-80) REVERT: D 640 MET cc_start: 0.7833 (tmm) cc_final: 0.7350 (ttp) outliers start: 45 outliers final: 32 residues processed: 338 average time/residue: 0.3264 time to fit residues: 169.2103 Evaluate side-chains 310 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 270 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 211 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN D 247 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20512 Z= 0.220 Angle : 0.520 6.272 27816 Z= 0.254 Chirality : 0.038 0.121 3116 Planarity : 0.004 0.059 3428 Dihedral : 7.652 59.978 2772 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.58 % Allowed : 16.28 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.25 (0.17), residues: 2412 helix: 0.90 (0.14), residues: 1432 sheet: -2.34 (0.45), residues: 124 loop : -1.62 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 454 HIS 0.004 0.001 HIS A 251 PHE 0.010 0.001 PHE B 540 TYR 0.021 0.001 TYR B 447 ARG 0.004 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 276 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6282 (mmtm) cc_final: 0.5704 (mttt) REVERT: A 111 TYR cc_start: 0.7815 (m-80) cc_final: 0.7273 (m-80) REVERT: A 205 THR cc_start: 0.9017 (t) cc_final: 0.8773 (m) REVERT: A 255 MET cc_start: 0.7858 (mmt) cc_final: 0.7384 (mmt) REVERT: A 375 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8237 (pp) REVERT: A 383 GLN cc_start: 0.7828 (tp-100) cc_final: 0.7149 (tm-30) REVERT: A 591 ARG cc_start: 0.8098 (ptm160) cc_final: 0.7645 (mmm160) REVERT: A 634 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: A 640 MET cc_start: 0.7974 (tmm) cc_final: 0.7484 (ttp) REVERT: B 104 LYS cc_start: 0.6296 (mmtm) cc_final: 0.5718 (mttt) REVERT: B 205 THR cc_start: 0.9010 (t) cc_final: 0.8763 (m) REVERT: B 255 MET cc_start: 0.7880 (mmt) cc_final: 0.7415 (mmt) REVERT: B 375 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8253 (pp) REVERT: B 383 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7144 (tm-30) REVERT: B 473 GLU cc_start: 0.7763 (mp0) cc_final: 0.7529 (mp0) REVERT: B 591 ARG cc_start: 0.8096 (ptm160) cc_final: 0.7647 (mmm160) REVERT: B 634 TYR cc_start: 0.8159 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: B 640 MET cc_start: 0.7892 (tmm) cc_final: 0.7506 (ttp) REVERT: C 104 LYS cc_start: 0.6362 (mmtm) cc_final: 0.5779 (mttt) REVERT: C 205 THR cc_start: 0.9001 (t) cc_final: 0.8756 (m) REVERT: C 255 MET cc_start: 0.7863 (mmt) cc_final: 0.7393 (mmt) REVERT: C 375 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8232 (pp) REVERT: C 383 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7146 (tm-30) REVERT: C 591 ARG cc_start: 0.8101 (ptm160) cc_final: 0.7644 (mmm160) REVERT: C 634 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7583 (m-80) REVERT: C 640 MET cc_start: 0.7897 (tmm) cc_final: 0.7511 (ttp) REVERT: D 104 LYS cc_start: 0.6363 (mmtm) cc_final: 0.5785 (mttt) REVERT: D 205 THR cc_start: 0.9007 (t) cc_final: 0.8758 (m) REVERT: D 255 MET cc_start: 0.7849 (mmt) cc_final: 0.7375 (mmt) REVERT: D 375 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8183 (pp) REVERT: D 383 GLN cc_start: 0.7824 (tp-100) cc_final: 0.7142 (tm-30) REVERT: D 591 ARG cc_start: 0.8100 (ptm160) cc_final: 0.7648 (mmm160) REVERT: D 634 TYR cc_start: 0.8158 (OUTLIER) cc_final: 0.7580 (m-80) REVERT: D 640 MET cc_start: 0.7906 (tmm) cc_final: 0.7545 (ttp) outliers start: 56 outliers final: 43 residues processed: 324 