Starting phenix.real_space_refine on Fri Feb 23 13:43:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm6_30402/02_2024/7cm6_30402_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm6_30402/02_2024/7cm6_30402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm6_30402/02_2024/7cm6_30402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm6_30402/02_2024/7cm6_30402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm6_30402/02_2024/7cm6_30402_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cm6_30402/02_2024/7cm6_30402_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 184 5.16 5 C 24384 2.51 5 N 6960 2.21 5 O 7136 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 146": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 146": "NH1" <-> "NH2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B ARG 244": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 468": "NH1" <-> "NH2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 543": "NH1" <-> "NH2" Residue "B ARG 615": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 468": "NH1" <-> "NH2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ARG 615": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D ARG 244": "NH1" <-> "NH2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D ARG 468": "NH1" <-> "NH2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D ARG 543": "NH1" <-> "NH2" Residue "D ARG 615": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ARG 244": "NH1" <-> "NH2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E ARG 322": "NH1" <-> "NH2" Residue "E ARG 338": "NH1" <-> "NH2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E ARG 468": "NH1" <-> "NH2" Residue "E ARG 517": "NH1" <-> "NH2" Residue "E ARG 543": "NH1" <-> "NH2" Residue "E ARG 615": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 201": "NH1" <-> "NH2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F ARG 307": "NH1" <-> "NH2" Residue "F ARG 322": "NH1" <-> "NH2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "F ARG 434": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 468": "NH1" <-> "NH2" Residue "F ARG 517": "NH1" <-> "NH2" Residue "F ARG 543": "NH1" <-> "NH2" Residue "F ARG 615": "NH1" <-> "NH2" Residue "G ARG 110": "NH1" <-> "NH2" Residue "G ARG 121": "NH1" <-> "NH2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G ARG 157": "NH1" <-> "NH2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 201": "NH1" <-> "NH2" Residue "G ARG 244": "NH1" <-> "NH2" Residue "G ARG 307": "NH1" <-> "NH2" Residue "G ARG 322": "NH1" <-> "NH2" Residue "G ARG 338": "NH1" <-> "NH2" Residue "G ARG 434": "NH1" <-> "NH2" Residue "G ARG 465": "NH1" <-> "NH2" Residue "G ARG 468": "NH1" <-> "NH2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "G ARG 543": "NH1" <-> "NH2" Residue "G ARG 615": "NH1" <-> "NH2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H ARG 146": "NH1" <-> "NH2" Residue "H ARG 157": "NH1" <-> "NH2" Residue "H ARG 159": "NH1" <-> "NH2" Residue "H ARG 201": "NH1" <-> "NH2" Residue "H ARG 244": "NH1" <-> "NH2" Residue "H ARG 307": "NH1" <-> "NH2" Residue "H ARG 322": "NH1" <-> "NH2" Residue "H ARG 338": "NH1" <-> "NH2" Residue "H ARG 434": "NH1" <-> "NH2" Residue "H ARG 465": "NH1" <-> "NH2" Residue "H ARG 468": "NH1" <-> "NH2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "H ARG 543": "NH1" <-> "NH2" Residue "H ARG 615": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38680 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "B" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "C" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "D" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "E" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "F" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "G" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "H" Number of atoms: 4791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4791 Classifications: {'peptide': 611} Link IDs: {'PTRANS': 21, 'TRANS': 589} Chain breaks: 3 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.94, per 1000 atoms: 0.52 Number of scatterers: 38680 At special positions: 0 Unit cell: (214.165, 214.165, 82.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 16 15.00 O 7136 8.00 N 6960 7.00 C 24384 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: 14.10 Conformation dependent library (CDL) restraints added in 7.3 seconds 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 296 helices and 8 sheets defined 59.7% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.39 Creating SS restraints... Processing helix chain 'A' and resid 63 through 81 Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 87 through 103 Processing helix chain 'A' and resid 109 through 123 Processing helix chain 'A' and resid 125 through 134 removed outlier: 4.077A pdb=" N GLN A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.941A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 168 through 171 No H-bonds generated for 'chain 'A' and resid 168 through 171' Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.211A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 235 Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.721A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 294 through 301 Proline residue: A 298 - end of helix Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 358 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 384 through 396 Processing helix chain 'A' and resid 414 through 424 removed outlier: 3.601A pdb=" N ILE A 424 " --> pdb=" O TRP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 434 Processing helix chain 'A' and resid 440 through 443 No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 460 through 475 Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.937A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 506 removed outlier: 4.406A pdb=" N TYR A 503 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A 506 " --> pdb=" O TYR A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 532 through 544 Processing helix chain 'A' and resid 574 through 585 Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 638 through 649 Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.875A pdb=" N LEU A 676 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR A 677 " --> pdb=" O ALA A 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 673 through 677' Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'B' and resid 63 through 81 Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 87 through 103 Processing helix chain 'B' and resid 109 through 123 Processing helix chain 'B' and resid 125 through 134 removed outlier: 4.077A pdb=" N GLN B 134 " --> pdb=" O LEU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 151 removed outlier: 3.941A pdb=" N GLN B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 168 through 171 No H-bonds generated for 'chain 'B' and resid 168 through 171' Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.212A pdb=" N SER B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 235 Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 265 through 279 removed outlier: 3.723A pdb=" N THR B 279 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 290 Processing helix chain 'B' and resid 294 through 301 Proline residue: B 298 - end of helix Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 358 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 384 through 396 Processing helix chain 'B' and resid 414 through 424 removed outlier: 3.600A pdb=" N ILE B 424 " --> pdb=" O TRP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 440 through 443 No H-bonds generated for 'chain 'B' and resid 440 through 443' Processing helix chain 'B' and resid 448 through 452 Processing helix chain 'B' and resid 460 through 475 Processing helix chain 'B' and resid 487 through 494 removed outlier: 3.937A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 506 removed outlier: 4.406A pdb=" N TYR B 503 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL B 506 " --> pdb=" O TYR B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 517 No H-bonds generated for 'chain 'B' and resid 515 through 517' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 532 through 544 Processing helix chain 'B' and resid 574 through 585 Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 638 through 649 Processing helix chain 'B' and resid 673 through 677 removed outlier: 3.875A pdb=" N LEU B 676 " --> pdb=" O GLN B 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR B 677 " --> pdb=" O ALA B 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 677' Processing helix chain 'B' and resid 688 through 697 Processing helix chain 'C' and resid 63 through 81 Proline residue: C 70 - end of helix Processing helix chain 'C' and resid 87 through 103 Processing helix chain 'C' and resid 109 through 123 Processing helix chain 'C' and resid 125 through 134 removed outlier: 4.077A pdb=" N GLN C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 151 removed outlier: 3.942A pdb=" N GLN C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 162 Processing helix chain 'C' and resid 168 through 171 No H-bonds generated for 'chain 'C' and resid 168 through 171' Processing helix chain 'C' and resid 178 through 193 removed outlier: 4.211A pdb=" N SER C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 204 Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 235 Processing helix chain 'C' and resid 239 through 247 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 265 through 279 removed outlier: 3.722A pdb=" N