Starting phenix.real_space_refine on Fri Feb 23 12:55:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjt_4567/02_2024/6qjt_4567.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjt_4567/02_2024/6qjt_4567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjt_4567/02_2024/6qjt_4567.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjt_4567/02_2024/6qjt_4567.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjt_4567/02_2024/6qjt_4567.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjt_4567/02_2024/6qjt_4567.pdb" } resolution = 3.74 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= 0.003 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 24792 2.51 5 N 6468 2.21 5 O 7080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ARG 238": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 434": "NH1" <-> "NH2" Residue "C ARG 120": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 434": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D ARG 238": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 434": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 238": "NH1" <-> "NH2" Residue "E ARG 253": "NH1" <-> "NH2" Residue "E ARG 274": "NH1" <-> "NH2" Residue "E ARG 434": "NH1" <-> "NH2" Residue "F ARG 120": "NH1" <-> "NH2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 434": "NH1" <-> "NH2" Residue "G ARG 120": "NH1" <-> "NH2" Residue "G ARG 238": "NH1" <-> "NH2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G ARG 274": "NH1" <-> "NH2" Residue "G ARG 434": "NH1" <-> "NH2" Residue "H ARG 120": "NH1" <-> "NH2" Residue "H ARG 238": "NH1" <-> "NH2" Residue "H ARG 253": "NH1" <-> "NH2" Residue "H ARG 274": "NH1" <-> "NH2" Residue "H ARG 434": "NH1" <-> "NH2" Residue "I ARG 120": "NH1" <-> "NH2" Residue "I ARG 238": "NH1" <-> "NH2" Residue "I ARG 253": "NH1" <-> "NH2" Residue "I ARG 274": "NH1" <-> "NH2" Residue "I ARG 434": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J ARG 238": "NH1" <-> "NH2" Residue "J ARG 253": "NH1" <-> "NH2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "J ARG 434": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "K ARG 238": "NH1" <-> "NH2" Residue "K ARG 253": "NH1" <-> "NH2" Residue "K ARG 274": "NH1" <-> "NH2" Residue "K ARG 434": "NH1" <-> "NH2" Residue "L ARG 120": "NH1" <-> "NH2" Residue "L ARG 238": "NH1" <-> "NH2" Residue "L ARG 253": "NH1" <-> "NH2" Residue "L ARG 274": "NH1" <-> "NH2" Residue "L ARG 434": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 38460 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "B" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "C" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "D" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "E" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "F" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "G" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "H" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "I" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "J" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "K" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Chain: "L" Number of atoms: 3205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3205 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 22, 'TRANS': 388} Time building chain proxies: 19.99, per 1000 atoms: 0.52 Number of scatterers: 38460 At special positions: 0 Unit cell: (158.153, 158.153, 132.593, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 7080 8.00 N 6468 7.00 C 24792 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: 15.29 Conformation dependent library (CDL) restraints added in 7.0 seconds 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9120 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 60 sheets defined 45.7% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 80 Processing helix chain 'A' and resid 92 through 107 Processing helix chain 'A' and resid 117 through 132 Processing helix chain 'A' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 272 Processing helix chain 'A' and resid 297 through 312 Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 423 Processing helix chain 'A' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 Processing helix chain 'B' and resid 92 through 107 Processing helix chain 'B' and resid 117 through 132 Processing helix chain 'B' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG B 238 " --> pdb=" O HIS B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 272 Processing helix chain 'B' and resid 297 through 312 Processing helix chain 'B' and resid 335 through 356 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU C 57 " --> pdb=" O LYS C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 80 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 117 through 132 Processing helix chain 'C' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 238 " --> pdb=" O HIS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 272 Processing helix chain 'C' and resid 297 through 312 Processing helix chain 'C' and resid 335 through 356 Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU C 407 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 423 Processing helix chain 'C' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 80 Processing helix chain 'D' and resid 92 through 107 Processing helix chain 'D' and resid 117 through 132 Processing helix chain 'D' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU D 237 " --> pdb=" O ASN D 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG D 238 " --> pdb=" O HIS D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 272 Processing helix chain 'D' and resid 297 through 312 Processing helix chain 'D' and resid 335 through 356 Processing helix chain 'D' and resid 357 through 362 Processing helix chain 'D' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU D 407 " --> pdb=" O ASP D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 423 Processing helix chain 'D' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 80 Processing helix chain 'E' and resid 92 through 107 Processing helix chain 'E' and resid 117 through 132 Processing helix chain 'E' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU E 237 " --> pdb=" O ASN E 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG E 238 " --> pdb=" O HIS E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 272 Processing helix chain 'E' and resid 297 through 312 Processing helix chain 'E' and resid 335 through 356 Processing helix chain 'E' and resid 357 through 362 Processing helix chain 'E' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU E 407 " --> pdb=" O ASP E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 423 Processing helix chain 'E' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU E 431 " --> pdb=" O ASP E 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU F 57 " --> pdb=" O LYS F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 80 Processing helix chain 'F' and resid 92 through 107 Processing helix chain 'F' and resid 117 through 132 Processing helix chain 'F' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU F 237 " --> pdb=" O ASN F 233 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG F 238 " --> pdb=" O HIS F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 272 Processing helix chain 'F' and resid 297 through 312 Processing helix chain 'F' and resid 335 through 356 Processing helix chain 'F' and resid 357 through 362 Processing helix chain 'F' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 423 Processing helix chain 'F' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU F 431 " --> pdb=" O ASP F 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU G 57 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 80 Processing helix chain 'G' and resid 92 through 107 Processing helix chain 'G' and resid 117 through 132 Processing helix chain 'G' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU G 237 " --> pdb=" O ASN G 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG G 238 " --> pdb=" O HIS G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 272 Processing helix chain 'G' and resid 297 through 312 Processing helix chain 'G' and resid 335 through 356 Processing helix chain 'G' and resid 357 through 362 Processing helix chain 'G' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA G 387 " --> pdb=" O ASP G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU G 407 " --> pdb=" O ASP G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 423 Processing helix chain 'G' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU G 431 " --> pdb=" O ASP G 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 