average time/residue: 0.3093 time to fit residues: 155.2017 Evaluate side-chains 319 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 268 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 6.9990 chunk 212 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 236 optimal weight: 0.4980 chunk 195 optimal weight: 0.0470 chunk 109 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 247 ASN B 129 GLN B 247 ASN C 129 GLN C 247 ASN D 129 GLN D 247 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20512 Z= 0.119 Angle : 0.476 7.093 27816 Z= 0.231 Chirality : 0.036 0.116 3116 Planarity : 0.004 0.056 3428 Dihedral : 7.014 57.071 2772 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.17 % Allowed : 17.02 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.15 (0.17), residues: 2412 helix: 1.23 (0.14), residues: 1432 sheet: -2.19 (0.46), residues: 124 loop : -1.48 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 454 HIS 0.003 0.001 HIS B 251 PHE 0.009 0.001 PHE B 547 TYR 0.019 0.001 TYR C 447 ARG 0.002 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 316 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6288 (mmtm) cc_final: 0.5801 (mtmt) REVERT: A 111 TYR cc_start: 0.7852 (m-80) cc_final: 0.7344 (m-80) REVERT: A 135 CYS cc_start: 0.7948 (t) cc_final: 0.7671 (p) REVERT: A 173 GLU cc_start: 0.8160 (tp30) cc_final: 0.7918 (tp30) REVERT: A 205 THR cc_start: 0.8960 (t) cc_final: 0.8721 (m) REVERT: A 255 MET cc_start: 0.7775 (mmt) cc_final: 0.7319 (mmt) REVERT: A 277 MET cc_start: 0.8555 (tpp) cc_final: 0.8072 (mmt) REVERT: A 375 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8169 (pp) REVERT: A 473 GLU cc_start: 0.7725 (mp0) cc_final: 0.7512 (mp0) REVERT: A 496 TRP cc_start: 0.7738 (m100) cc_final: 0.7318 (m100) REVERT: A 591 ARG cc_start: 0.8067 (ptm160) cc_final: 0.7616 (mmm160) REVERT: A 634 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: A 640 MET cc_start: 0.7825 (tmm) cc_final: 0.7432 (ttp) REVERT: B 104 LYS cc_start: 0.6299 (mmtm) cc_final: 0.5851 (mtmt) REVERT: B 135 CYS cc_start: 0.7874 (t) cc_final: 0.7614 (p) REVERT: B 173 GLU cc_start: 0.8163 (tp30) cc_final: 0.7923 (tp30) REVERT: B 205 THR cc_start: 0.8962 (t) cc_final: 0.8717 (m) REVERT: B 255 MET cc_start: 0.7774 (mmt) cc_final: 0.7319 (mmt) REVERT: B 277 MET cc_start: 0.8533 (tpp) cc_final: 0.8044 (mmt) REVERT: B 345 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8150 (mt) REVERT: B 375 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8165 (pp) REVERT: B 591 ARG cc_start: 0.8069 (ptm160) cc_final: 0.7617 (mmm160) REVERT: B 634 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: B 640 MET cc_start: 0.7779 (tmm) cc_final: 0.7482 (ttp) REVERT: C 104 LYS cc_start: 0.6306 (mmtm) cc_final: 0.5871 (mtmt) REVERT: C 111 TYR cc_start: 0.7632 (m-80) cc_final: 0.7093 (m-80) REVERT: C 135 CYS cc_start: 0.7904 (t) cc_final: 0.7512 (p) REVERT: C 173 GLU cc_start: 0.8160 (tp30) cc_final: 0.7927 (tp30) REVERT: C 205 THR cc_start: 0.8956 (t) cc_final: 0.8710 (m) REVERT: C 255 MET cc_start: 0.7760 (mmt) cc_final: 0.7279 (mmt) REVERT: C 277 MET cc_start: 0.8544 (tpp) cc_final: 0.8067 (mmt) REVERT: C 375 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8165 (pp) REVERT: C 473 GLU cc_start: 0.7732 (mp0) cc_final: 0.7509 (mp0) REVERT: C 591 ARG cc_start: 0.8065 (ptm160) cc_final: 0.7616 (mmm160) REVERT: C 634 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7531 (m-80) REVERT: C 640 MET