THR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 290 Processing helix chain 'C' and resid 294 through 301 Proline residue: C 298 - end of helix Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 358 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 384 through 396 Processing helix chain 'C' and resid 414 through 424 removed outlier: 3.600A pdb=" N ILE C 424 " --> pdb=" O TRP C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 440 through 443 No H-bonds generated for 'chain 'C' and resid 440 through 443' Processing helix chain 'C' and resid 448 through 452 Processing helix chain 'C' and resid 460 through 475 Processing helix chain 'C' and resid 487 through 494 removed outlier: 3.938A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 506 removed outlier: 4.407A pdb=" N TYR C 503 " --> pdb=" O GLN C 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL C 506 " --> pdb=" O TYR C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 532 through 544 Processing helix chain 'C' and resid 574 through 585 Processing helix chain 'C' and resid 608 through 613 Processing helix chain 'C' and resid 638 through 649 Processing helix chain 'C' and resid 673 through 677 removed outlier: 3.875A pdb=" N LEU C 676 " --> pdb=" O GLN C 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR C 677 " --> pdb=" O ALA C 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 673 through 677' Processing helix chain 'C' and resid 688 through 697 Processing helix chain 'D' and resid 63 through 81 Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 87 through 103 Processing helix chain 'D' and resid 109 through 123 Processing helix chain 'D' and resid 125 through 134 removed outlier: 4.078A pdb=" N GLN D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.941A pdb=" N GLN D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 162 Processing helix chain 'D' and resid 168 through 171 No H-bonds generated for 'chain 'D' and resid 168 through 171' Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.212A pdb=" N SER D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 235 Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 265 through 279 removed outlier: 3.722A pdb=" N THR D 279 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 294 through 301 Proline residue: D 298 - end of helix Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 358 Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 384 through 396 Processing helix chain 'D' and resid 414 through 424 removed outlier: 3.601A pdb=" N ILE D 424 " --> pdb=" O TRP D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 Processing helix chain 'D' and resid 440 through 443 No H-bonds generated for 'chain 'D' and resid 440 through 443' Processing helix chain 'D' and resid 448 through 452 Processing helix chain 'D' and resid 460 through 475 Processing helix chain 'D' and resid 487 through 494 removed outlier: 3.937A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 506 removed outlier: 4.407A pdb=" N TYR D 503 " --> pdb=" O GLN D 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL D 506 " --> pdb=" O TYR D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 517 No H-bonds generated for 'chain 'D' and resid 515 through 517' Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 532 through 544 Processing helix chain 'D' and resid 574 through 585 Processing helix chain 'D' and resid 608 through 613 Processing helix chain 'D' and resid 638 through 649 Processing helix chain 'D' and resid 673 through 677 removed outlier: 3.876A pdb=" N LEU D 676 " --> pdb=" O GLN D 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR D 677 " --> pdb=" O ALA D 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 673 through 677' Processing helix chain 'D' and resid 688 through 697 Processing helix chain 'E' and resid 63 through 81 Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 87 through 103 Processing helix chain 'E' and resid 109 through 123 Processing helix chain 'E' and resid 125 through 134 removed outlier: 4.077A pdb=" N GLN E 134 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 151 removed outlier: 3.942A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 162 Processing helix chain 'E' and resid 168 through 171 No H-bonds generated for 'chain 'E' and resid 168 through 171' Processing helix chain 'E' and resid 178 through 193 removed outlier: 4.212A pdb=" N SER E 183 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 204 Processing helix chain 'E' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 235 Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 265 through 279 removed outlier: 3.721A pdb=" N THR E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 290 Processing helix chain 'E' and resid 294 through 301 Proline residue: E 298 - end of helix Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 358 Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 384 through 396 Processing helix chain 'E' and resid 414 through 424 removed outlier: 3.600A pdb=" N ILE E 424 " --> pdb=" O TRP E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 Processing helix chain 'E' and resid 440 through 443 No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 448 through 452 Processing helix chain 'E' and resid 460 through 475 Processing helix chain 'E' and resid 487 through 494 removed outlier: 3.938A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 506 removed outlier: 4.406A pdb=" N TYR E 503 " --> pdb=" O GLN E 500 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL E 506 " --> pdb=" O TYR E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 517 No H-bonds generated for 'chain 'E' and resid 515 through 517' Processing helix chain 'E' and resid 520 through 525 Processing helix chain 'E' and resid 532 through 544 Processing helix chain 'E' and resid 574 through 585 Processing helix chain 'E' and resid 608 through 613 Processing helix chain 'E' and resid 638 through 649 Processing helix chain 'E' and resid 673 through 677 removed outlier: 3.876A pdb=" N LEU E 676 " --> pdb=" O GLN E 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR E 677 " --> pdb=" O ALA E 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 673 through 677' Processing helix chain 'E' and resid 688 through 697 Processing helix chain 'F' and resid 63 through 81 Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 125 through 134 removed outlier: 4.078A pdb=" N GLN F 134 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 151 removed outlier: 3.942A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 162 Processing helix chain 'F' and resid 168 through 171 No H-bonds generated for 'chain 'F' and resid 168 through 171' Processing helix chain 'F' and resid 178 through 193 removed outlier: 4.212A pdb=" N SER F 183 " --> pdb=" O GLU F 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 204 Processing helix chain 'F' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 235 Processing helix chain 'F' and resid 239 through 247 Processing helix chain 'F' and resid 255 through 259 Processing helix chain 'F' and resid 265 through 279 removed outlier: 3.722A pdb=" N THR F 279 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 290 Processing helix chain 'F' and resid 294 through 301 Proline residue: F 298 - end of helix Processing helix chain 'F' and resid 305 through 311 Processing helix chain 'F' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG F 329 " --> pdb=" O ASP F 325 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 358 Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 384 through 396 Processing helix chain 'F' and resid 414 through 424 removed outlier: 3.601A pdb=" N ILE F 424 " --> pdb=" O TRP F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 434 Processing helix chain 'F' and resid 440 through 443 No H-bonds generated for 'chain 'F' and resid 440 through 443' Processing helix chain 'F' and resid 448 through 452 Processing helix chain 'F' and resid 460 through 475 Processing helix chain 'F' and resid 487 through 494 removed outlier: 3.938A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 506 removed outlier: 4.406A pdb=" N TYR F 503 " --> pdb=" O GLN F 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL F 506 " --> pdb=" O TYR F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 517 No H-bonds generated for 'chain 'F' and resid 515 through 517' Processing helix chain 'F' and resid 520 through 525 Processing helix chain 'F' and resid 532 through 544 Processing helix chain 'F' and resid 574 through 585 Processing helix chain 'F' and resid 608 through 613 Processing helix chain 'F' and resid 638 through 649 Processing helix chain 'F' and resid 673 through 677 removed outlier: 3.875A pdb=" N LEU F 676 " --> pdb=" O GLN F 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR F 677 " --> pdb=" O ALA F 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 673 through 677' Processing helix chain 'F' and resid 688 through 697 Processing helix chain 'G' and resid 63 through 81 Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 87 through 103 Processing helix chain 'G' and resid 109 through 123 Processing helix chain 'G' and resid 125 through 134 removed outlier: 4.076A pdb=" N GLN G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.943A pdb=" N GLN G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 162 Processing helix chain 'G' and resid 168 through 171 No H-bonds generated for 'chain 'G' and resid 168 through 171' Processing helix chain 'G' and resid 178 through 193 removed outlier: 4.211A pdb=" N SER G 183 " --> pdb=" O GLU G 179 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 