80 Processing helix chain 'H' and resid 92 through 107 Processing helix chain 'H' and resid 117 through 132 Processing helix chain 'H' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU H 237 " --> pdb=" O ASN H 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG H 238 " --> pdb=" O HIS H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 272 Processing helix chain 'H' and resid 297 through 312 Processing helix chain 'H' and resid 335 through 356 Processing helix chain 'H' and resid 357 through 362 Processing helix chain 'H' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA H 387 " --> pdb=" O ASP H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU H 407 " --> pdb=" O ASP H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 423 Processing helix chain 'H' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU H 431 " --> pdb=" O ASP H 427 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU I 57 " --> pdb=" O LYS I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 80 Processing helix chain 'I' and resid 92 through 107 Processing helix chain 'I' and resid 117 through 132 Processing helix chain 'I' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU I 237 " --> pdb=" O ASN I 233 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG I 238 " --> pdb=" O HIS I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 256 through 272 Processing helix chain 'I' and resid 297 through 312 Processing helix chain 'I' and resid 335 through 356 Processing helix chain 'I' and resid 357 through 362 Processing helix chain 'I' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA I 387 " --> pdb=" O ASP I 383 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU I 407 " --> pdb=" O ASP I 403 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 423 Processing helix chain 'I' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU I 431 " --> pdb=" O ASP I 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU J 57 " --> pdb=" O LYS J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 80 Processing helix chain 'J' and resid 92 through 107 Processing helix chain 'J' and resid 117 through 132 Processing helix chain 'J' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU J 237 " --> pdb=" O ASN J 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG J 238 " --> pdb=" O HIS J 234 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 272 Processing helix chain 'J' and resid 297 through 312 Processing helix chain 'J' and resid 335 through 356 Processing helix chain 'J' and resid 357 through 362 Processing helix chain 'J' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA J 387 " --> pdb=" O ASP J 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU J 407 " --> pdb=" O ASP J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 423 Processing helix chain 'J' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU J 431 " --> pdb=" O ASP J 427 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU K 57 " --> pdb=" O LYS K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 80 Processing helix chain 'K' and resid 92 through 107 Processing helix chain 'K' and resid 117 through 132 Processing helix chain 'K' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU K 237 " --> pdb=" O ASN K 233 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG K 238 " --> pdb=" O HIS K 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 272 Processing helix chain 'K' and resid 297 through 312 Processing helix chain 'K' and resid 335 through 356 Processing helix chain 'K' and resid 357 through 362 Processing helix chain 'K' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA K 387 " --> pdb=" O ASP K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU K 407 " --> pdb=" O ASP K 403 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 423 Processing helix chain 'K' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU K 431 " --> pdb=" O ASP K 427 " (cutoff:3.500A) Processing helix chain 'L' and resid 53 through 62 removed outlier: 3.521A pdb=" N LEU L 57 " --> pdb=" O LYS L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 80 Processing helix chain 'L' and resid 92 through 107 Processing helix chain 'L' and resid 117 through 132 Processing helix chain 'L' and resid 218 through 240 removed outlier: 4.001A pdb=" N GLU L 237 " --> pdb=" O ASN L 233 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG L 238 " --> pdb=" O HIS L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 256 through 272 Processing helix chain 'L' and resid 297 through 312 Processing helix chain 'L' and resid 335 through 356 Processing helix chain 'L' and resid 357 through 362 Processing helix chain 'L' and resid 383 through 399 removed outlier: 3.635A pdb=" N ALA L 387 " --> pdb=" O ASP L 383 " (cutoff:3.500A) Processing helix chain 'L' and resid 403 through 414 removed outlier: 4.044A pdb=" N GLU L 407 " --> pdb=" O ASP L 403 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 423 Processing helix chain 'L' and resid 427 through 435 removed outlier: 3.896A pdb=" N GLU L 431 " --> pdb=" O ASP L 427 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 84 through 87 Processing sheet with id= 2, first strand: chain 'A' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA A 135 " --> pdb=" O ILE A 156 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 139 through 142 removed outlier: 7.022A pdb=" N VAL A 139 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU A 163 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 174 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR A 247 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 284 " --> pdb=" O THR A 247 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 84 through 87 Processing sheet with id= 7, first strand: chain 'B' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA B 135 " --> pdb=" O ILE B 156 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL B 139 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU B 163 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 174 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR B 247 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 284 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 84 through 87 Processing sheet with id= 12, first strand: chain 'C' and resid 155 through 156 removed outlier: 3.690A pdb=" N ALA C 135 " --> pdb=" O ILE C 156 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL C 139 " --> pdb=" O ASP C 151 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU C 163 " --> pdb=" O LYS C 176 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 174 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR C 247 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS C 284 " --> pdb=" O THR C 247 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 84 through 87 Processing sheet with id= 17, first strand: chain 'D' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA D 135 " --> pdb=" O ILE D 156 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 139 through 142 removed outlier: 7.022A pdb=" N VAL D 139 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'D' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU D 163 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA D 174 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'D' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR D 247 " --> pdb=" O LYS D 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 284 " --> pdb=" O THR D 247 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'E' and resid 84 through 87 Processing sheet with id= 22, first strand: chain 'E' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA E 135 " --> pdb=" O ILE E 156 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'E' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL E 139 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'E' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU E 163 " --> pdb=" O LYS E 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA E 174 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'E' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR E 247 " --> pdb=" O LYS E 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS E 284 " --> pdb=" O THR E 247 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'F' and resid 84 through 87 Processing sheet with id= 27, first strand: chain 'F' and resid 155 through 156 removed outlier: 3.690A pdb=" N ALA F 135 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'F' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL F 139 " --> pdb=" O ASP F 151 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'F' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU F 163 " --> pdb=" O LYS F 176 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA F 174 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'F' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR F 247 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS F 284 " --> pdb=" O THR F 247 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'G' and resid 84 through 87 Processing sheet with id= 32, first strand: chain 'G' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA G 135 " --> pdb=" O ILE G 156 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'G' and resid 139 through 142 removed outlier: 7.022A pdb=" N VAL G 139 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'G' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU G 163 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA G 174 " --> pdb=" O LEU G 165 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'G' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR G 247 " --> pdb=" O LYS G 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS G 284 " --> pdb=" O THR G 247 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'H' and resid 84 through 87 Processing sheet with id= 37, first strand: chain 'H' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA H 135 " --> pdb=" O ILE H 156 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'H' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL H 139 " --> pdb=" O ASP H 151 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'H' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU H 163 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA H 174 " --> pdb=" O LEU H 165 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'H' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR H 247 " --> pdb=" O LYS H 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS H 284 " --> pdb=" O THR H 247 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'I' and resid 84 through 87 Processing sheet with id= 42, first strand: chain 'I' and resid 155 through 156 removed outlier: 3.690A pdb=" N ALA I 135 " --> pdb=" O ILE I 156 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'I' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL I 139 " --> pdb=" O ASP I 151 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'I' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU I 163 " --> pdb=" O LYS I 176 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA I 174 " --> pdb=" O LEU I 165 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'I' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR I 247 " --> pdb=" O LYS I 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS I 284 " --> pdb=" O THR I 247 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'J' and resid 84 through 87 Processing sheet with id= 47, first strand: chain 'J' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA J 135 " --> pdb=" O ILE J 156 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'J' and resid 139 through 142 removed outlier: 7.022A pdb=" N VAL J 139 " --> pdb=" O ASP J 151 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'J' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU J 163 " --> pdb=" O LYS J 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA J 174 " --> pdb=" O LEU J 165 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'J' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR J 247 " --> pdb=" O LYS J 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS J 284 " --> pdb=" O THR J 247 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'K' and resid 84 through 87 Processing sheet with id= 52, first strand: chain 'K' and resid 155 through 156 removed outlier: 3.691A pdb=" N ALA K 135 " --> pdb=" O ILE K 156 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'K' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL K 139 " --> pdb=" O ASP K 151 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'K' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU K 163 " --> pdb=" O LYS K 176 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA K 174 " --> pdb=" O LEU K 165 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'K' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR K 247 " --> pdb=" O LYS K 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS K 284 " --> pdb=" O THR K 247 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'L' and resid 84 through 87 Processing sheet with id= 57, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.690A pdb=" N ALA L 135 " --> pdb=" O ILE L 156 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'L' and resid 139 through 142 removed outlier: 7.021A pdb=" N VAL L 139 " --> pdb=" O ASP L 151 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'L' and resid 161 through 166 removed outlier: 3.675A pdb=" N GLU L 163 " --> pdb=" O LYS L 176 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA L 174 " --> pdb=" O LEU L 165 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'L' and resid 244 through 247 removed outlier: 3.523A pdb=" N THR L 247 " --> pdb=" O LYS L 284 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS L 284 " --> pdb=" O THR L 247 " (cutoff:3.500A) 1800 hydrogen bonds defined for protein. 5328 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: 13.69 Time building geometry restraints manager: 16.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12332 1.34 - 1.45: 5462 1.45 - 1.57: 21278 1.57 - 1.69: 0 1.69 - 1.80: 240 Bond restraints: 39312 Sorted by residual: bond pdb=" N ASP L 110 " pdb=" CA ASP L 110 " ideal model delta sigma weight residual 1.459 1.482 -0.024 1.16e-02 7.43e+03 4.11e+00 bond pdb=" N ASP C 110 " pdb=" CA ASP C 110 " ideal model delta sigma weight residual 1.459 1.482 -0.024 1.16e-02 7.43e+03 4.11e+00 bond pdb=" N ASP I 110 " pdb=" CA ASP I 110 " ideal model delta sigma weight residual 1.459 1.482 -0.024 1.16e-02 7.43e+03 4.11e+00 bond pdb=" N ASP F 110 " pdb=" CA ASP F 110 " ideal model delta sigma weight residual 1.459 1.482 -0.024 1.16e-02 7.43e+03 4.11e+00 bond pdb=" N ASP A 110 " pdb=" CA ASP A 110 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.16e-02 7.43e+03 4.06e+00 ... (remaining 39307 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.57: 1380 106.57 - 113.43: 21840 113.43 - 120.28: 14698 120.28 - 127.14: 15018 127.14 - 133.99: 464 Bond angle restraints: 53400 Sorted by residual: angle pdb=" C LEU J 356 " pdb=" N ILE J 357 " pdb=" CA ILE J 357 " ideal model delta sigma weight residual 120.33 124.33 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" C LEU A 356 " pdb=" N ILE A 357 " pdb=" CA ILE A 357 " ideal model delta sigma weight residual 120.33 124.33 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" C LEU G 356 " pdb=" N ILE G 357 " pdb=" CA ILE G 357 " ideal model delta sigma weight residual 120.33 124.33 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" C LEU D 356 " pdb=" N ILE D 357 " pdb=" CA ILE D 357 " ideal model delta sigma weight residual 120.33 124.33 -4.00 8.00e-01 1.56e+00 2.50e+01 angle pdb=" C LEU I 356 " pdb=" N ILE I 357 " pdb=" CA ILE I 357 " ideal model delta sigma weight residual 120.33 124.32 -3.99 8.00e-01 1.56e+00 2.48e+01 ... (remaining 53395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.42: 22380 14.42 - 28.84: 924 28.84 - 43.25: 216 43.25 - 57.67: 12 57.67 - 72.09: 36 Dihedral angle restraints: 23568 sinusoidal: 9384 harmonic: 14184 Sorted by residual: dihedral pdb=" CA ASP K 109 " pdb=" C ASP K 109 " pdb=" N ASP K 110 " pdb=" CA ASP K 110 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASP H 109 " pdb=" C ASP H 109 " pdb=" N ASP H 110 " pdb=" CA ASP H 110 " ideal model delta harmonic sigma weight residual 180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASP B 109 " pdb=" C ASP B 109 " pdb=" N ASP B 110 " pdb=" CA ASP B 110 " ideal model delta harmonic sigma weight residual -180.00 -155.48 -24.52 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 23565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 4309 0.048 - 0.095: 1220 0.095 - 0.143: 491 0.143 - 0.191: 16 0.191 - 0.239: 24 Chirality restraints: 6060 Sorted by residual: chirality pdb=" CA ASN E 204 " pdb=" N ASN E 204 " pdb=" C ASN E 204 " pdb=" CB ASN E 204 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASN B 204 " pdb=" N ASN B 204 " pdb=" C ASN B 204 " pdb=" CB ASN B 204 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASN K 204 " pdb=" N ASN K 204 " pdb=" C ASN K 204 " pdb=" CB ASN K 204 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 6057 not shown) Planarity restraints: 6888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN E 435 