cc_start: 0.7802 (tmm) cc_final: 0.7460 (ttp) REVERT: D 104 LYS cc_start: 0.6297 (mmtm) cc_final: 0.5857 (mtmt) REVERT: D 111 TYR cc_start: 0.7659 (m-80) cc_final: 0.7108 (m-80) REVERT: D 135 CYS cc_start: 0.7872 (t) cc_final: 0.7523 (p) REVERT: D 173 GLU cc_start: 0.8170 (tp30) cc_final: 0.7926 (tp30) REVERT: D 205 THR cc_start: 0.8956 (t) cc_final: 0.8712 (m) REVERT: D 255 MET cc_start: 0.7771 (mmt) cc_final: 0.7314 (mmt) REVERT: D 277 MET cc_start: 0.8550 (tpp) cc_final: 0.8048 (mmt) REVERT: D 375 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8093 (pp) REVERT: D 473 GLU cc_start: 0.7730 (mp0) cc_final: 0.7501 (mp0) REVERT: D 591 ARG cc_start: 0.8065 (ptm160) cc_final: 0.7620 (mmm160) REVERT: D 634 TYR cc_start: 0.8140 (OUTLIER) cc_final: 0.7532 (m-80) REVERT: D 640 MET cc_start: 0.7760 (tmm) cc_final: 0.7465 (ttp) outliers start: 47 outliers final: 25 residues processed: 356 average time/residue: 0.3173 time to fit residues: 172.9248 Evaluate side-chains 324 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 290 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 134 optimal weight: 0.2980 chunk 172 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 198 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN D 247 ASN D 316 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20512 Z= 0.225 Angle : 0.535 7.788 27816 Z= 0.258 Chirality : 0.038 0.154 3116 Planarity : 0.004 0.056 3428 Dihedral : 7.088 58.467 2772 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.44 % Allowed : 17.02 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 2412 helix: 1.22 (0.14), residues: 1432 sheet: -2.33 (0.46), residues: 116 loop : -1.47 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 677 HIS 0.004 0.001 HIS B 251 PHE 0.011 0.001 PHE D 394 TYR 0.017 0.001 TYR C 447 ARG 0.003 0.000 ARG D 617 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 271 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6301 (mmtm) cc_final: 0.5698 (mttt) REVERT: A 111 TYR cc_start: 0.7769 (m-80) cc_final: 0.7250 (m-80) REVERT: A 205 THR cc_start: 0.8978 (t) cc_final: 0.8730 (m) REVERT: A 375 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8163 (pp) REVERT: A 383 GLN cc_start: 0.7822 (tp-100) cc_final: 0.7159 (tm-30) REVERT: A 473 GLU cc_start: 0.7755 (mp0) cc_final: 0.7553 (mp0) REVERT: A 591 ARG cc_start: 0.8100 (ptm160) cc_final: 0.7636 (mmm160) REVERT: A 634 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: A 640 MET cc_start: 0.7997 (tmm) cc_final: 0.7604 (ttp) REVERT: B 104 LYS cc_start: 0.6360 (mmtm) cc_final: 0.5719 (mttt) REVERT: B 205 THR cc_start: 0.8975 (t) cc_final: 0.8726 (m) REVERT: B 345 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8416 (mt) REVERT: B 375 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8163 (pp) REVERT: B 383 GLN cc_start: 0.7825 (tp-100) cc_final: 0.7170 (tm-30) REVERT: B 591 ARG cc_start: 0.8102 (ptm160) cc_final: 0.7649 (mmm160) REVERT: B 634 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7580 (m-80) REVERT: B 645 MET cc_start: 0.7223 (tpp) cc_final: 0.7020 (tpp) REVERT: C 104 LYS cc_start: 0.6365 (mmtm) cc_final: 0.5732 (mttt) REVERT: C 111 TYR cc_start: 0.7652 (m-80) cc_final: 0.7143 (m-80) REVERT: C 255 MET cc_start: 0.7813 (mmt) cc_final: 0.7343 (mmt) REVERT: C 375 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8161 (pp) REVERT: C 383 GLN cc_start: 0.7820 (tp-100) cc_final: 0.7159 (tm-30) REVERT: C 473 GLU cc_start: 