204 Processing helix chain 'G' and resid 208 through 216 removed outlier: 4.785A pdb=" N ARG G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 235 Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'G' and resid 255 through 259 Processing helix chain 'G' and resid 265 through 279 removed outlier: 3.721A pdb=" N THR G 279 " --> pdb=" O ALA G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 290 Processing helix chain 'G' and resid 294 through 301 Proline residue: G 298 - end of helix Processing helix chain 'G' and resid 305 through 311 Processing helix chain 'G' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG G 329 " --> pdb=" O ASP G 325 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL G 331 " --> pdb=" O LEU G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 358 Processing helix chain 'G' and resid 364 through 368 Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 384 through 396 Processing helix chain 'G' and resid 414 through 424 removed outlier: 3.601A pdb=" N ILE G 424 " --> pdb=" O TRP G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 434 Processing helix chain 'G' and resid 440 through 443 No H-bonds generated for 'chain 'G' and resid 440 through 443' Processing helix chain 'G' and resid 448 through 452 Processing helix chain 'G' and resid 460 through 475 Processing helix chain 'G' and resid 487 through 494 removed outlier: 3.938A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 499 through 506 removed outlier: 4.406A pdb=" N TYR G 503 " --> pdb=" O GLN G 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL G 506 " --> pdb=" O TYR G 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 515 through 517 No H-bonds generated for 'chain 'G' and resid 515 through 517' Processing helix chain 'G' and resid 520 through 525 Processing helix chain 'G' and resid 532 through 544 Processing helix chain 'G' and resid 574 through 585 Processing helix chain 'G' and resid 608 through 613 Processing helix chain 'G' and resid 638 through 649 Processing helix chain 'G' and resid 673 through 677 removed outlier: 3.875A pdb=" N LEU G 676 " --> pdb=" O GLN G 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR G 677 " --> pdb=" O ALA G 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 673 through 677' Processing helix chain 'G' and resid 688 through 697 Processing helix chain 'H' and resid 63 through 81 Proline residue: H 70 - end of helix Processing helix chain 'H' and resid 87 through 103 Processing helix chain 'H' and resid 109 through 123 Processing helix chain 'H' and resid 125 through 134 removed outlier: 4.078A pdb=" N GLN H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 151 removed outlier: 3.942A pdb=" N GLN H 150 " --> pdb=" O ARG H 146 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE H 151 " --> pdb=" O LEU H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 162 Processing helix chain 'H' and resid 168 through 171 No H-bonds generated for 'chain 'H' and resid 168 through 171' Processing helix chain 'H' and resid 178 through 193 removed outlier: 4.211A pdb=" N SER H 183 " --> pdb=" O GLU H 179 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS H 193 " --> pdb=" O GLU H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 204 Processing helix chain 'H' and resid 208 through 216 removed outlier: 4.784A pdb=" N ARG H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 235 Processing helix chain 'H' and resid 239 through 247 Processing helix chain 'H' and resid 255 through 259 Processing helix chain 'H' and resid 265 through 279 removed outlier: 3.722A pdb=" N THR H 279 " --> pdb=" O ALA H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 290 Processing helix chain 'H' and resid 294 through 301 Proline residue: H 298 - end of helix Processing helix chain 'H' and resid 305 through 311 Processing helix chain 'H' and resid 324 through 331 removed outlier: 4.092A pdb=" N ARG H 329 " --> pdb=" O ASP H 325 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL H 331 " --> pdb=" O LEU H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 358 Processing helix chain 'H' and resid 364 through 368 Processing helix chain 'H' and resid 370 through 379 Processing helix chain 'H' and resid 384 through 396 Processing helix chain 'H' and resid 414 through 424 removed outlier: 3.600A pdb=" N ILE H 424 " --> pdb=" O TRP H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 434 Processing helix chain 'H' and resid 440 through 443 No H-bonds generated for 'chain 'H' and resid 440 through 443' Processing helix chain 'H' and resid 448 through 452 Processing helix chain 'H' and resid 460 through 475 Processing helix chain 'H' and resid 487 through 494 removed outlier: 3.938A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 499 through 506 removed outlier: 4.407A pdb=" N TYR H 503 " --> pdb=" O GLN H 500 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL H 506 " --> pdb=" O TYR H 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 517 No H-bonds generated for 'chain 'H' and resid 515 through 517' Processing helix chain 'H' and resid 520 through 525 Processing helix chain 'H' and resid 532 through 544 Processing helix chain 'H' and resid 574 through 585 Processing helix chain 'H' and resid 608 through 613 Processing helix chain 'H' and resid 638 through 649 Processing helix chain 'H' and resid 673 through 677 removed outlier: 3.875A pdb=" N LEU H 676 " --> pdb=" O GLN H 673 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR H 677 " --> pdb=" O ALA H 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 673 through 677' Processing helix chain 'H' and resid 688 through 697 Processing sheet with id= A, first strand: chain 'A' and resid 564 through 567 removed outlier: 6.496A pdb=" N ASN A 616 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N SER A 567 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 618 " --> pdb=" O SER A 567 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 564 through 567 removed outlier: 6.496A pdb=" N ASN B 616 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N SER B 567 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL B 618 " --> pdb=" O SER B 567 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 564 through 567 removed outlier: 6.496A pdb=" N ASN C 616 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER C 567 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL C 618 " --> pdb=" O SER C 567 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 564 through 567 removed outlier: 6.495A pdb=" N ASN D 616 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N SER D 567 " --> pdb=" O ASN D 616 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 618 " --> pdb=" O SER D 567 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 564 through 567 removed outlier: 6.495A pdb=" N ASN E 616 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER E 567 " --> pdb=" O ASN E 616 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL E 618 " --> pdb=" O SER E 567 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 564 through 567 removed outlier: 6.496A pdb=" N ASN F 616 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER F 567 " --> pdb=" O ASN F 616 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL F 618 " --> pdb=" O SER F 567 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 564 through 567 removed outlier: 6.495A pdb=" N ASN G 616 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER G 567 " --> pdb=" O ASN G 616 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL G 618 " --> pdb=" O SER G 567 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 564 through 567 removed outlier: 6.495A pdb=" N ASN H 616 " --> pdb=" O PHE H 565 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER H 567 " --> pdb=" O ASN H 616 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL H 618 " --> pdb=" O SER H 567 " (cutoff:3.500A) 1608 hydrogen bonds defined for protein. 4752 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: 12.93 Time building geometry restraints manager: 15.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8549 1.33 - 1.45: 7943 1.45 - 1.57: 22572 1.57 - 1.69: 24 1.69 - 1.81: 248 Bond restraints: 39336 Sorted by residual: bond pdb=" C2D NAD A1000 " pdb=" O2D NAD A1000 " ideal model delta sigma weight residual 1.393 1.478 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C2D NAD D1000 " pdb=" O2D NAD D1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C2D NAD B1000 " pdb=" O2D NAD B1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C2D NAD H1000 " pdb=" O2D NAD H1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C2D NAD G1000 " pdb=" O2D NAD G1000 " ideal model delta sigma weight residual 1.393 1.477 -0.084 2.00e-02 2.50e+03 1.78e+01 ... (remaining 39331 not shown) Histogram of bond angle deviations from ideal: 99.14 - 106.18: 857 106.18 - 113.22: 21301 113.22 - 120.25: 16008 120.25 - 127.29: 14644 127.29 - 134.32: 414 Bond angle restraints: 53224 Sorted by residual: angle pdb=" C SER F 336 " pdb=" N ASN F 337 " pdb=" CA ASN F 337 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" N VAL H 108 " pdb=" CA VAL H 108 " pdb=" C VAL H 108 " ideal model delta sigma weight residual 112.12 108.41 3.71 8.40e-01 1.42e+00 1.95e+01 angle pdb=" C SER B 336 " pdb=" N ASN B 337 " pdb=" CA ASN B 337 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 angle pdb=" N VAL B 108 " pdb=" CA VAL B 108 " pdb=" C VAL B 108 " ideal model delta sigma weight residual 112.12 108.42 3.70 8.40e-01 1.42e+00 1.94e+01 angle pdb=" C SER D 336 " pdb=" N ASN D 337 " pdb=" CA ASN D 337 