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO E 436 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO E 436 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 436 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 435 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO B 436 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 436 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 436 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 435 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO H 436 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO H 436 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 436 " -0.037 5.00e-02 4.00e+02 ... (remaining 6885 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 11176 2.82 - 3.34: 35440 3.34 - 3.86: 63828 3.86 - 4.38: 70092 4.38 - 4.90: 121669 Nonbonded interactions: 302205 Sorted by model distance: nonbonded pdb=" O ILE F 130 " pdb=" OG SER F 213 " model vdw 2.298 2.440 nonbonded pdb=" O ILE G 130 " pdb=" OG SER G 213 " model vdw 2.298 2.440 nonbonded pdb=" O ILE A 130 " pdb=" OG SER A 213 " model vdw 2.298 2.440 nonbonded pdb=" O ILE J 130 " pdb=" OG SER J 213 " model vdw 2.298 2.440 nonbonded pdb=" O ILE D 130 " pdb=" OG SER D 213 " model vdw 2.298 2.440 ... (remaining 302200 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' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 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: 3.230 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 97.230 Find NCS groups from input model: 2.840 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 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 : 0.005 0.051 39312 Z= 0.345 Angle : 0.850 9.621 53400 Z= 0.470 Chirality : 0.051 0.239 6060 Planarity : 0.007 0.061 6888 Dihedral : 9.403 72.091 14448 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -3.36 (0.10), residues: 4908 helix: -2.00 (0.08), residues: 2220 sheet: -2.40 (0.16), residues: 660 loop : -2.24 (0.12), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 259 HIS 0.005 0.002 HIS B 60 PHE 0.017 0.002 PHE D 76 TYR 0.029 0.003 TYR H 116 ARG 0.004 0.001 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 919 time to evaluate : 5.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8556 (t0) cc_final: 0.7825 (t70) REVERT: A 49 LEU cc_start: 0.9015 (tp) cc_final: 0.8373 (mp) REVERT: A 125 TYR cc_start: 0.9302 (t80) cc_final: 0.9083 (t80) REVERT: A 126 GLU cc_start: 0.8436 (pt0) cc_final: 0.8107 (pt0) REVERT: A 180 GLU cc_start: 0.7872 (mp0) cc_final: 0.7385 (mm-30) REVERT: A 237 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8081 (tt0) REVERT: A 289 ASP cc_start: 0.8091 (m-30) cc_final: 0.6937 (m-30) REVERT: A 314 ILE cc_start: 0.9335 (tt) cc_final: 0.8860 (pt) REVERT: A 383 ASP cc_start: 0.7657 (t0) cc_final: 0.7384 (t0) REVERT: A 385 SER cc_start: 0.9092 (t) cc_final: 0.8760 (m) REVERT: A 393 MET cc_start: 0.8580 (mmm) cc_final: 0.8144 (mtt) REVERT: B 47 ASP cc_start: 0.8624 (t0) cc_final: 0.7210 (t70) REVERT: B 50 LEU cc_start: 0.9139 (mp) cc_final: 0.8744 (mt) REVERT: B 180 GLU cc_start: 0.8136 (mp0) cc_final: 0.7687 (mm-30) REVERT: B 308 ILE cc_start: 0.9484 (mt) cc_final: 0.9251 (mm) REVERT: B 321 LEU cc_start: 0.8871 (tp) cc_final: 0.8412 (tp) REVERT: B 339 GLN cc_start: 0.9313 (tp40) cc_final: 0.8816 (tp40) REVERT: B 385 SER cc_start: 0.9131 (t) cc_final: 0.8760 (m) REVERT: C 47 ASP cc_start: 0.8686 (t0) cc_final: 0.7975 (t70) REVERT: C 50 LEU cc_start: 0.9232 (mp) cc_final: 0.8932 (mt) REVERT: C 54 ASP cc_start: 0.8532 (m-30) cc_final: 0.8115 (p0) REVERT: C 180 GLU cc_start: 0.8234 (mp0) cc_final: 0.7940 (mm-30) REVERT: C 308 ILE cc_start: 0.9308 (mt) cc_final: 0.9108 (mm) REVERT: C 314 ILE cc_start: 0.9060 (tt) cc_final: 0.8624 (pt) REVERT: C 339 GLN cc_start: 0.9254 (tp40) cc_final: 0.8958 (tp40) REVERT: C 383 ASP cc_start: 0.7713 (t0) cc_final: 0.7479 (t0) REVERT: C 385 SER cc_start: 0.9394 (t) cc_final: 0.8847 (t) REVERT: C 393 MET cc_start: 0.8480 (mmm) cc_final: 0.7872 (mtp) REVERT: D 47 ASP cc_start: 0.8557 (t0) cc_final: 0.7821 (t70) REVERT: D 49 LEU cc_start: 0.9019 (tp) cc_final: 0.8376 (mp) REVERT: D 125 TYR cc_start: 0.9298 (t80) cc_final: 0.9079 (t80) REVERT: D 126 GLU cc_start: 0.8436 (pt0) cc_final: 0.8113 (pt0) REVERT: D 180 GLU cc_start: 0.7876 (mp0) cc_final: 0.7388 (mm-30) REVERT: D 237 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8082 (tt0) REVERT: D 314 ILE cc_start: 0.9336 (tt) cc_final: 0.8865 (pt) REVERT: D 383 ASP cc_start: 0.7650 (t0) cc_final: 0.7386 (t0) REVERT: D 385 SER cc_start: 0.9092 (t) cc_final: 0.8761 (m) REVERT: D 393 MET cc_start: 0.8573 (mmm) cc_final: 0.8135 (mtt) REVERT: E 47 ASP cc_start: 0.8627 (t0) cc_final: 0.7205 (t70) REVERT: E 50 LEU cc_start: 0.9139 (mp) cc_final: 0.8746 (mt) REVERT: E 180 GLU cc_start: 0.8130 (mp0) cc_final: 0.7684 (mm-30) REVERT: E 308 ILE cc_start: 0.9480 (mt) cc_final: 0.9257 (mm) REVERT: E 321 LEU cc_start: 0.8874 (tp) cc_final: 0.8413 (tp) REVERT: E 339 GLN cc_start: 0.9299 (tp40) cc_final: 0.8806 (tp40) REVERT: E 385 SER cc_start: 0.9131 (t) cc_final: 0.8757 (m) REVERT: F 47 ASP cc_start: 0.8690 (t0) cc_final: 0.7985 (t70) REVERT: F 50 LEU cc_start: 0.9225 (mp) cc_final: 0.8930 (mt) REVERT: F 54 ASP cc_start: 0.8528 (m-30) cc_final: 0.8112 (p0) REVERT: F 180 GLU cc_start: 0.8242 (mp0) cc_final: 0.7944 (mm-30) REVERT: F 314 ILE cc_start: 0.9061 (tt) cc_final: 0.8622 (pt) REVERT: F 339 GLN cc_start: 0.9259 (tp40) cc_final: 0.8953 (tp40) REVERT: F 383 ASP cc_start: 0.7710 (t0) cc_final: 0.7484 (t0) REVERT: F 385 SER cc_start: 0.9397 (t) cc_final: 0.8852 (t) REVERT: F 393 MET cc_start: 0.8477 (mmm) cc_final: 0.7874 (mtp) REVERT: G 47 ASP cc_start: 0.8559 (t0) cc_final: 0.7826 (t70) REVERT: G 49 LEU cc_start: 0.9018 (tp) cc_final: 0.8374 (mp) REVERT: G 125 TYR cc_start: 0.9300 (t80) cc_final: 0.9080 (t80) REVERT: G 126 GLU cc_start: 0.8441 (pt0) cc_final: 0.8116 (pt0) REVERT: G 180 GLU cc_start: 0.7876 (mp0) cc_final: 0.7388 (mm-30) REVERT: G 237 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8083 (tt0) REVERT: G 314 ILE cc_start: 0.9335 (tt) cc_final: 0.8867 (pt) REVERT: G 383 ASP cc_start: 0.7664 (t0) cc_final: 0.7391 (t0) REVERT: G 385 SER cc_start: 0.9093 (t) cc_final: 0.8762 (m) REVERT: G 393 MET cc_start: 0.8578 (mmm) cc_final: 0.8140 (mtt) REVERT: H 47 ASP cc_start: 0.8622 (t0) cc_final: 0.7205 (t70) REVERT: H 50 LEU cc_start: 0.9138 (mp) cc_final: 0.8739 (mt) REVERT: H 180 GLU cc_start: 0.8132 (mp0) cc_final: 0.7683 (mm-30) REVERT: H 308 ILE cc_start: 0.9477 (mt) cc_final: 0.9247 (mm) REVERT: H 321 LEU cc_start: 0.8881 (tp) cc_final: 0.8420 (tp) REVERT: H 339 GLN cc_start: 0.9296 (tp40) cc_final: 0.8809 (tp40) REVERT: H 385 SER cc_start: 0.9130 (t) cc_final: 0.8759 (m) REVERT: I 47 ASP cc_start: 0.8686 (t0) cc_final: 0.7977 (t70) REVERT: I 50 LEU cc_start: 0.9233 (mp) cc_final: 0.8933 (mt) REVERT: I 54 ASP cc_start: 0.8534 (m-30) cc_final: 0.8115 (p0) REVERT: I 180 GLU cc_start: 0.8238 (mp0) cc_final: 0.7948 (mm-30) REVERT: I 308 ILE cc_start: 0.9323 (mt) cc_final: 0.9122 (mm) REVERT: I 314 ILE cc_start: 0.9062 (tt) cc_final: 0.8625 (pt) REVERT: I 339 GLN cc_start: 0.9266 (tp40) cc_final: 0.8955 (tp40) REVERT: I 383 ASP cc_start: 0.7704 (t0) cc_final: 0.7482 (t0) REVERT: I 385 SER cc_start: 0.9396 (t) cc_final: 0.8850 (t) REVERT: I 393 MET cc_start: 0.8480 (mmm) cc_final: 0.7875 (mtp) REVERT: J 47 ASP cc_start: 0.8559 (t0) cc_final: 0.7825 (t70) REVERT: J 49 LEU cc_start: 0.9016 (tp) cc_final: 0.8371 (mp) REVERT: J 125 TYR cc_start: 0.9302 (t80) cc_final: 0.9084 (t80) REVERT: J 126 GLU cc_start: 0.8442 (pt0) cc_final: 0.8112 (pt0) REVERT: J 180 GLU cc_start: 0.7871 (mp0) cc_final: 0.7382 (mm-30) REVERT: J 237 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8083 (tt0) REVERT: J 314 ILE cc_start: 0.9335 (tt) cc_final: 0.8863 (pt) REVERT: J 383 ASP cc_start: 0.7661 (t0) cc_final: 0.7388 (t0) REVERT: J 385 SER cc_start: 0.9091 (t) cc_final: 0.8759 (m) REVERT: J 393 MET cc_start: 0.8576 (mmm) cc_final: 0.8142 (mtt) REVERT: K 47 ASP cc_start: 0.8626 (t0) cc_final: 0.7207 (t70) REVERT: K 50 LEU cc_start: 0.9137 (mp) cc_final: 0.8742 (mt) REVERT: K 180 GLU cc_start: 0.8132 (mp0) cc_final: 0.7681 (mm-30) REVERT: K 308 ILE cc_start: 0.9477 (mt) cc_final: 0.9236 (mm) REVERT: K 321 LEU cc_start: 0.8887 (tp) cc_final: 0.8424 (tp) REVERT: K 339 GLN cc_start: 0.9312 (tp40) cc_final: 0.8821 (tp40) REVERT: K 385 SER cc_start: 0.9131 (t) cc_final: 0.8760 (m) REVERT: K 393 MET cc_start: 0.8567 (mmm) cc_final: 0.8366 (mtp) REVERT: L 47 ASP cc_start: 0.8684 (t0) cc_final: 0.7977 (t70) REVERT: L 50 LEU cc_start: 0.9234 (mp) cc_final: 0.8935 (mt) REVERT: L 54 ASP cc_start: 0.8538 (m-30) cc_final: 0.8116 (p0) REVERT: L 180 GLU cc_start: 0.8236 (mp0) cc_final: 0.7949 (mm-30) REVERT: L 308 ILE cc_start: 0.9312 (mt) cc_final: 0.9110 (mm) REVERT: L 314 ILE cc_start: 0.9064 (tt) cc_final: 0.8628 (pt) REVERT: L 339 GLN cc_start: 0.9259 (tp40) cc_final: 0.8960 (tp40) REVERT: L 383 ASP cc_start: 0.7709 (t0) cc_final: 0.7484 (t0) REVERT: L 385 SER cc_start: 0.9393 (t) cc_final: 0.8849 (t) REVERT: L 393 MET cc_start: 0.8477 (mmm) cc_final: 0.7872 (mtp) outliers start: 0 outliers final: 0 residues processed: 919 average time/residue: 0.5423 time to fit residues: 800.0351 Evaluate side-chains 486 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 4.