0.7766 (mp0) cc_final: 0.7560 (mp0) REVERT: C 591 ARG cc_start: 0.8105 (ptm160) cc_final: 0.7648 (mmm160) REVERT: C 634 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.7575 (m-80) REVERT: D 104 LYS cc_start: 0.6365 (mmtm) cc_final: 0.5739 (mttt) REVERT: D 111 TYR cc_start: 0.7707 (m-80) cc_final: 0.7197 (m-80) REVERT: D 205 THR cc_start: 0.8976 (t) cc_final: 0.8726 (m) REVERT: D 375 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8192 (pp) REVERT: D 383 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7170 (tm-30) REVERT: D 591 ARG cc_start: 0.8106 (ptm160) cc_final: 0.7649 (mmm160) REVERT: D 634 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7571 (m-80) outliers start: 53 outliers final: 39 residues processed: 317 average time/residue: 0.3142 time to fit residues: 154.1003 Evaluate side-chains 313 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 265 time to evaluate : 2.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 149 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 20512 Z= 0.130 Angle : 0.490 7.520 27816 Z= 0.236 Chirality : 0.036 0.193 3116 Planarity : 0.004 0.054 3428 Dihedral : 6.759 56.784 2772 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.31 % Allowed : 17.30 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.42 (0.17), residues: 2412 helix: 1.44 (0.14), residues: 1432 sheet: -2.16 (0.46), residues: 124 loop : -1.33 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 454 HIS 0.003 0.001 HIS A 251 PHE 0.008 0.001 PHE B 540 TYR 0.017 0.001 TYR C 447 ARG 0.002 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 295 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6311 (mmtm) cc_final: 0.5679 (mttt) REVERT: A 111 TYR cc_start: 0.7782 (m-80) cc_final: 0.7284 (m-80) REVERT: A 277 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7986 (mmt) REVERT: A 345 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8253 (mt) REVERT: A 375 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8096 (pp) REVERT: A 383 GLN cc_start: 0.7773 (tp-100) cc_final: 0.7207 (tm-30) REVERT: A 591 ARG cc_start: 0.8072 (ptm160) cc_final: 0.7613 (mmm160) REVERT: A 634 TYR cc_start: 0.8152 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: A 640 MET cc_start: 0.7814 (tmm) cc_final: 0.7488 (ttp) REVERT: B 104 LYS cc_start: 0.6306 (mmtm) cc_final: 0.5672 (mttt) REVERT: B 111 TYR cc_start: 0.7611 (m-80) cc_final: 0.7128 (m-80) REVERT: B 277 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8030 (mmt) REVERT: B 345 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8276 (mt) REVERT: B 375 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8100 (pp) REVERT: B 383 GLN cc_start: 0.7775 (tp-100) cc_final: 0.7208 (tm-30) REVERT: B 473 GLU cc_start: 0.7729 (mp0) cc_final: 0.7529 (mp0) REVERT: B 591 ARG cc_start: 0.8069 (ptm160) cc_final: 0.7615 (mmm160) REVERT: B 634 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7550 (m-80) REVERT: C 104 LYS cc_start: 0.6319 (mmtm) cc_final: 0.5673 (mttt) REVERT: C 111 TYR cc_start: 0.7613 (m-80) cc_final: 0.7120 (m-80) REVERT: C 135 CYS cc_start: 0.7903 (t) cc_final: 0.7489 (p) REVERT: C 205 THR cc_start: 0.8898 (t) cc_final: 0.8595 (m) REVERT: C 277 MET cc_start: 0.8463 (tpp) cc_final: 0.8011 (mmt) REVERT: C 345 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8259 (mt) REVERT: C 375 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8102 (pp) REVERT: C 383 GLN cc_start: 0.7769 (tp-100) cc_final: 0.7204 (tm-30) REVERT: C 591 ARG cc_start: 0.8070 (ptm160) cc_final: 0.7613 (mmm160) REVERT: C 634 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7588 (m-80) REVERT: D 104 LYS cc_start: 0.6321 (mmtm) cc_final: 0.5678 (mttt) REVERT: D 111 TYR cc_start: 0.7618 (m-80) cc_final: 0.7131 (m-80) REVERT: D 135 CYS cc_start: 0.7899 (t) cc_final: 0.7494 (p) REVERT: D 277 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7990 (mmt) REVERT: D 345 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8258 (mt) REVERT: D 375 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8167 (pp) REVERT: D 383 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7211 (tm-30) REVERT: D 473 GLU cc_start: 0.7675 (mp0) cc_final: 0.7457 (mp0) REVERT: D 591 ARG cc_start: 0.8069 (ptm160) cc_final: 0.7613 (mmm160) REVERT: D 634 TYR cc_start: 0.8135 (OUTLIER) cc_final: 0.7583 (m-80) outliers start: 50 outliers final: 32 residues processed: 337 average time/residue: 0.3134 time to fit residues: 162.3953 Evaluate side-chains 335 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 288 time to evaluate : 2.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 0.9980 chunk 225 optimal weight: 0.9990 chunk 205 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 172 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 218 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN B 247 ASN C 247 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20512 Z= 0.158 Angle : 0.507 7.405 27816 Z= 0.245 Chirality : 0.037 0.200 3116 Planarity : 0.004 0.054 3428 Dihedral : 6.721 53.880 2772 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.49 % Allowed : 17.16 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.54 (0.17), residues: 2412 helix: 1.49 (0.14), residues: 1428 sheet: -2.14 (0.46), residues: 124 loop : -1.18 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 677 HIS 0.003 0.001 HIS B 251 PHE 0.009 0.001 PHE B 540 TYR 0.016 0.001 TYR C 447 ARG 0.002 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 292 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6323 (mmtm) cc_final: 0.5702 (mttt) REVERT: A 111 TYR cc_start: 0.7752 (m-80) cc_final: 0.7296 (m-80) REVERT: A 205 THR cc_start: 0.8925 (t) cc_final: 0.8623 (m) REVERT: A 277 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7985 (mmt) REVERT: A 345 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8351 (mt) REVERT: A 375 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8099 (pp) REVERT: A 383 GLN cc_start: 0.7811 (tp-100) cc_final: 0.7255 (tm-30) REVERT: A 591 ARG cc_start: 0.8084 (ptm160) cc_final: 0.7625 (mmm160) REVERT: A 634 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: A 640 MET cc_start: 0.7891 (tmm) cc_final: 0.7564 (ttp) REVERT: B 104 LYS cc_start: 0.6310 (mmtm) cc_final: 0.5684 (mttt) REVERT: B 111 TYR cc_start: 0.7641 (m-80) cc_final: 0.7177 (m-80) REVERT: B 205 THR cc_start: 0.8924 (t) cc_final: 0.8619 (m) REVERT: B 277 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7989 (mmt) REVERT: B 375 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8101 (pp) REVERT: B 383 GLN cc_start: 0.7806 (tp-100) cc_final: 0.7250 (tm-30) REVERT: B 591 ARG cc_start: 0.8083 (ptm160) cc_final: 0.7630 (mmm160) REVERT: B 634 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7597 (m-80) REVERT: C 104 LYS cc_start: 0.6320 (mmtm) cc_final: 0.5691 (mttt) REVERT: C 111 TYR cc_start: 0.7599 (m-80) cc_final: 0.7187 (m-80) REVERT: C 205 THR cc_start: 0.8910 (t) cc_final: 0.8597 (m) REVERT: C 345 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8347 (mt) REVERT: C 375 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8103 (pp) REVERT: C 383 GLN cc_start: 0.7810 (tp-100) cc_final: 0.7253 (tm-30) REVERT: C 591 ARG cc_start: 0.8082 (ptm160) cc_final: 0.7627 (mmm160) REVERT: C 634 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7596 (m-80) REVERT: D 104 LYS cc_start: 0.6332 (mmtm) cc_final: 0.5701 (mttt) REVERT: D 111 TYR cc_start: 0.7606 (m-80) cc_final: 0.7194 (m-80) REVERT: D 205 THR cc_start: 0.8918 (t) cc_final: 0.8615 (m) REVERT: D 277 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8006 (mmt) REVERT: D 345 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8350 (mt) REVERT: D 375 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8188 (pp) REVERT: D 383 GLN cc_start: 0.7814 (tp-100) cc_final: 0.7258 (tm-30) REVERT: D 473 GLU cc_start: 0.7666 (mp0) cc_final: 0.7449 (mp0) REVERT: D 591 ARG cc_start: 0.8084 (ptm160) cc_final: 0.7629 (mmm160) REVERT: D 634 TYR cc_start: 0.8149 (OUTLIER) cc_final: 0.7589 (m-80) outliers start: 54 outliers final: 36 residues processed: 338 average time/residue: 0.3164 time to fit residues: 164.2775 Evaluate side-chains 339 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 289 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 725 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 9.9990 chunk 231 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 118 optimal weight: 0.0170 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20512 Z= 0.145 Angle : 0.495 7.064 27816 Z= 0.239 Chirality : 0.037 0.180 3116 Planarity : 0.004 0.054 3428 Dihedral : 6.468 52.388 2772 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.40 % Allowed : 17.39 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.17), residues: 2412 helix: 1.54 (0.14), residues: 1428 sheet: -2.20 (0.47), residues: 116 loop : -1.19 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 677 HIS 0.003 0.001 HIS C 251 PHE 0.007 0.001 PHE B 540 TYR 0.016 0.001 TYR C 447 ARG 0.002 0.000 ARG D 617 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 293 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6341 (mmtm) cc_final: 0.5708 (mttt) REVERT: A 111 TYR cc_start: 0.7738 (m-80) cc_final: 0.7321 (m-80) REVERT: A 173 GLU cc_start: 0.8085 (tp30) cc_final: 0.7800 (tp30) REVERT: A 205 THR cc_start: 0.8911 (t) cc_final: 0.8601 (m) REVERT: A 277 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7979 (mmt) REVERT: A 345 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8315 (mt) REVERT: A 375 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8101 (pp) REVERT: A 383 GLN cc_start: 0.7798 (tp-100) cc_final: 0.7237 (tm-30) REVERT: A 496 TRP cc_start: 0.7607 (m100) cc_final: 0.7272 (m100) REVERT: A 591 ARG cc_start: 0.8074 (ptm160) cc_final: 0.7622 (mmm160) REVERT: A 634 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.7584 (m-80) REVERT: A 640 MET cc_start: 0.7878 (tmm) cc_final: 0.7549 (ttp) REVERT: B 104 LYS cc_start: 0.6303 (mmtm) cc_final: 0.5668 (mttt) REVERT: B 111 TYR cc_start: 0.7627 (m-80) cc_final: 0.7187 (m-80) REVERT: B 173 GLU cc_start: 0.8092 (tp30) cc_final: 0.7811 (tp30) REVERT: B 205 THR cc_start: 0.8919 (t) cc_final: 0.8606 (m) REVERT: B 277 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8056 (mmt) REVERT: B 375 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8107 (pp) REVERT: B 383 GLN cc_start: 0.7800 (tp-100) cc_final: 0.7233 (tm-30) REVERT: B 473 GLU cc_start: 0.7725 (mp0) cc_final: 0.7518 (mp0) REVERT: B 591 ARG cc_start: 0.8076 (ptm160) cc_final: 0.7626 (mmm160) REVERT: B 634 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7552 (m-80) REVERT: C 104 LYS cc_start: 0.6322 (mmtm) cc_final: 0.5674 (mttt) REVERT: C 111 TYR cc_start: 0.7615 (m-80) cc_final: 0.7189 (m-80) REVERT: C 173 GLU cc_start: 0.8090 (tp30) cc_final: 0.7804 (tp30) REVERT: C 205 THR cc_start: 0.8906 (t) cc_final: 0.8595 (m) REVERT: C 263 ASN cc_start: 0.9000 (t0) cc_final: 0.8715 (t0) REVERT: C 345 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8313 (mt) REVERT: C 375 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8108 (pp) REVERT: C 383 GLN cc_start: 0.7797 (tp-100) cc_final: 0.7232 (tm-30) REVERT: C 591 ARG cc_start: 0.8074 (ptm160) cc_final: 0.7622 (mmm160) REVERT: C 634 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.7589 (m-80) REVERT: D 104 LYS cc_start: 0.6327 (mmtm) cc_final: 0.5672 (mttt) REVERT: D 111 TYR cc_start: 0.7639 (m-80) cc_final: 0.7211 (m-80) REVERT: D 173 GLU cc_start: 0.8077 (tp30) cc_final: 0.7792 (tp30) REVERT: D 205 THR cc_start: 0.8912 (t) cc_final: 0.8599 (m) REVERT: D 277 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8076 (mmt) REVERT: D 345 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8311 (mt) REVERT: D 375 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8204 (pp) REVERT: D 383 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7259 (tm-30) REVERT: D 473 GLU cc_start: 0.7689 (mp0) cc_final: 0.7478 (mp0) REVERT: D 591 ARG cc_start: 0.8077 (ptm160) cc_final: 0.7623 (mmm160) REVERT: D 634 TYR cc_start: 0.8143 (OUTLIER) cc_final: 0.7586 (m-80) outliers start: 52 outliers final: 36 residues processed: 337 average time/residue: 0.3189 time to fit residues: 164.1772 Evaluate side-chains 338 residues out of total 2176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 288 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain A residue 725 ASP Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 148 ASN Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 59 optimal weight: 0.0010 chunk 178 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 0.0670 chunk 193 optimal weight: 0.9980 chunk 81 optimal weight: 0.0170 chunk 199 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 overall best weight: 0.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 247 ASN B 129 GLN B 247 ASN C 129 GLN D 129 GLN D 247 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.117350 restraints weight = 26493.755| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.18 r_work: 0.3205 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 20512 Z= 0.110 Angle : 0.470 6.811 27816 Z= 0.228 Chirality : 0.036 0.179 3116 Planarity : 0.004 0.054 3428 Dihedral : 5.867 50.200 2772 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.49 % Allowed : 17.99 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.81 (0.18), residues: 2412 helix: 1.76 (0.14), residues: 1420 sheet: -1.97 (0.46), residues: 124 loop : -1.15 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 509 HIS 0.002 0.000 HIS D 251 PHE 0.006 0.001 PHE A 407 TYR 0.015 0.001 TYR C 447 ARG 0.002 0.000 ARG B 539 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4501.60 seconds wall clock time: 82 minutes 14.86 seconds (4934.86 seconds total)