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 ... (remaining 53219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.00: 23256 15.00 - 30.00: 704 30.00 - 45.01: 160 45.01 - 60.01: 48 60.01 - 75.01: 16 Dihedral angle restraints: 24184 sinusoidal: 10136 harmonic: 14048 Sorted by residual: dihedral pdb=" CA TRP B 412 " pdb=" C TRP B 412 " pdb=" N LYS B 413 " pdb=" CA LYS B 413 " ideal model delta harmonic sigma weight residual 180.00 164.22 15.78 0 5.00e+00 4.00e-02 9.96e+00 dihedral pdb=" CA TRP H 412 " pdb=" C TRP H 412 " pdb=" N LYS H 413 " pdb=" CA LYS H 413 " ideal model delta harmonic sigma weight residual 180.00 164.24 15.76 0 5.00e+00 4.00e-02 9.94e+00 dihedral pdb=" CA TRP G 412 " pdb=" C TRP G 412 " pdb=" N LYS G 413 " pdb=" CA LYS G 413 " ideal model delta harmonic sigma weight residual 180.00 164.24 15.76 0 5.00e+00 4.00e-02 9.93e+00 ... (remaining 24181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5433 0.069 - 0.138: 592 0.138 - 0.207: 36 0.207 - 0.276: 19 0.276 - 0.345: 8 Chirality restraints: 6088 Sorted by residual: chirality pdb=" C2D NAD D1000 " pdb=" C1D NAD D1000 " pdb=" C3D NAD D1000 " pdb=" O2D NAD D1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.91 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C2D NAD F1000 " pdb=" C1D NAD F1000 " pdb=" C3D NAD F1000 " pdb=" O2D NAD F1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.90 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C2D NAD H1000 " pdb=" C1D NAD H1000 " pdb=" C3D NAD H1000 " pdb=" O2D NAD H1000 " both_signs ideal model delta sigma weight residual False -2.56 -2.90 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 6085 not shown) Planarity restraints: 6848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 283 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" C VAL G 283 " -0.039 2.00e-02 2.50e+03 pdb=" O VAL G 283 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU G 284 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 283 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C VAL F 283 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL F 283 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU F 284 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 283 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C VAL B 283 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL B 283 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU B 284 " 0.013 2.00e-02 2.50e+03 ... (remaining 6845 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 10059 2.80 - 3.33: 33540 3.33 - 3.85: 61659 3.85 - 4.38: 73030 4.38 - 4.90: 124944 Nonbonded interactions: 303232 Sorted by model distance: nonbonded pdb=" OE1 GLN D 436 " pdb=" OG SER E 459 " model vdw 2.281 2.440 nonbonded pdb=" OE1 GLN A 436 " pdb=" OG SER B 459 " model vdw 2.320 2.440 nonbonded pdb=" OH TYR B 568 " pdb=" OD1 ASP B 594 " model vdw 2.359 2.440 nonbonded pdb=" OH TYR F 568 " pdb=" OD1 ASP F 594 " model vdw 2.359 2.440 nonbonded pdb=" OH TYR A 568 " pdb=" OD1 ASP A 594 " model vdw 2.359 2.440 ... (remaining 303227 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' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.960 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: 0.030 Extract box with map and model: 15.590 Check model and map are aligned: 0.600 Set scattering table: 0.390 Process input model: 98.540 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 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 : 0.004 0.085 39336 Z= 0.262 Angle : 0.822 13.125 53224 Z= 0.435 Chirality : 0.047 0.345 6088 Planarity : 0.006 0.053 6848 Dihedral : 8.990 75.011 15064 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.09), residues: 4824 helix: -2.88 (0.06), residues: 3184 sheet: -1.48 (0.42), residues: 136 loop : -2.00 (0.14), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 490 HIS 0.010 0.002 HIS G 269 PHE 0.036 0.002 PHE D 192 TYR 0.010 0.001 TYR E 568 ARG 0.008 0.001 ARG A 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1045 time to evaluate : 4.869 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.6678 (tt) cc_final: 0.6456 (mp) REVERT: A 307 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6814 (ttp80) REVERT: A 638 TRP cc_start: 0.4921 (m100) cc_final: 0.4622 (m100) REVERT: A 672 MET cc_start: 0.3714 (ptm) cc_final: 0.3416 (ppp) REVERT: B 118 ASP cc_start: 0.6643 (m-30) cc_final: 0.6424 (m-30) REVERT: B 191 MET cc_start: 0.8527 (mmm) cc_final: 0.8215 (mmp) REVERT: B 638 TRP cc_start: 0.5266 (m100) cc_final: 0.4932 (m100) REVERT: C 307 ARG cc_start: 0.7078 (ttp-110) cc_final: 0.6667 (ttp80) REVERT: C 638 TRP cc_start: 0.4918 (m100) cc_final: 0.4501 (m100) REVERT: D 191 MET cc_start: 0.8640 (mmm) cc_final: 0.8428 (mmp) REVERT: D 638 TRP cc_start: 0.5379 (m100) cc_final: 0.5050 (m100) REVERT: E 191 MET cc_start: 0.8423 (mmm) cc_final: 0.8173 (mmp) REVERT: E 672 MET cc_start: 0.3662 (ptm) cc_final: 0.3401 (ppp) REVERT: F 638 TRP cc_start: 0.5395 (m100) cc_final: 0.5093 (m100) REVERT: G 638 TRP cc_start: 0.4926 (m100) cc_final: 0.4503 (m100) REVERT: G 672 MET cc_start: 0.3436 (ptm) cc_final: 0.3132 (ptm) REVERT: H 118 ASP cc_start: 0.6612 (m-30) cc_final: 0.6310 (m-30) REVERT: H 191 MET cc_start: 0.8516 (mmm) cc_final: 0.8210 (mmp) REVERT: H 638 TRP cc_start: 0.5274 (m100) cc_final: 0.4820 (m100) outliers start: 0 outliers final: 8 residues processed: 1045 average time/residue: 1.8384 time to fit residues: 2243.0728 Evaluate side-chains 410 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 402 time to evaluate : 4.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain D residue 406 LEU Chi-restraints excluded: chain F residue 406 LEU Chi-restraints excluded: chain G residue 472 GLU Chi-restraints excluded: chain H residue 406 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 412 optimal weight: 2.9990 chunk 369 optimal weight: 0.8980 chunk 205 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 249 optimal weight: 9.9990 chunk 197 optimal weight: 0.6980 chunk 382 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 chunk 443 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 134 GLN A 236 HIS A 239 GLN A 280 ASN A 575 GLN A 652 ASN B 170 ASN B 236 HIS B 280 ASN B 585 GLN B 652 ASN C 236 HIS C 652 ASN D 134 GLN D 236 HIS D 585 GLN D 652 ASN E 236 HIS E 652 ASN F 134 GLN F 236 HIS F 585 GLN F 616 ASN F 652 ASN G 134 GLN G 236 HIS G 280 ASN G 575 GLN G 616 ASN G 652 ASN G 700 GLN H 236 HIS H 280 ASN H 585 GLN H 652 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39336 Z= 0.224 Angle : 0.542 8.235 53224 Z= 0.275 Chirality : 0.038 0.131 6088 Planarity : 0.004 0.038 6848 Dihedral : 7.154 168.845 5771 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.94 % Allowed : 11.18 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.11), residues: 4824 helix: -1.03 (0.08), residues: 3320 sheet: -1.14 (0.44), residues: 136 loop : -1.32 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 412 HIS 0.005 0.001 HIS E 236 PHE 0.027 0.003 PHE D 433 TYR 0.017 0.002 TYR G 687 ARG 0.007 0.001 ARG H 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 454 time to evaluate : 4.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6812 (tp) REVERT: A 114 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6865 (tp40) REVERT: A 147 LEU cc_start: 0.8517 (tm) cc_final: 0.8145 (tp) REVERT: A 326 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: A 472 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: A 570 ARG cc_start: 0.5953 (OUTLIER) cc_final: 0.5423 (mmt90) REVERT: B 545 MET cc_start: 0.5626 (OUTLIER) cc_final: 0.5083 (ppp) REVERT: B 638 TRP cc_start: 0.5611 (m100) cc_final: 0.5204 (m100) REVERT: C 114 GLN cc_start: 0.7189 (OUTLIER) cc_final: 0.6738 (tt0) REVERT: C 126 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7574 (mt) REVERT: C 472 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: C 638 TRP cc_start: 0.5009 (m100) cc_final: 0.4784 (m100) REVERT: D 363 LYS cc_start: 0.7538 (OUTLIER) cc_final: 0.7333 (tppp) REVERT: D 545 MET cc_start: 0.5586 (OUTLIER) cc_final: 0.5099 (ppp) REVERT: D 638 TRP cc_start: 0.5550 (m100) cc_final: 0.5121 (m100) REVERT: E 376 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7291 (mtm-85) REVERT: E 472 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: E 638 TRP cc_start: 0.5099 (m100) cc_final: 0.4883 (m100) REVERT: E 672 MET cc_start: 0.3764 (ptm) cc_final: 0.3463 (ppp) REVERT: F 114 GLN cc_start: 0.7193 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: F 638 TRP cc_start: 0.5610 (m100) cc_final: 0.5248 (m100) REVERT: G 114 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6477 (tp40) REVERT: G 126 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7492 (mt) REVERT: G 472 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7242 (tm-30) REVERT: H 170 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7694 (t0) REVERT: H 638 TRP cc_start: 0.5539 (m100) cc_final: 0.5119 (m100) outliers start: 120 outliers final: 41 residues processed: 548 average time/residue: 1.6804 time to fit residues: 1089.2068 Evaluate side-chains 349 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 290 time to evaluate : 4.