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 206 optimal weight: 0.0170 chunk 127 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 199 optimal weight: 10.0000 chunk 385 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 287 optimal weight: 30.0000 chunk 446 optimal weight: 20.0000 overall best weight: 3.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 275 HIS A 320 GLN ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN C 320 GLN D 160 ASN D 275 HIS D 320 GLN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 GLN F 320 GLN G 160 ASN G 275 HIS G 320 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 320 GLN I 320 GLN J 160 ASN J 275 HIS J 320 GLN ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 320 GLN L 320 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 39312 Z= 0.210 Angle : 0.602 9.832 53400 Z= 0.298 Chirality : 0.043 0.145 6060 Planarity : 0.005 0.064 6888 Dihedral : 4.728 21.830 5280 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.10 % Allowed : 7.99 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.12), residues: 4908 helix: 0.29 (0.11), residues: 2184 sheet: -1.91 (0.17), residues: 636 loop : -1.25 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 259 HIS 0.005 0.001 HIS A 60 PHE 0.030 0.002 PHE B 76 TYR 0.011 0.002 TYR D 303 ARG 0.005 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 580 time to evaluate : 4.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8479 (t0) cc_final: 0.8171 (t70) REVERT: A 91 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8625 (m) REVERT: A 121 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9255 (mp) REVERT: A 125 TYR cc_start: 0.9392 (t80) cc_final: 0.9187 (t80) REVERT: A 126 GLU cc_start: 0.8696 (pt0) cc_final: 0.8469 (pt0) REVERT: A 314 ILE cc_start: 0.9331 (tt) cc_final: 0.8901 (pt) REVERT: A 383 ASP cc_start: 0.7470 (t0) cc_final: 0.6983 (t0) REVERT: A 385 SER cc_start: 0.8850 (t) cc_final: 0.8595 (p) REVERT: A 393 MET cc_start: 0.8599 (mmm) cc_final: 0.7990 (mtt) REVERT: B 47 ASP cc_start: 0.8064 (t0) cc_final: 0.7796 (t70) REVERT: B 240 MET cc_start: 0.9053 (mmm) cc_final: 0.8650 (mmm) REVERT: B 323 MET cc_start: 0.7370 (mmm) cc_final: 0.7049 (mmt) REVERT: B 333 PHE cc_start: 0.7555 (t80) cc_final: 0.7188 (t80) REVERT: C 47 ASP cc_start: 0.8364 (t0) cc_final: 0.8034 (t70) REVERT: C 54 ASP cc_start: 0.8496 (m-30) cc_final: 0.7912 (p0) REVERT: C 237 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8056 (tt0) REVERT: C 240 MET cc_start: 0.9123 (mmm) cc_final: 0.8873 (mmm) REVERT: C 305 ASP cc_start: 0.9014 (m-30) cc_final: 0.8793 (m-30) REVERT: C 308 ILE cc_start: 0.9310 (mt) cc_final: 0.9068 (mm) REVERT: C 314 ILE cc_start: 0.9059 (tt) cc_final: 0.8653 (pt) REVERT: C 315 ASP cc_start: 0.8688 (p0) cc_final: 0.8283 (p0) REVERT: C 339 GLN cc_start: 0.9252 (tp40) cc_final: 0.8957 (tp40) REVERT: C 383 ASP cc_start: 0.7474 (t0) cc_final: 0.7221 (t0) REVERT: C 393 MET cc_start: 0.8572 (mmm) cc_final: 0.7828 (mtp) REVERT: D 47 ASP cc_start: 0.8471 (t0) cc_final: 0.8161 (t70) REVERT: D 91 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8625 (m) REVERT: D 121 LEU cc_start: 0.9521 (OUTLIER) cc_final: 0.9253 (mp) REVERT: D 125 TYR cc_start: 0.9391 (t80) cc_final: 0.9183 (t80) REVERT: D 126 GLU cc_start: 0.8699 (pt0) cc_final: 0.8464 (pt0) REVERT: D 314 ILE cc_start: 0.9330 (tt) cc_final: 0.8908 (pt) REVERT: D 383 ASP cc_start: 0.7468 (t0) cc_final: 0.6996 (t0) REVERT: D 385 SER cc_start: 0.8845 (t) cc_final: 0.8598 (p) REVERT: D 393 MET cc_start: 0.8591 (mmm) cc_final: 0.7979 (mtt) REVERT: E 47 ASP cc_start: 0.8058 (t0) cc_final: 0.7792 (t70) REVERT: E 240 MET cc_start: 0.9055 (mmm) cc_final: 0.8653 (mmm) REVERT: E 323 MET cc_start: 0.7376 (mmm) cc_final: 0.7067 (mmt) REVERT: E 333 PHE cc_start: 0.7554 (t80) cc_final: 0.7189 (t80) REVERT: F 47 ASP cc_start: 0.8381 (t0) cc_final: 0.8045 (t70) REVERT: F 54 ASP cc_start: 0.8487 (m-30) cc_final: 0.7913 (p0) REVERT: F 237 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8060 (tt0) REVERT: F 240 MET cc_start: 0.9130 (mmm) cc_final: 0.8876 (mmm) REVERT: F 305 ASP cc_start: 0.9049 (m-30) cc_final: 0.8815 (m-30) REVERT: F 314 ILE cc_start: 0.9009 (tt) cc_final: 0.8592 (pt) REVERT: F 315 ASP cc_start: 0.8681 (p0) cc_final: 0.8283 (p0) REVERT: F 339 GLN cc_start: 0.9249 (tp40) cc_final: 0.8946 (tp40) REVERT: F 383 ASP cc_start: 0.7479 (t0) cc_final: 0.7226 (t0) REVERT: F 393 MET cc_start: 0.8576 (mmm) cc_final: 0.7830 (mtp) REVERT: G 47 ASP cc_start: 0.8474 (t0) cc_final: 0.8165 (t70) REVERT: G 91 THR cc_start: 0.8921 (OUTLIER) cc_final: 0.8628 (m) REVERT: G 121 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9249 (mp) REVERT: G 125 TYR cc_start: 0.9391 (t80) cc_final: 0.9184 (t80) REVERT: G 126 GLU cc_start: 0.8706 (pt0) cc_final: 0.8470 (pt0) REVERT: G 314 ILE cc_start: 0.9341 (tt) cc_final: 0.8919 (pt) REVERT: G 383 ASP cc_start: 0.7485 (t0) cc_final: 0.7003 (t0) REVERT: G 385 SER cc_start: 0.8851 (t) cc_final: 0.8603 (p) REVERT: G 393 MET cc_start: 0.8591 (mmm) cc_final: 0.7981 (mtt) REVERT: H 47 ASP cc_start: 0.8063 (t0) cc_final: 0.7795 (t70) REVERT: H 240 MET cc_start: 0.9056 (mmm) cc_final: 0.8645 (mmm) REVERT: H 323 MET cc_start: 0.7373 (mmm) cc_final: 0.7062 (mmt) REVERT: H 333 PHE cc_start: 0.7559 (t80) cc_final: 0.7192 (t80) REVERT: I 47 ASP cc_start: 0.8364 (t0) cc_final: 0.8038 (t70) REVERT: I 54 ASP cc_start: 0.8488 (m-30) cc_final: 0.7912 (p0) REVERT: I 237 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8064 (tt0) REVERT: I 240 MET cc_start: 0.9129 (mmm) cc_final: 0.8875 (mmm) REVERT: I 305 ASP cc_start: 0.9010 (m-30) cc_final: 0.8802 (m-30) REVERT: I 308 ILE cc_start: 0.9326 (mt) cc_final: 0.9081 (mm) REVERT: I 314 ILE cc_start: 0.9059 (tt) cc_final: 0.8655 (pt) REVERT: I 315 ASP cc_start: 0.8668 (p0) cc_final: 0.8279 (p0) REVERT: I 339 GLN cc_start: 0.9258 (tp40) cc_final: 0.8952 (tp40) REVERT: I 383 ASP cc_start: 0.7461 (t0) cc_final: 0.7225 (t0) REVERT: I 393 MET cc_start: 0.8573 (mmm) cc_final: 0.7832 (mtp) REVERT: J 47 ASP cc_start: 0.8477 (t0) cc_final: 0.8166 (t70) REVERT: J 91 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8626 (m) REVERT: J 121 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9254 (mp) REVERT: J 125 TYR cc_start: 0.9394 (t80) cc_final: 0.9189 (t80) REVERT: J 126 GLU cc_start: 0.8700 (pt0) cc_final: 0.8472 (pt0) REVERT: J 314 ILE cc_start: 0.9336 (tt) cc_final: 0.8910 (pt) REVERT: J 383 ASP cc_start: 0.7482 (t0) cc_final: 0.6999 (t0) REVERT: J 385 SER cc_start: 0.8845 (t) cc_final: 0.8599 (p) REVERT: J 393 MET cc_start: 0.8600 (mmm) cc_final: 0.7984 (mtt) REVERT: K 47 ASP cc_start: 0.8062 (t0) cc_final: 0.7792 (t70) REVERT: K 240 MET cc_start: 0.9056 (mmm) cc_final: 0.8650 (mmm) REVERT: K 323 MET cc_start: 0.7379 (mmm) cc_final: 0.7056 (mmt) REVERT: K 333 PHE cc_start: 0.7554 (t80) cc_final: 0.7194 (t80) REVERT: K 393 MET cc_start: 0.8651 (mmm) cc_final: 0.8313 (mtp) REVERT: L 47 ASP cc_start: 0.8369 (t0) cc_final: 0.8039 (t70) REVERT: L 54 ASP cc_start: 0.8493 (m-30) cc_final: 0.7912 (p0) REVERT: L 237 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8060 (tt0) REVERT: L 240 MET cc_start: 0.9126 (mmm) cc_final: 0.8873 (mmm) REVERT: L 305 ASP cc_start: 0.9008 (m-30) cc_final: 0.8785 (m-30) REVERT: L 308 ILE cc_start: 0.9312 (mt) cc_final: 0.9065 (mm) REVERT: L 314 ILE cc_start: 0.9062 (tt) cc_final: 0.8655 (pt) REVERT: L 315 ASP cc_start: 0.8674 (p0) cc_final: 0.8279 (p0) REVERT: L 339 GLN cc_start: 0.9257 (tp40) cc_final: 0.8959 (tp40) REVERT: L 383 ASP cc_start: 0.7469 (t0) cc_final: 0.7229 (t0) REVERT: L 393 MET cc_start: 0.8590 (mmm) cc_final: 0.7791 (mtp) outliers start: 127 outliers final: 83 residues processed: 663 average time/residue: 0.4697 time to fit residues: 530.0254 Evaluate side-chains 486 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 395 time to evaluate : 4.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 121 LEU Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 378 MET Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 401 SER Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 289 ASP Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 121 LEU Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 312 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 20.0000 chunk 138 optimal weight: 30.0000 chunk 371 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 123 optimal weight: 30.0000 chunk 447 optimal weight: 30.0000 chunk 483 optimal weight: 9.9990 chunk 398 optimal weight: 10.0000 chunk 443 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 359 optimal weight: 1.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 39312 Z= 0.394 Angle : 0.676 8.756 53400 Z= 0.338 Chirality : 0.045 0.141 6060 Planarity : 0.005 0.073 6888 Dihedral : 4.647 20.638 5280 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.25 % Allowed : 10.87 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.12), residues: 4908 helix: 1.25 (0.11), residues: 2172 sheet: -1.66 (0.18), residues: 660 loop : -0.86 (0.15), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 84 HIS 0.007 0.002 HIS A 60 PHE 0.037 0.002 PHE B 76 TYR 0.018 0.002 TYR E 125 ARG 0.003 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 382 time to evaluate : 4.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8537 (m) REVERT: A 126 GLU cc_start: 0.8563 (pt0) cc_final: 0.8196 (pt0) REVERT: A 314 ILE cc_start: 0.9383 (tt) cc_final: 0.9033 (pt) REVERT: A 383 ASP cc_start: 0.7369 (t0) cc_final: 0.6881 (t0) REVERT: A 385 SER cc_start: 0.8845 (t) cc_final: 0.8522 (p) REVERT: A 393 MET cc_start: 0.8773 (mmm) cc_final: 0.7965 (mtt) REVERT: B 47 ASP cc_start: 0.8448 (t0) cc_final: 0.8220 (t0) REVERT: B 61 LYS cc_start: 0.9650 (mttt) cc_final: 0.9265 (mttm) REVERT: C 54 ASP cc_start: 0.8500 (m-30) cc_final: 0.7904 (p0) REVERT: C 240 MET cc_start: 0.9374 (mmm) cc_final: 0.9169 (mmm) REVERT: C 314 ILE cc_start: 0.9228 (tt) cc_final: 0.8912 (pt) REVERT: C 393 MET cc_start: 0.8643 (mmm) cc_final: 0.8067 (mmm) REVERT: D 91 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8532 (m) REVERT: D 126 GLU cc_start: 0.8567 (pt0) cc_final: 0.8194 (pt0) REVERT: D 314 ILE cc_start: 0.9386 (tt) cc_final: 0.9044 (pt) REVERT: D 383 ASP cc_start: 0.7367 (t0) cc_final: 0.6881 (t0) REVERT: D 385 SER cc_start: 0.8845 (t) cc_final: 0.8530 (p) REVERT: D 393 MET cc_start: 0.8781 (mmm) cc_final: 0.7957 (mtt) REVERT: E 47 ASP cc_start: 0.8446 (t0) cc_final: 0.8221 (t0) REVERT: E 61 LYS cc_start: 0.9650 (mttt) cc_final: 0.9268 (mttm) REVERT: F 54 ASP cc_start: 0.8494 (m-30) cc_final: 0.7911 (p0) REVERT: F 240 MET cc_start: 0.9372 (mmm) cc_final: 0.8922 (mmm) REVERT: F 314 ILE cc_start: 0.9215 (tt) cc_final: 0.8901 (pt) REVERT: F 393 MET cc_start: 0.8649 (mmm) cc_final: 0.8076 (mmm) REVERT: G 91 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8531 (m) REVERT: G 126 GLU cc_start: 0.8574 (pt0) cc_final: 0.8202 (pt0) REVERT: G 314 ILE cc_start: 0.9394 (tt) cc_final: 0.9050 (pt) REVERT: G 383 ASP cc_start: 0.7377 (t0) cc_final: 0.6881 (t0) REVERT: G 385 SER cc_start: 0.8848 (t) cc_final: 0.8531 (p) REVERT: G 393 MET cc_start: 0.8774 (mmm) cc_final: 0.7955 (mtt) REVERT: H 47 ASP cc_start: 0.8446 (t0) cc_final: 0.8221 (t0) REVERT: H 61 LYS cc_start: 0.9650 (mttt) cc_final: 0.9266 (mttm) REVERT: I 54 ASP cc_start: 0.8492 (m-30) cc_final: 0.7904 (p0) REVERT: I 240 MET cc_start: 0.9372 (mmm) cc_final: 0.8927 (mmm) REVERT: I 314 ILE cc_start: 0.9231 (tt) cc_final: 0.8912 (pt) REVERT: I 393 MET cc_start: 0.8650 (mmm) cc_final: 0.8078 (mmm) REVERT: J 91 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8537 (m) REVERT: J 126 GLU cc_start: 0.8568 (pt0) cc_final: 0.8200 (pt0) REVERT: J 314 ILE cc_start: 0.9387 (tt) cc_final: 0.9039 (pt) REVERT: J 383 ASP cc_start: 0.7375 (t0) cc_final: 0.6881 (t0) REVERT: J 385 SER cc_start: 0.8843 (t) cc_final: 0.8527 (p) REVERT: J 393 MET cc_start: 0.8774 (mmm) cc_final: 0.7961 (mtt) REVERT: K 47 ASP cc_start: 0.8446 (t0) cc_final: 0.8220 (t0) REVERT: K 61 LYS cc_start: 0.9648 (mttt) cc_final: 0.9263 (mttm) REVERT: K 393 MET cc_start: 0.8762 (mmm) cc_final: 0.8445 (mtp) REVERT: L 54 ASP cc_start: 0.8499 (m-30) cc_final: 0.7902 (p0) REVERT: L 240 MET cc_start: 0.9370 (mmm) cc_final: 0.8921 (mmm) REVERT: L 314 ILE cc_start: 0.9232 (tt) cc_final: 0.8913 (pt) REVERT: L 393 MET cc_start: 0.8658 (mmm) cc_final: 0.8084 (mmm) outliers start: 174 outliers final: 126 residues processed: 513 average time/residue: 0.4378 time to fit residues: 389.6371 Evaluate side-chains 502 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 372 time to evaluate : 4.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 378 MET Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 312 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 289 ASP Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 9.9990 chunk 336 optimal weight: 30.0000 chunk 232 optimal weight: 0.9990 chunk 49 optimal weight: 30.0000 chunk 213 optimal weight: 30.0000 chunk 300 optimal weight: 8.9990 chunk 449 optimal weight: 1.9990 chunk 475 optimal weight: 0.1980 chunk 234 optimal weight: 10.0000 chunk 425 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 39312 Z= 0.183 Angle : 0.587 10.109 53400 Z= 0.283 Chirality : 0.042 0.136 6060 Planarity : 0.004 0.066 6888 Dihedral : 4.456 19.890 5280 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.64 % Allowed : 12.37 % Favored : 83.99 % 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: 0.38 (0.13), residues: 4908 helix: 1.64 (0.11), residues: 2196 sheet: -1.35 (0.18), residues: 660 loop : -0.66 (0.15), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 84 HIS 0.003 0.001 HIS A 60 PHE 0.022 0.001 PHE E 333 TYR 0.012 0.001 TYR B 125 ARG 0.002 0.000 ARG L 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 409 time to evaluate : 4.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8513 (m) REVERT: A 126 GLU cc_start: 0.8527 (pt0) cc_final: 0.8125 (pt0) REVERT: A 314 ILE cc_start: 0.9310 (tt) cc_final: 0.8947 (pt) REVERT: A 383 ASP cc_start: 0.7412 (t0) cc_final: 0.6917 (t0) REVERT: A 385 SER cc_start: 0.8816 (t) cc_final: 0.8461 (p) REVERT: A 393 MET cc_start: 0.8758 (mmm) cc_final: 0.7899 (mtt) REVERT: B 47 ASP cc_start: 0.8450 (t0) cc_final: 0.8155 (t0) REVERT: B 61 LYS cc_start: 0.9641 (mttt) cc_final: 0.9263 (mttm) REVERT: B 321 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8670 (tp) REVERT: C 54 ASP cc_start: 0.8451 (m-30) cc_final: 0.7873 (p0) REVERT: C 314 ILE cc_start: 0.9080 (tt) cc_final: 0.8745 (pt) REVERT: C 315 ASP cc_start: 0.8704 (p0) cc_final: 0.8455 (p0) REVERT: C 393 MET cc_start: 0.8597 (mmm) cc_final: 0.8041 (mmm) REVERT: D 91 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8509 (m) REVERT: D 126 GLU cc_start: 0.8524 (pt0) cc_final: 0.8123 (pt0) REVERT: D 314 ILE cc_start: 0.9310 (tt) cc_final: 0.8958 (pt) REVERT: D 383 ASP cc_start: 0.7422 (t0) cc_final: 0.6931 (t0) REVERT: D 385 SER cc_start: 0.8814 (t) cc_final: 0.8463 (p) REVERT: D 393 MET cc_start: 0.8761 (mmm) cc_final: 0.7903 (mtt) REVERT: E 47 ASP cc_start: 0.8451 (t0) cc_final: 0.8159 (t0) REVERT: E 61 LYS cc_start: 0.9642 (mttt) cc_final: 0.9266 (mttm) REVERT: E 321 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8672 (tp) REVERT: F 54 ASP cc_start: 0.8454 (m-30) cc_final: 0.7875 (p0) REVERT: F 314 ILE cc_start: 0.9057 (tt) cc_final: 0.8724 (pt) REVERT: F 315 ASP cc_start: 0.8705 (p0) cc_final: 0.8463 (p0) REVERT: F 393 MET cc_start: 0.8599 (mmm) cc_final: 0.8047 (mmm) REVERT: G 91 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8510 (m) REVERT: G 126 GLU cc_start: 0.8530 (pt0) cc_final: 0.8128 (pt0) REVERT: G 314 ILE cc_start: 0.9321 (tt) cc_final: 0.8962 (pt) REVERT: G 383 ASP cc_start: 0.7432 (t0) cc_final: 0.6936 (t0) REVERT: G 385 SER cc_start: 0.8815 (t) cc_final: 0.8464 (p) REVERT: G 393 MET cc_start: 0.8758 (mmm) cc_final: 0.7902 (mtt) REVERT: H 47 ASP cc_start: 0.8451 (t0) cc_final: 0.8161 (t0) REVERT: H 61 LYS cc_start: 0.9640 (mttt) cc_final: 0.9264 (mttm) REVERT: H 321 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8678 (tp) REVERT: I 54 ASP cc_start: 0.8445 (m-30) cc_final: 0.7865 (p0) REVERT: I 314 ILE cc_start: 0.9077 (tt) cc_final: 0.8740 (pt) REVERT: I 315 ASP cc_start: 0.8694 (p0) cc_final: 0.8453 (p0) REVERT: I 393 MET cc_start: 0.8599 (mmm) cc_final: 0.8047 (mmm) REVERT: J 91 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8514 (m) REVERT: J 126 GLU cc_start: 0.8526 (pt0) cc_final: 0.8127 (pt0) REVERT: J 314 ILE cc_start: 0.9314 (tt) cc_final: 0.8955 (pt) REVERT: J 383 ASP cc_start: 0.7425 (t0) cc_final: 0.6932 (t0) REVERT: J 385 SER cc_start: 0.8812 (t) cc_final: 0.8460 (p) REVERT: J 393 MET cc_start: 0.8764 (mmm) cc_final: 0.7918 (mtt) REVERT: K 47 ASP cc_start: 0.8450 (t0) cc_final: 0.8171 (t0) REVERT: K 61 LYS cc_start: 0.9641 (mttt) cc_final: 0.9261 (mttm) REVERT: K 321 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8677 (tp) REVERT: K 393 MET cc_start: 0.8649 (mmm) cc_final: 0.8262 (mtp) REVERT: L 54 ASP cc_start: 0.8455 (m-30) cc_final: 0.7869 (p0) REVERT: L 314 ILE cc_start: 0.9086 (tt) cc_final: 0.8743 (pt) REVERT: L 315 ASP cc_start: 0.8697 (p0) cc_final: 0.8455 (p0) REVERT: L 393 MET cc_start: 0.8618 (mmm) cc_final: 0.8026 (mmm) outliers start: 149 outliers final: 101 residues processed: 503 average time/residue: 0.4336 time to fit residues: 380.4069 Evaluate side-chains 491 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 382 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 378 MET Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 344 LEU Chi-restraints excluded: chain H residue 401 SER Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 289 ASP Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 385 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 6.9990 chunk 269 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 354 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 405 optimal weight: 6.9990 chunk 328 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 242 optimal weight: 20.0000 chunk 426 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 203 HIS ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 203 HIS ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN G 203 HIS ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 160 ASN J 203 HIS ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 39312 Z= 0.333 Angle : 0.633 9.844 53400 Z= 0.311 Chirality : 0.043 0.140 6060 Planarity : 0.004 0.063 6888 Dihedral : 4.423 18.876 5280 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.03 % Allowed : 12.83 % Favored : 83.14 % 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: 0.50 (0.13), residues: 4908 helix: 1.80 (0.11), residues: 2196 sheet: -1.30 (0.18), residues: 660 loop : -0.68 (0.15), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 283 HIS 0.004 0.001 HIS L 60 PHE 0.021 0.001 PHE K 76 TYR 0.019 0.002 TYR K 125 ARG 0.003 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 396 time to evaluate : 4.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8568 (m) REVERT: A 126 GLU cc_start: 0.8610 (pt0) cc_final: 0.8212 (pt0) REVERT: A 314 ILE cc_start: 0.9377 (tt) cc_final: 0.8988 (pt) REVERT: A 383 ASP cc_start: 0.7479 (t0) cc_final: 0.6977 (t0) REVERT: A 385 SER cc_start: 0.8857 (t) cc_final: 0.8477 (p) REVERT: A 393 MET cc_start: 0.8849 (mmm) cc_final: 0.8179 (mmm) REVERT: B 47 ASP cc_start: 0.8546 (t0) cc_final: 0.8174 (t0) REVERT: B 61 LYS cc_start: 0.9647 (mttt) cc_final: 0.9300 (mttm) REVERT: B 240 MET cc_start: 0.9370 (tpp) cc_final: 0.9097 (mmp) REVERT: B 393 MET cc_start: 0.8137 (mtp) cc_final: 0.7812 (mtt) REVERT: C 54 ASP cc_start: 0.8507 (m-30) cc_final: 0.7901 (p0) REVERT: C 314 ILE cc_start: 0.9205 (tt) cc_final: 0.8847 (pt) REVERT: C 393 MET cc_start: 0.8619 (mmm) cc_final: 0.8200 (mmm) REVERT: D 91 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8562 (m) REVERT: D 126 GLU cc_start: 0.8606 (pt0) cc_final: 0.8207 (pt0) REVERT: D 383 ASP cc_start: 0.7479 (t0) cc_final: 0.6985 (t0) REVERT: D 385 SER cc_start: 0.8854 (t) cc_final: 0.8482 (p) REVERT: D 393 MET cc_start: 0.8848 (mmm) cc_final: 0.8579 (mmt) REVERT: E 47 ASP cc_start: 0.8544 (t0) cc_final: 0.8174 (t0) REVERT: E 61 LYS cc_start: 0.9647 (mttt) cc_final: 0.9303 (mttm) REVERT: F 54 ASP cc_start: 0.8497 (m-30) cc_final: 0.7905 (p0) REVERT: F 314 ILE cc_start: 0.9192 (tt) cc_final: 0.8846 (pt) REVERT: F 393 MET cc_start: 0.8619 (mmm) cc_final: 0.8210 (mmm) REVERT: G 91 THR cc_start: 0.8846 (OUTLIER) cc_final: 0.8567 (m) REVERT: G 126 GLU cc_start: 0.8613 (pt0) cc_final: 0.8212 (pt0) REVERT: G 314 ILE cc_start: 0.9390 (tt) cc_final: 0.9001 (pt) REVERT: G 383 ASP cc_start: 0.7491 (t0) cc_final: 0.6987 (t0) REVERT: G 385 SER cc_start: 0.8856 (t) cc_final: 0.8485 (p) REVERT: G 393 MET cc_start: 0.8843 (mmm) cc_final: 0.8578 (mmt) REVERT: H 47 ASP cc_start: 0.8548 (t0) cc_final: 0.8181 (t0) REVERT: H 61 LYS cc_start: 0.9646 (mttt) cc_final: 0.9302 (mttm) REVERT: I 54 ASP cc_start: 0.8496 (m-30) cc_final: 0.7896 (p0) REVERT: I 314 ILE cc_start: 0.9206 (tt) cc_final: 0.8851 (pt) REVERT: I 393 MET cc_start: 0.8623 (mmm) cc_final: 0.8204 (mmm) REVERT: J 91 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8569 (m) REVERT: J 126 GLU cc_start: 0.8612 (pt0) cc_final: 0.8214 (pt0) REVERT: J 314 ILE cc_start: 0.9382 (tt) cc_final: 0.8993 (pt) REVERT: J 383 ASP cc_start: 0.7489 (t0) cc_final: 0.6986 (t0) REVERT: J 385 SER cc_start: 0.8852 (t) cc_final: 0.8486 (p) REVERT: J 393 MET cc_start: 0.8850 (mmm) cc_final: 0.7973 (mtt) REVERT: K 47 ASP cc_start: 0.8538 (t0) cc_final: 0.8190 (t0) REVERT: K 61 LYS cc_start: 0.9645 (mttt) cc_final: 0.9298 (mttm) REVERT: K 393 MET cc_start: 0.8784 (mmm) cc_final: 0.8461 (mtp) REVERT: L 54 ASP cc_start: 0.8498 (m-30) cc_final: 0.7894 (p0) REVERT: L 314 ILE cc_start: 0.9208 (tt) cc_final: 0.8853 (pt) REVERT: L 393 MET cc_start: 0.8713 (mmm) cc_final: 0.8235 (mmm) outliers start: 165 outliers final: 134 residues processed: 517 average time/residue: 0.4201 time to fit residues: 379.6335 Evaluate side-chains 530 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 392 time to evaluate : 4.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 378 MET Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 344 LEU Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 289 ASP Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 312 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 419 MET Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 229 ILE Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 5.9990 chunk 428 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 279 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 476 optimal weight: 0.7980 chunk 395 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 249 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 39312 Z= 0.249 Angle : 0.615 10.566 53400 Z= 0.296 Chirality : 0.043 0.171 6060 Planarity : 0.004 0.058 6888 Dihedral : 4.375 18.403 5280 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.15 % Allowed : 13.54 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.13), residues: 4908 helix: 1.85 (0.12), residues: 2208 sheet: -1.18 (0.19), residues: 660 loop : -0.62 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 84 HIS 0.003 0.001 HIS L 60 PHE 0.019 0.001 PHE K 76 TYR 0.014 0.001 TYR B 125 ARG 0.002 0.000 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 402 time to evaluate : 4.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8630 (m) REVERT: A 126 GLU cc_start: 0.8680 (pt0) cc_final: 0.8305 (pt0) REVERT: A 383 ASP cc_start: 0.7653 (t0) cc_final: 0.7297 (t0) REVERT: A 385 SER cc_start: 0.8840 (t) cc_final: 0.8457 (p) REVERT: A 393 MET cc_start: 0.8841 (mmm) cc_final: 0.7979 (mtt) REVERT: B 47 ASP cc_start: 0.8566 (t0) cc_final: 0.8173 (t0) REVERT: B 61 LYS cc_start: 0.9647 (mttt) cc_final: 0.9286 (mttm) REVERT: B 240 MET cc_start: 0.9386 (tpp) cc_final: 0.9120 (mmp) REVERT: B 314 ILE cc_start: 0.9328 (mt) cc_final: 0.9073 (pt) REVERT: B 415 LEU cc_start: 0.9293 (tp) cc_final: 0.9043 (tp) REVERT: C 54 ASP cc_start: 0.8503 (m-30) cc_final: 0.7909 (p0) REVERT: C 314 ILE cc_start: 0.9161 (tt) cc_final: 0.8800 (pt) REVERT: C 315 ASP cc_start: 0.8684 (p0) cc_final: 0.8468 (p0) REVERT: C 393 MET cc_start: 0.8663 (mmm) cc_final: 0.8372 (mmm) REVERT: D 91 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8630 (m) REVERT: D 126 GLU cc_start: 0.8682 (pt0) cc_final: 0.8306 (pt0) REVERT: D 383 ASP cc_start: 0.7555 (t0) cc_final: 0.7184 (t0) REVERT: D 385 SER cc_start: 0.8837 (t) cc_final: 0.8460 (p) REVERT: D 393 MET cc_start: 0.8831 (mmm) cc_final: 0.7948 (mtt) REVERT: E 47 ASP cc_start: 0.8560 (t0) cc_final: 0.8173 (t0) REVERT: E 61 LYS cc_start: 0.9647 (mttt) cc_final: 0.9287 (mttm) REVERT: E 314 ILE cc_start: 0.9331 (mt) cc_final: 0.9072 (pt) REVERT: E 415 LEU cc_start: 0.9294 (tp) cc_final: 0.9043 (tp) REVERT: F 54 ASP cc_start: 0.8497 (m-30) cc_final: 0.7912 (p0) REVERT: F 314 ILE cc_start: 0.9144 (tt) cc_final: 0.8790 (pt) REVERT: F 315 ASP cc_start: 0.8685 (p0) cc_final: 0.8470 (p0) REVERT: F 393 MET cc_start: 0.8686 (mmm) cc_final: 0.8377 (mmm) REVERT: G 91 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8633 (m) REVERT: G 126 