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 363 LYS Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 376 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 472 GLU Chi-restraints excluded: chain H residue 170 ASN Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 468 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 246 optimal weight: 8.9990 chunk 137 optimal weight: 0.8980 chunk 368 optimal weight: 9.9990 chunk 301 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 443 optimal weight: 0.9980 chunk 479 optimal weight: 9.9990 chunk 395 optimal weight: 5.9990 chunk 440 optimal weight: 7.9990 chunk 151 optimal weight: 0.2980 chunk 356 optimal weight: 10.0000 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 97 GLN B 280 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 150 GLN C 280 ASN C 575 GLN C 609 GLN D 62 GLN ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN F 62 GLN G 280 ASN G 609 GLN H 62 GLN H 97 GLN H 575 GLN H 609 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39336 Z= 0.258 Angle : 0.545 8.166 53224 Z= 0.272 Chirality : 0.039 0.142 6088 Planarity : 0.004 0.039 6848 Dihedral : 7.038 171.948 5761 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.73 % Allowed : 12.30 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.12), residues: 4824 helix: -0.22 (0.09), residues: 3304 sheet: -1.39 (0.43), residues: 144 loop : -0.87 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 214 HIS 0.006 0.001 HIS A 194 PHE 0.028 0.002 PHE G 259 TYR 0.015 0.002 TYR H 380 ARG 0.006 0.000 ARG G 249 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 343 time to evaluate : 4.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 ASP cc_start: 0.7546 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: A 472 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: A 570 ARG cc_start: 0.6159 (OUTLIER) cc_final: 0.5267 (mmt90) REVERT: A 609 GLN cc_start: 0.5566 (mp10) cc_final: 0.5248 (tp-100) REVERT: A 612 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6672 (mmt) REVERT: B 434 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7902 (ttt-90) REVERT: B 545 MET cc_start: 0.5829 (OUTLIER) cc_final: 0.5379 (ppp) REVERT: B 638 TRP cc_start: 0.5441 (m100) cc_final: 0.5119 (m100) REVERT: C 114 GLN cc_start: 0.7310 (OUTLIER) cc_final: 0.6773 (tt0) REVERT: C 149 GLU cc_start: 0.7258 (tm-30) cc_final: 0.6838 (tm-30) REVERT: C 150 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7407 (mp-120) REVERT: C 162 ARG cc_start: 0.7285 (OUTLIER) cc_final: 0.6830 (mpt90) REVERT: C 472 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: C 628 LYS cc_start: 0.4713 (mttt) cc_final: 0.4211 (mmtp) REVERT: C 630 MET cc_start: 0.4218 (OUTLIER) cc_final: 0.3194 (mtt) REVERT: D 434 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7893 (ttt-90) REVERT: D 545 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.5425 (ppp) REVERT: D 612 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6919 (mmt) REVERT: D 638 TRP cc_start: 0.5473 (m100) cc_final: 0.5029 (m100) REVERT: E 149 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6998 (tm-30) REVERT: E 472 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: E 569 ARG cc_start: 0.6263 (tpp-160) cc_final: 0.6046 (tpm170) REVERT: E 570 ARG cc_start: 0.6308 (OUTLIER) cc_final: 0.5278 (mmt90) REVERT: E 638 TRP cc_start: 0.4932 (m100) cc_final: 0.4720 (m100) REVERT: E 672 MET cc_start: 0.3513 (ptm) cc_final: 0.3215 (ppp) REVERT: E 699 LEU cc_start: 0.6421 (mt) cc_final: 0.6152 (tp) REVERT: F 434 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7877 (ttt-90) REVERT: F 545 MET cc_start: 0.5812 (OUTLIER) cc_final: 0.5273 (ppp) REVERT: F 575 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6456 (pt0) REVERT: F 638 TRP cc_start: 0.5670 (m100) cc_final: 0.5401 (m100) REVERT: F 699 LEU cc_start: 0.7044 (tp) cc_final: 0.6762 (mt) REVERT: G 149 GLU cc_start: 0.7276 (tm-30) cc_final: 0.7018 (tm-30) REVERT: G 162 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6832 (mpt90) REVERT: G 259 PHE cc_start: 0.8126 (t80) cc_final: 0.7916 (t80) REVERT: G 472 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7220 (tm-30) REVERT: G 569 ARG cc_start: 0.6525 (tpp-160) cc_final: 0.6307 (tpm170) REVERT: G 656 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7727 (mm) REVERT: H 434 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7842 (ttt-90) REVERT: H 545 MET cc_start: 0.5894 (OUTLIER) cc_final: 0.5472 (ppp) REVERT: H 638 TRP cc_start: 0.5475 (m100) cc_final: 0.5108 (m100) outliers start: 152 outliers final: 61 residues processed: 454 average time/residue: 1.6509 time to fit residues: 895.1470 Evaluate side-chains 368 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 283 time to evaluate : 4.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 150 GLN Chi-restraints excluded: chain C residue 162 ARG Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 570 ARG Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 545 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 472 GLU Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain G residue 656 ILE Chi-restraints excluded: chain G residue 672 MET Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 545 MET Chi-restraints excluded: chain H residue 672 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 438 optimal weight: 10.0000 chunk 333 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 chunk 445 optimal weight: 1.9990 chunk 471 optimal weight: 0.8980 chunk 232 optimal weight: 10.0000 chunk 422 optimal weight: 0.0010 chunk 127 optimal weight: 7.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN A 616 ASN A 700 GLN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN D 575 GLN D 700 GLN E 383 ASN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 700 GLN F 134 GLN G 62 GLN G 700 GLN H 700 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 39336 Z= 0.294 Angle : 0.561 7.668 53224 Z= 0.280 Chirality : 0.040 0.212 6088 Planarity : 0.004 0.040 6848 Dihedral : 7.026 172.764 5761 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.80 % Allowed : 12.82 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.12), residues: 4824 helix: 0.13 (0.09), residues: 3296 sheet: -1.38 (0.43), residues: 144 loop : -0.72 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 638 HIS 0.006 0.001 HIS C 194 PHE 0.028 0.002 PHE H 259 TYR 0.017 0.002 TYR F 380 ARG 0.007 0.000 ARG B 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 292 time to evaluate : 4.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8510 (tm) cc_final: 0.8204 (tp) REVERT: A 326 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7318 (m-30) REVERT: A 472 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: A 570 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5139 (mmt90) REVERT: A 609 GLN cc_start: 0.5691 (mp10) cc_final: 0.5231 (tp-100) REVERT: A 612 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6624 (mmt) REVERT: A 656 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7715 (mm) REVERT: B 322 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7324 (ptp-170) REVERT: B 545 MET cc_start: 0.5825 (OUTLIER) cc_final: 0.5440 (ppp) REVERT: B 638 TRP cc_start: 0.5572 (m100) cc_final: 0.5220 (m100) REVERT: B 699 LEU cc_start: 0.7051 (mt) cc_final: 0.6820 (tp) REVERT: C 147 LEU cc_start: 0.8475 (tm) cc_final: 0.8124 (tp) REVERT: C 149 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6911 (tm-30) REVERT: C 472 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: C 609 GLN cc_start: 0.6177 (mp10) cc_final: 0.5461 (tp-100) REVERT: C 612 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6960 (mmt) REVERT: C 628 LYS cc_start: 0.4590 (mttt) cc_final: 0.4107 (mmtp) REVERT: C 630 MET cc_start: 0.4156 (OUTLIER) cc_final: 0.3023 (mtt) REVERT: D 139 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6086 (pm20) REVERT: D 170 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7913 (t160) REVERT: D 545 MET cc_start: 0.5671 (OUTLIER) cc_final: 0.5291 (ppp) REVERT: D 612 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6866 (mmt) REVERT: D 638 TRP cc_start: 0.5560 (m100) cc_final: 0.5220 (m100) REVERT: E 147 LEU cc_start: 0.8516 (tm) cc_final: 0.8158 (tp) REVERT: E 376 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7450 (mtm-85) REVERT: E 472 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: E 569 ARG cc_start: 0.6376 (tpp-160) cc_final: 0.6124 (tpm170) REVERT: E 612 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6668 (mmt) REVERT: E 672 MET cc_start: 0.3489 (ptm) cc_final: 0.3219 (ppp) REVERT: F 545 MET cc_start: 0.5836 (OUTLIER) cc_final: 0.5405 (ppp) REVERT: F 575 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6443 (pt0) REVERT: F 638 TRP cc_start: 0.5680 (m100) cc_final: 0.5408 (m100) REVERT: F 699 LEU cc_start: 0.7119 (tp) cc_final: 0.6848 (mt) REVERT: G 149 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6986 (tm-30) REVERT: G 472 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: G 609 GLN cc_start: 0.6217 (mp10) cc_final: 0.5425 (tp-100) REVERT: G 656 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7787 (mm) REVERT: H 545 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5550 (ppp) REVERT: H 638 TRP cc_start: 0.5609 (m100) cc_final: 0.5088 (m100) REVERT: H 699 LEU cc_start: 0.7286 (tp) cc_final: 0.7080 (mt) outliers start: 155 outliers final: 68 residues processed: 408 average time/residue: 1.5744 time to fit residues: 773.9247 Evaluate side-chains 355 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 265 time to evaluate : 4.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 612 MET Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 672 MET Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 612 MET Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 612 MET Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 376 ARG Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 612 MET Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 545 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 472 GLU Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain G residue 656 ILE Chi-restraints excluded: chain H residue 263 ASP Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 545 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 392 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 351 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 402 optimal weight: 3.9990 chunk 326 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 240 optimal weight: 20.0000 chunk 423 optimal weight: 0.2980 chunk 119 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN B 575 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN C 328 GLN D 700 GLN E 62 GLN E 328 GLN E 609 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 700 GLN G 328 GLN G 616 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 700 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 39336 Z= 0.234 Angle : 0.520 11.318 53224 Z= 0.257 Chirality : 0.039 0.175 6088 Planarity : 0.004 0.079 6848 Dihedral : 6.893 173.279 5761 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.48 % Allowed : 13.58 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.12), residues: 4824 helix: 0.44 (0.09), residues: 3256 sheet: -1.22 (0.44), residues: 144 loop : -0.35 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 253 HIS 0.004 0.001 HIS A 194 PHE 0.016 0.001 PHE H 476 TYR 0.017 0.002 TYR A 687 ARG 0.008 0.000 ARG H 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 288 time to evaluate : 4.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: A 472 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: A 570 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5106 (mmt90) REVERT: A 609 GLN cc_start: 0.5632 (mp10) cc_final: 0.5244 (tp-100) REVERT: B 162 ARG cc_start: 0.7092 (mmt90) cc_final: 0.6877 (mmm-85) REVERT: B 322 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7314 (ptp-170) REVERT: B 434 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7918 (ttt-90) REVERT: B 545 MET cc_start: 0.5765 (OUTLIER) cc_final: 0.5373 (ppp) REVERT: B 638 TRP cc_start: 0.5433 (m100) cc_final: 0.5102 (m100) REVERT: B 699 LEU cc_start: 0.7048 (mt) cc_final: 0.6824 (tp) REVERT: C 149 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6885 (tm-30) REVERT: C 472 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: C 609 GLN cc_start: 0.6018 (mp10) cc_final: 0.5431 (tp-100) REVERT: C 612 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6815 (mmt) REVERT: C 628 LYS cc_start: 0.4493 (mttt) cc_final: 0.4222 (mmtp) REVERT: C 630 MET cc_start: 0.4205 (OUTLIER) cc_final: 0.3044 (mtt) REVERT: C 699 LEU cc_start: 0.6370 (mt) cc_final: 0.6102 (tp) REVERT: D 139 GLU cc_start: 0.6355 (OUTLIER) cc_final: 0.6130 (pm20) REVERT: D 170 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7891 (t160) REVERT: D 545 MET cc_start: 0.5772 (OUTLIER) cc_final: 0.5414 (ppp) REVERT: D 638 TRP cc_start: 0.5547 (m100) cc_final: 0.5189 (m100) REVERT: E 147 LEU cc_start: 0.8514 (tm) cc_final: 0.8178 (tp) REVERT: E 472 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: E 569 ARG cc_start: 0.6357 (tpp-160) cc_final: 0.6120 (tpm170) REVERT: E 672 MET cc_start: 0.3439 (ptm) cc_final: 0.3208 (ppp) REVERT: E 699 LEU cc_start: 0.6536 (mt) cc_final: 0.6182 (tp) REVERT: F 434 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7905 (ttt-90) REVERT: F 545 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.5401 (ppp) REVERT: F 575 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6407 (pt0) REVERT: F 638 TRP cc_start: 0.5857 (m100) cc_final: 0.5607 (m100) REVERT: F 699 LEU cc_start: 0.7230 (tp) cc_final: 0.6891 (mt) REVERT: G 149 GLU cc_start: 0.7214 (tm-30) cc_final: 0.6959 (tm-30) REVERT: G 162 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6847 (mpt90) REVERT: G 472 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: G 569 ARG cc_start: 0.6604 (tpp-160) cc_final: 0.6344 (tpm170) REVERT: G 609 GLN cc_start: 0.6080 (mp10) cc_final: 0.5393 (tp-100) REVERT: G 656 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7775 (mm) REVERT: H 434 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7884 (ttt-90) REVERT: H 545 MET cc_start: 0.5825 (OUTLIER) cc_final: 0.5476 (ppp) REVERT: H 568 TYR cc_start: 0.7729 (p90) cc_final: 0.7528 (p90) REVERT: H 638 TRP cc_start: 0.5690 (m100) cc_final: 0.5346 (m100) REVERT: H 699 LEU cc_start: 0.7422 (tp) cc_final: 0.7063 (mt) outliers start: 142 outliers final: 75 residues processed: 395 average time/residue: 1.5556 time to fit residues: 739.5495 Evaluate side-chains 359 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 263 time to evaluate : 4.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 570 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 545 MET Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 612 MET Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 545 MET Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 468 ARG Chi-restraints excluded: chain F residue 545 MET Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 472 GLU Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain G residue 656 ILE Chi-restraints excluded: chain G residue 672 MET Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Chi-restraints excluded: chain H residue 468 ARG Chi-restraints excluded: chain H residue 545 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 158 optimal weight: 0.4980 chunk 424 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 276 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 472 optimal weight: 1.9990 chunk 391 optimal weight: 8.9990 chunk 218 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 GLN C 328 GLN E 328 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 GLN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 39336 Z= 0.150 Angle : 0.472 11.693 53224 Z= 0.233 Chirality : 0.037 0.150 6088 Planarity : 0.003 0.056 6848 Dihedral : 6.649 176.668 5761 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.82 % Allowed : 14.93 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.12), residues: 4824 helix: 0.77 (0.09), residues: 3272 sheet: -1.04 (0.45), residues: 144 loop : -0.14 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 253 HIS 0.002 0.001 HIS D 269 PHE 0.015 0.001 PHE E 476 TYR 0.017 0.001 TYR E 213 ARG 0.007 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 313 time to evaluate : 4.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8459 (tm) cc_final: 0.8090 (tp) REVERT: A 609 GLN cc_start: 0.5587 (mp10) cc_final: 0.5229 (tp-100) REVERT: A 699 LEU cc_start: 0.6286 (mt) cc_final: 0.6020 (tp) REVERT: B 322 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7337 (ptp-170) REVERT: B 568 TYR cc_start: 0.7561 (p90) cc_final: 0.7319 (p90) REVERT: B 638 TRP cc_start: 0.5464 (m100) cc_final: 0.5172 (m100) REVERT: C 147 LEU cc_start: 0.8369 (tm) cc_final: 0.8071 (tp) REVERT: C 609 GLN cc_start: 0.6063 (mp10) cc_final: 0.5488 (tp-100) REVERT: C 630 MET cc_start: 0.4181 (OUTLIER) cc_final: 0.3046 (mtt) REVERT: C 694 LYS cc_start: 0.7240 (ttmm) cc_final: 0.6803 (mttp) REVERT: C 699 LEU cc_start: 0.6416 (mt) cc_final: 0.6160 (tp) REVERT: D 139 GLU cc_start: 0.6322 (OUTLIER) cc_final: 0.6108 (pm20) REVERT: D 170 ASN cc_start: 0.8229 (OUTLIER) cc_final: 0.7860 (t160) REVERT: D 434 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7898 (ttt-90) REVERT: D 568 TYR cc_start: 0.7610 (p90) cc_final: 0.7366 (p90) REVERT: D 638 TRP cc_start: 0.5581 (m100) cc_final: 0.5205 (m100) REVERT: E 147 LEU cc_start: 0.8511 (tm) cc_final: 0.8183 (tp) REVERT: E 472 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: E 699 LEU cc_start: 0.6561 (mt) cc_final: 0.6229 (tp) REVERT: F 322 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7293 (ptp-170) REVERT: F 575 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.6262 (pt0) REVERT: F 638 TRP cc_start: 0.6004 (m100) cc_final: 0.5731 (m100) REVERT: F 700 GLN cc_start: 0.5839 (mt0) cc_final: 0.5637 (mt0) REVERT: G 114 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6848 (tt0) REVERT: G 162 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6891 (mpt90) REVERT: G 569 ARG cc_start: 0.6567 (tpp-160) cc_final: 0.6327 (tpm170) REVERT: G 609 GLN cc_start: 0.6109 (mp10) cc_final: 0.5445 (tp-100) REVERT: G 656 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7778 (mm) REVERT: G 699 LEU cc_start: 0.6434 (mt) cc_final: 0.6040 (tp) REVERT: H 322 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7733 (ptp-170) REVERT: H 638 TRP cc_start: 0.5680 (m100) cc_final: 0.5343 (m100) REVERT: H 657 ILE cc_start: 0.7141 (mp) cc_final: 0.6768 (tp) REVERT: H 699 LEU cc_start: 0.7428 (tp) cc_final: 0.7093 (mt) REVERT: H 700 GLN cc_start: 0.5790 (mt0) cc_final: 0.5449 (mm-40) outliers start: 115 outliers final: 63 residues processed: 400 average time/residue: 1.5213 time to fit residues: 735.6496 Evaluate side-chains 330 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 255 time to evaluate : 4.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 114 GLN Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain G residue 656 ILE Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 325 ASP Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 630 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 269 optimal weight: 8.9990 chunk 344 optimal weight: 1.9990 chunk 267 optimal weight: 0.4980 chunk 397 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 470 optimal weight: 2.9990 chunk 294 optimal weight: 9.9990 chunk 286 optimal weight: 1.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 616 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39336 Z= 0.199 Angle : 0.504 11.563 53224 Z= 0.249 Chirality : 0.038 0.152 6088 Planarity : 0.003 0.059 6848 Dihedral : 5.146 46.483 5752 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.97 % Allowed : 15.71 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.12), residues: 4824 helix: 0.79 (0.09), residues: 3344 sheet: -0.93 (0.46), residues: 144 loop : -0.13 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 253 HIS 0.003 0.001 HIS D 269 PHE 0.014 0.001 PHE H 476 TYR 0.013 0.001 TYR E 213 ARG 0.007 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 270 time to evaluate : 5.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8486 (tm) cc_final: 0.8149 (tp) REVERT: A 545 MET cc_start: 0.5229 (OUTLIER) cc_final: 0.5025 (pmm) REVERT: A 699 LEU cc_start: 0.6385 (mt) cc_final: 0.6141 (tp) REVERT: B 101 GLU cc_start: 0.6621 (mt-10) cc_final: 0.6175 (mp0) REVERT: B 568 TYR cc_start: 0.7598 (p90) cc_final: 0.7396 (p90) REVERT: B 638 TRP cc_start: 0.5550 (m100) cc_final: 0.5264 (m100) REVERT: C 147 LEU cc_start: 0.8405 (tm) cc_final: 0.8110 (tp) REVERT: C 609 GLN cc_start: 0.6043 (mp10) cc_final: 0.5504 (tp-100) REVERT: C 612 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6805 (mmt) REVERT: C 630 MET cc_start: 0.4133 (OUTLIER) cc_final: 0.2988 (mtt) REVERT: C 694 LYS cc_start: 0.7288 (ttmm) cc_final: 0.6817 (mttp) REVERT: C 699 LEU cc_start: 0.6467 (mt) cc_final: 0.6092 (tp) REVERT: D 139 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.6108 (pm20) REVERT: D 170 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7872 (t160) REVERT: D 434 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7891 (ttt-90) REVERT: D 638 TRP cc_start: 0.5658 (m100) cc_final: 0.5323 (m100) REVERT: D 699 LEU cc_start: 0.7660 (tp) cc_final: 0.7220 (mt) REVERT: D 700 GLN cc_start: 0.5613 (mt0) cc_final: 0.5242 (mm-40) REVERT: E 472 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7269 (tm-30) REVERT: E 699 LEU cc_start: 0.6549 (mt) cc_final: 0.6237 (tp) REVERT: F 146 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7536 (ttp-170) REVERT: F 434 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7894 (ttt-90) REVERT: F 575 GLN cc_start: 0.6778 (OUTLIER) cc_final: 0.6284 (pt0) REVERT: F 612 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6949 (mmt) REVERT: F 638 TRP cc_start: 0.6077 (m100) cc_final: 0.5829 (m100) REVERT: G 147 LEU cc_start: 0.8399 (tm) cc_final: 0.8055 (tp) REVERT: G 545 MET cc_start: 0.5171 (OUTLIER) cc_final: 0.4428 (pmm) REVERT: G 569 ARG cc_start: 0.6597 (tpp-160) cc_final: 0.6340 (tpm170) REVERT: G 609 GLN cc_start: 0.6103 (mp10) cc_final: 0.5408 (tp-100) REVERT: G 612 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6845 (mmt) REVERT: G 656 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7789 (mm) REVERT: G 699 LEU cc_start: 0.6430 (mt) cc_final: 0.6054 (tp) REVERT: H 322 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7663 (ptp-170) REVERT: H 638 TRP cc_start: 0.5709 (m100) cc_final: 0.5219 (m100) REVERT: H 699 LEU cc_start: 0.7494 (tp) cc_final: 0.7115 (mt) REVERT: H 700 GLN cc_start: 0.5697 (mt0) cc_final: 0.5426 (mm-40) outliers start: 121 outliers final: 74 residues processed: 354 average time/residue: 1.4190 time to fit residues: 615.0005 Evaluate side-chains 348 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 259 time to evaluate : 4.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 612 MET Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 322 ARG Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain D residue 630 MET Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 146 ARG Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 612 MET Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 545 MET Chi-restraints excluded: chain G residue 612 MET Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain G residue 656 ILE Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 290 optimal weight: 0.8980 chunk 187 optimal weight: 0.0370 chunk 280 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 chunk 232 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 369 optimal weight: 0.9980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN F 700 GLN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 700 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.5074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 39336 Z= 0.149 Angle : 0.485 12.558 53224 Z= 0.238 Chirality : 0.037 0.177 6088 Planarity : 0.003 0.038 6848 Dihedral : 4.924 45.567 5752 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.50 % Allowed : 16.25 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.13), residues: 4824 helix: 0.97 (0.09), residues: 3352 sheet: -1.01 (0.45), residues: 152 loop : 0.05 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 253 HIS 0.002 0.001 HIS D 269 PHE 0.014 0.001 PHE C 476 TYR 0.012 0.001 TYR E 213 ARG 0.009 0.000 ARG H 162 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 281 time to evaluate : 4.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8463 (tm) cc_final: 0.8127 (tp) REVERT: A 609 GLN cc_start: 0.5954 (mp10) cc_final: 0.5369 (tp-100) REVERT: A 699 LEU cc_start: 0.6418 (mt) cc_final: 0.6080 (tp) REVERT: B 101 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6473 (mt-10) REVERT: B 162 ARG cc_start: 0.7141 (mmm-85) cc_final: 0.6861 (mmm160) REVERT: B 322 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7539 (ptp-170) REVERT: B 638 TRP cc_start: 0.5477 (m100) cc_final: 0.5195 (m100) REVERT: B 700 GLN cc_start: 0.5585 (mt0) cc_final: 0.5271 (mm-40) REVERT: C 114 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6938 (tt0) REVERT: C 147 LEU cc_start: 0.8373 (tm) cc_final: 0.8080 (tp) REVERT: C 609 GLN cc_start: 0.6023 (mp10) cc_final: 0.5502 (tp-100) REVERT: C 630 MET cc_start: 0.4098 (OUTLIER) cc_final: 0.3002 (mtt) REVERT: C 694 LYS cc_start: 0.7217 (ttmm) cc_final: 0.6802 (mttp) REVERT: C 699 LEU cc_start: 0.6529 (mt) cc_final: 0.6203 (tp) REVERT: D 170 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7836 (t160) REVERT: D 434 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7867 (ttt-90) REVERT: D 638 TRP cc_start: 0.5594 (m100) cc_final: 0.5259 (m100) REVERT: D 699 LEU cc_start: 0.7759 (tp) cc_final: 0.7255 (mt) REVERT: D 700 GLN cc_start: 0.5615 (mt0) cc_final: 0.5249 (mm-40) REVERT: E 147 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7955 (tp) REVERT: E 472 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: E 545 MET cc_start: 0.5394 (OUTLIER) cc_final: 0.4956 (pmm) REVERT: E 699 LEU cc_start: 0.6495 (mt) cc_final: 0.6225 (tp) REVERT: F 322 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7585 (ptp-170) REVERT: F 575 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6240 (pt0) REVERT: F 612 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6903 (mmt) REVERT: F 630 MET cc_start: 0.4596 (OUTLIER) cc_final: 0.4359 (ttt) REVERT: F 638 TRP cc_start: 0.6146 (m100) cc_final: 0.5870 (m100) REVERT: G 147 LEU cc_start: 0.8362 (tm) cc_final: 0.8011 (tp) REVERT: G 569 ARG cc_start: 0.6614 (tpp-160) cc_final: 0.6360 (tpm170) REVERT: G 609 GLN cc_start: 0.6076 (mp10) cc_final: 0.5433 (tp-100) REVERT: G 656 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7776 (mm) REVERT: G 699 LEU cc_start: 0.6408 (mt) cc_final: 0.6066 (tp) REVERT: H 638 TRP cc_start: 0.5629 (m100) cc_final: 0.5140 (m100) outliers start: 102 outliers final: 64 residues processed: 354 average time/residue: 1.5093 time to fit residues: 654.1060 Evaluate side-chains 334 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 257 time to evaluate : 4.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 325 ASP Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 325 ASP Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain E residue 545 MET Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 612 MET Chi-restraints excluded: chain F residue 630 MET Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain G residue 656 ILE Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 427 optimal weight: 10.0000 chunk 450 optimal weight: 2.9990 chunk 411 optimal weight: 0.9980 chunk 438 optimal weight: 0.9980 chunk 263 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 chunk 344 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 396 optimal weight: 1.9990 chunk 414 optimal weight: 3.9990 chunk 436 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 ASN G 97 GLN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39336 Z= 0.213 Angle : 0.520 12.093 53224 Z= 0.256 Chirality : 0.038 0.166 6088 Planarity : 0.003 0.038 6848 Dihedral : 5.096 46.979 5752 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.75 % Allowed : 16.27 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.13), residues: 4824 helix: 0.94 (0.09), residues: 3344 sheet: -0.93 (0.45), residues: 152 loop : 0.18 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 253 HIS 0.004 0.001 HIS D 269 PHE 0.013 0.001 PHE H 308 TYR 0.012 0.001 TYR B 380 ARG 0.009 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 270 time to evaluate : 4.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8484 (tm) cc_final: 0.8154 (tp) REVERT: A 545 MET cc_start: 0.5152 (OUTLIER) cc_final: 0.4562 (pmm) REVERT: A 609 GLN cc_start: 0.5973 (mp10) cc_final: 0.5359 (tp-100) REVERT: A 699 LEU cc_start: 0.6396 (mt) cc_final: 0.6055 (tp) REVERT: B 162 ARG cc_start: 0.7135 (mmm-85) cc_final: 0.6851 (mmm160) REVERT: B 434 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7895 (ttt-90) REVERT: B 638 TRP cc_start: 0.5552 (m100) cc_final: 0.5259 (m100) REVERT: B 700 GLN cc_start: 0.5652 (mt0) cc_final: 0.5320 (mm-40) REVERT: C 114 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6915 (tt0) REVERT: C 147 LEU cc_start: 0.8407 (tm) cc_final: 0.8109 (tp) REVERT: C 472 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: C 609 GLN cc_start: 0.5977 (mp10) cc_final: 0.5396 (tp-100) REVERT: C 612 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6807 (mmt) REVERT: C 630 MET cc_start: 0.4085 (OUTLIER) cc_final: 0.2979 (mtt) REVERT: C 694 LYS cc_start: 0.7282 (ttmm) cc_final: 0.6811 (mttp) REVERT: C 699 LEU cc_start: 0.6424 (mt) cc_final: 0.6097 (tp) REVERT: D 170 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7869 (t160) REVERT: D 434 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7883 (ttt-90) REVERT: D 638 TRP cc_start: 0.5607 (m100) cc_final: 0.5283 (m100) REVERT: D 699 LEU cc_start: 0.7777 (tp) cc_final: 0.7250 (mt) REVERT: D 700 GLN cc_start: 0.5702 (mt0) cc_final: 0.5349 (mm-40) REVERT: E 147 LEU cc_start: 0.8370 (tm) cc_final: 0.8017 (tp) REVERT: E 472 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: E 699 LEU cc_start: 0.6573 (mt) cc_final: 0.6318 (tp) REVERT: F 575 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.6285 (pt0) REVERT: F 612 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6947 (mmt) REVERT: F 638 TRP cc_start: 0.6240 (m100) cc_final: 0.6024 (m100) REVERT: G 147 LEU cc_start: 0.8434 (tm) cc_final: 0.8086 (tp) REVERT: G 545 MET cc_start: 0.5290 (OUTLIER) cc_final: 0.4673 (pmm) REVERT: G 569 ARG cc_start: 0.6642 (tpp-160) cc_final: 0.6338 (tpm170) REVERT: G 609 GLN cc_start: 0.6114 (mp10) cc_final: 0.5442 (tp-100) REVERT: G 612 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6840 (mmt) REVERT: G 656 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7811 (mm) REVERT: G 699 LEU cc_start: 0.6403 (mt) cc_final: 0.6043 (tp) REVERT: H 322 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7558 (ptp-170) REVERT: H 434 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7859 (ttt-90) REVERT: H 638 TRP cc_start: 0.5679 (m100) cc_final: 0.5318 (m100) outliers start: 112 outliers final: 69 residues processed: 349 average time/residue: 1.4689 time to fit residues: 625.8492 Evaluate side-chains 347 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 262 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 434 ARG Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 612 MET Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain E residue 143 GLN Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 612 MET Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain F residue 656 ILE Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 545 MET Chi-restraints excluded: chain G residue 612 MET Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain G residue 656 ILE Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 322 ARG Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Chi-restraints excluded: chain H residue 434 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 287 optimal weight: 1.9990 chunk 463 optimal weight: 0.0050 chunk 282 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 322 optimal weight: 4.9990 chunk 486 optimal weight: 0.4980 chunk 447 optimal weight: 1.9990 chunk 387 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 143 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 700 GLN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39336 Z= 0.168 Angle : 0.501 12.933 53224 Z= 0.246 Chirality : 0.037 0.162 6088 Planarity : 0.003 0.041 6848 Dihedral : 4.950 46.300 5752 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.28 % Allowed : 16.84 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.13), residues: 4824 helix: 1.01 (0.09), residues: 3392 sheet: -0.78 (0.45), residues: 152 loop : 0.18 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 103 HIS 0.003 0.001 HIS D 269 PHE 0.013 0.001 PHE E 476 TYR 0.011 0.001 TYR E 213 ARG 0.008 0.000 ARG C 615 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 266 time to evaluate : 4.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.8480 (tm) cc_final: 0.8153 (tp) REVERT: A 699 LEU cc_start: 0.6530 (mt) cc_final: 0.6226 (tp) REVERT: B 162 ARG cc_start: 0.7152 (mmm-85) cc_final: 0.6884 (mmm160) REVERT: B 322 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7665 (ptp-170) REVERT: B 638 TRP cc_start: 0.5521 (m100) cc_final: 0.5245 (m100) REVERT: B 700 GLN cc_start: 0.5713 (mt0) cc_final: 0.5381 (mm-40) REVERT: C 114 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6887 (tt0) REVERT: C 147 LEU cc_start: 0.8403 (tm) cc_final: 0.8116 (tp) REVERT: C 545 MET cc_start: 0.5321 (OUTLIER) cc_final: 0.5118 (pmm) REVERT: C 609 GLN cc_start: 0.6012 (mp10) cc_final: 0.5406 (tp-100) REVERT: C 612 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6762 (mmt) REVERT: C 630 MET cc_start: 0.4048 (OUTLIER) cc_final: 0.2964 (mtt) REVERT: C 694 LYS cc_start: 0.7228 (ttmm) cc_final: 0.6802 (mttp) REVERT: C 699 LEU cc_start: 0.6573 (mt) cc_final: 0.6273 (tp) REVERT: D 170 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7840 (t160) REVERT: D 434 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7871 (ttt-90) REVERT: D 638 TRP cc_start: 0.5605 (m100) cc_final: 0.5268 (m100) REVERT: D 699 LEU cc_start: 0.7736 (tp) cc_final: 0.7270 (mt) REVERT: D 700 GLN cc_start: 0.5680 (mt0) cc_final: 0.5292 (mm-40) REVERT: E 147 LEU cc_start: 0.8333 (tm) cc_final: 0.7998 (tp) REVERT: E 472 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: E 699 LEU cc_start: 0.6523 (mt) cc_final: 0.6277 (tp) REVERT: F 322 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7750 (ptp-170) REVERT: F 434 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7865 (ttt-90) REVERT: F 575 GLN cc_start: 0.6657 (OUTLIER) cc_final: 0.6125 (pt0) REVERT: F 612 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6899 (mmt) REVERT: F 638 TRP cc_start: 0.6226 (m100) cc_final: 0.6017 (m100) REVERT: G 147 LEU cc_start: 0.8400 (tm) cc_final: 0.8050 (tp) REVERT: G 545 MET cc_start: 0.5154 (OUTLIER) cc_final: 0.4610 (pmm) REVERT: G 569 ARG cc_start: 0.6666 (tpp-160) cc_final: 0.6345 (tpm170) REVERT: G 609 GLN cc_start: 0.6087 (mp10) cc_final: 0.5452 (tp-100) REVERT: G 656 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7800 (mm) REVERT: G 699 LEU cc_start: 0.6450 (mt) cc_final: 0.6134 (tp) REVERT: H 638 TRP cc_start: 0.5665 (m100) cc_final: 0.5182 (m100) outliers start: 93 outliers final: 63 residues processed: 332 average time/residue: 1.4429 time to fit residues: 585.8162 Evaluate side-chains 339 residues out of total 4080 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 262 time to evaluate : 4.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 468 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 362 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 362 THR Chi-restraints excluded: chain C residue 468 ARG Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 612 MET Chi-restraints excluded: chain C residue 630 MET Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 ASN Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 362 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 434 ARG Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 362 THR Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 468 ARG Chi-restraints excluded: chain E residue 472 GLU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 163 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 362 THR Chi-restraints excluded: chain F residue 408 SER Chi-restraints excluded: chain F residue 434 ARG Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 612 MET Chi-restraints excluded: chain F residue 648 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 325 ASP Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain G residue 408 SER Chi-restraints excluded: chain G residue 468 ARG Chi-restraints excluded: chain G residue 545 MET Chi-restraints excluded: chain G residue 648 SER Chi-restraints excluded: chain G residue 656 ILE Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain H residue 283 VAL Chi-restraints excluded: chain H residue 362 THR Chi-restraints excluded: chain H residue 408 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 307 optimal weight: 0.9980 chunk 412 optimal weight: 2.9990 chunk 118 optimal weight: 8.9990 chunk 356 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 387 optimal weight: 0.6980 chunk 162 optimal weight: 0.1980 chunk 398 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 328 GLN A 616 ASN ** B 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** E 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 ASN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 700 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.154030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121739 restraints weight = 53741.139| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.53 r_work: 0.3004 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 39336 Z= 0.150 Angle : 0.487 12.635 53224 Z= 0.240 Chirality : 0.037 0.159 6088 Planarity : 0.003 0.037 6848 Dihedral : 4.797 45.674 5752 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.23 % Allowed : 16.94 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.13), residues: 4824 helix: 1.24 (0.09), residues: 3328 sheet: -0.69 (0.45), residues: 152 loop : 0.36 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 103 HIS 0.002 0.001 HIS D 269 PHE 0.014 0.001 PHE C 476 TYR 0.011 0.001 TYR E 213 ARG 0.009 0.000 ARG H 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13290.90 seconds wall clock time: 236 minutes 41.18 seconds (14201.18 seconds total)