GLU cc_start: 0.8688 (pt0) cc_final: 0.8309 (pt0) REVERT: G 314 ILE cc_start: 0.9364 (tt) cc_final: 0.8952 (pt) REVERT: G 383 ASP cc_start: 0.7568 (t0) cc_final: 0.7193 (t0) REVERT: G 385 SER cc_start: 0.8836 (t) cc_final: 0.8461 (p) REVERT: G 393 MET cc_start: 0.8828 (mmm) cc_final: 0.7948 (mtt) REVERT: H 47 ASP cc_start: 0.8563 (t0) cc_final: 0.8178 (t0) REVERT: H 61 LYS cc_start: 0.9645 (mttt) cc_final: 0.9286 (mttm) REVERT: H 314 ILE cc_start: 0.9333 (mt) cc_final: 0.9076 (pt) REVERT: H 415 LEU cc_start: 0.9289 (tp) cc_final: 0.9033 (tp) REVERT: I 54 ASP cc_start: 0.8495 (m-30) cc_final: 0.7907 (p0) REVERT: I 314 ILE cc_start: 0.9160 (tt) cc_final: 0.8797 (pt) REVERT: I 315 ASP cc_start: 0.8677 (p0) cc_final: 0.8465 (p0) REVERT: I 393 MET cc_start: 0.8689 (mmm) cc_final: 0.8380 (mmm) REVERT: J 91 THR cc_start: 0.8930 (OUTLIER) cc_final: 0.8635 (m) REVERT: J 126 GLU cc_start: 0.8687 (pt0) cc_final: 0.8310 (pt0) REVERT: J 314 ILE cc_start: 0.9356 (tt) cc_final: 0.8943 (pt) REVERT: J 383 ASP cc_start: 0.7563 (t0) cc_final: 0.7185 (t0) REVERT: J 385 SER cc_start: 0.8834 (t) cc_final: 0.8456 (p) REVERT: J 393 MET cc_start: 0.8828 (mmm) cc_final: 0.7950 (mtt) REVERT: K 47 ASP cc_start: 0.8548 (t0) cc_final: 0.8181 (t0) REVERT: K 61 LYS cc_start: 0.9645 (mttt) cc_final: 0.9283 (mttm) REVERT: K 314 ILE cc_start: 0.9334 (mt) cc_final: 0.9074 (pt) REVERT: K 393 MET cc_start: 0.8768 (mmm) cc_final: 0.8435 (mtp) REVERT: L 54 ASP cc_start: 0.8499 (m-30) cc_final: 0.7907 (p0) REVERT: L 314 ILE cc_start: 0.9168 (tt) cc_final: 0.8793 (pt) REVERT: L 315 ASP cc_start: 0.8677 (p0) cc_final: 0.8454 (p0) REVERT: L 393 MET cc_start: 0.8707 (mmm) cc_final: 0.8201 (mmm) outliers start: 170 outliers final: 150 residues processed: 522 average time/residue: 0.4176 time to fit residues: 382.5927 Evaluate side-chains 534 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 380 time to evaluate : 4.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 419 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 378 MET Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 312 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 344 LEU Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 289 ASP Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 419 MET Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 271 optimal weight: 0.6980 chunk 347 optimal weight: 4.9990 chunk 269 optimal weight: 9.9990 chunk 400 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 chunk 474 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 289 optimal weight: 20.0000 chunk 218 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 GLN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 339 GLN ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 39312 Z= 0.221 Angle : 0.609 11.801 53400 Z= 0.291 Chirality : 0.043 0.165 6060 Planarity : 0.004 0.055 6888 Dihedral : 4.324 17.801 5280 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.20 % Allowed : 14.25 % Favored : 81.55 % 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: 0.53 (0.13), residues: 4908 helix: 1.72 (0.11), residues: 2244 sheet: -1.06 (0.19), residues: 660 loop : -0.68 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 84 HIS 0.004 0.001 HIS G 60 PHE 0.019 0.001 PHE H 76 TYR 0.013 0.001 TYR K 125 ARG 0.002 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 417 time to evaluate : 4.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8631 (m) REVERT: A 126 GLU cc_start: 0.8680 (pt0) cc_final: 0.8360 (pt0) REVERT: A 323 MET cc_start: 0.7619 (mmm) cc_final: 0.7267 (mmm) REVERT: A 383 ASP cc_start: 0.7603 (t0) cc_final: 0.7209 (t0) REVERT: A 385 SER cc_start: 0.8844 (t) cc_final: 0.8418 (p) REVERT: A 393 MET cc_start: 0.8790 (mmm) cc_final: 0.8502 (mmt) REVERT: B 47 ASP cc_start: 0.8575 (t0) cc_final: 0.8167 (t0) REVERT: B 61 LYS cc_start: 0.9645 (mttt) cc_final: 0.9272 (mttm) REVERT: B 240 MET cc_start: 0.9410 (tpp) cc_final: 0.9137 (mmp) REVERT: C 54 ASP cc_start: 0.8503 (m-30) cc_final: 0.7885 (p0) REVERT: C 314 ILE cc_start: 0.9138 (tt) cc_final: 0.8760 (pt) REVERT: C 323 MET cc_start: 0.7583 (mmm) cc_final: 0.7331 (mmm) REVERT: C 393 MET cc_start: 0.8630 (mmm) cc_final: 0.8207 (mmm) REVERT: D 91 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8633 (m) REVERT: D 126 GLU cc_start: 0.8684 (pt0) cc_final: 0.8361 (pt0) REVERT: D 323 MET cc_start: 0.7603 (mmm) cc_final: 0.7248 (mmm) REVERT: D 383 ASP cc_start: 0.7583 (t0) cc_final: 0.7202 (t0) REVERT: D 385 SER cc_start: 0.8916 (t) cc_final: 0.8458 (p) REVERT: D 393 MET cc_start: 0.8790 (mmm) cc_final: 0.7926 (mtt) REVERT: E 47 ASP cc_start: 0.8566 (t0) cc_final: 0.8158 (t0) REVERT: E 61 LYS cc_start: 0.9645 (mttt) cc_final: 0.9274 (mttm) REVERT: F 54 ASP cc_start: 0.8500 (m-30) cc_final: 0.7896 (p0) REVERT: F 314 ILE cc_start: 0.9124 (tt) cc_final: 0.8756 (pt) REVERT: F 323 MET cc_start: 0.7591 (mmm) cc_final: 0.7334 (mmm) REVERT: F 393 MET cc_start: 0.8691 (mmm) cc_final: 0.8065 (mtp) REVERT: G 91 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8634 (m) REVERT: G 126 GLU cc_start: 0.8690 (pt0) cc_final: 0.8361 (pt0) REVERT: G 314 ILE cc_start: 0.9322 (tt) cc_final: 0.8873 (pt) REVERT: G 323 MET cc_start: 0.7609 (mmm) cc_final: 0.7262 (mmm) REVERT: G 383 ASP cc_start: 0.7602 (t0) cc_final: 0.7208 (t0) REVERT: G 385 SER cc_start: 0.8918 (t) cc_final: 0.8462 (p) REVERT: G 393 MET cc_start: 0.8787 (mmm) cc_final: 0.8008 (mtt) REVERT: H 47 ASP cc_start: 0.8572 (t0) cc_final: 0.8168 (t0) REVERT: H 61 LYS cc_start: 0.9643 (mttt) cc_final: 0.9271 (mttm) REVERT: I 54 ASP cc_start: 0.8496 (m-30) cc_final: 0.7887 (p0) REVERT: I 314 ILE cc_start: 0.9136 (tt) cc_final: 0.8753 (pt) REVERT: I 323 MET cc_start: 0.7594 (mmm) cc_final: 0.7342 (mmm) REVERT: I 393 MET cc_start: 0.8634 (mmm) cc_final: 0.8216 (mmm) REVERT: J 91 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8636 (m) REVERT: J 126 GLU cc_start: 0.8688 (pt0) cc_final: 0.8364 (pt0) REVERT: J 314 ILE cc_start: 0.9315 (tt) cc_final: 0.8865 (pt) REVERT: J 323 MET cc_start: 0.7602 (mmm) cc_final: 0.7254 (mmm) REVERT: J 383 ASP cc_start: 0.7602 (t0) cc_final: 0.7212 (t0) REVERT: J 385 SER cc_start: 0.8919 (t) cc_final: 0.8463 (p) REVERT: J 393 MET cc_start: 0.8790 (mmm) cc_final: 0.7926 (mtt) REVERT: K 47 ASP cc_start: 0.8550 (t0) cc_final: 0.8154 (t0) REVERT: K 61 LYS cc_start: 0.9643 (mttt) cc_final: 0.9270 (mttm) REVERT: K 393 MET cc_start: 0.8770 (mmm) cc_final: 0.8389 (mtp) REVERT: L 54 ASP cc_start: 0.8498 (m-30) cc_final: 0.7884 (p0) REVERT: L 314 ILE cc_start: 0.9145 (tt) cc_final: 0.8759 (pt) REVERT: L 323 MET cc_start: 0.7599 (mmm) cc_final: 0.7341 (mmm) REVERT: L 393 MET cc_start: 0.8703 (mmm) cc_final: 0.8324 (mmm) outliers start: 172 outliers final: 155 residues processed: 535 average time/residue: 0.4192 time to fit residues: 393.5478 Evaluate side-chains 550 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 391 time to evaluate : 4.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 419 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 378 MET Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 344 LEU Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 289 ASP Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 419 MET Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 283 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 301 optimal weight: 0.0170 chunk 323 optimal weight: 20.0000 chunk 234 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 372 optimal weight: 7.9990 overall best weight: 5.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 GLN ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 339 GLN L 339 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 39312 Z= 0.301 Angle : 0.651 12.888 53400 Z= 0.311 Chirality : 0.043 0.162 6060 Planarity : 0.004 0.054 6888 Dihedral : 4.353 17.801 5280 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.72 % Allowed : 14.83 % Favored : 80.45 % 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: 0.60 (0.13), residues: 4908 helix: 1.84 (0.11), residues: 2244 sheet: -1.09 (0.19), residues: 660 loop : -0.69 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 283 HIS 0.004 0.001 HIS A 60 PHE 0.029 0.001 PHE H 76 TYR 0.014 0.002 TYR H 125 ARG 0.003 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 389 time to evaluate : 4.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8954 (OUTLIER) cc_final: 0.8657 (m) REVERT: A 126 GLU cc_start: 0.8705 (pt0) cc_final: 0.8368 (pt0) REVERT: A 323 MET cc_start: 0.7644 (mmm) cc_final: 0.7293 (mmm) REVERT: A 383 ASP cc_start: 0.7628 (t0) cc_final: 0.7242 (t0) REVERT: A 385 SER cc_start: 0.8924 (t) cc_final: 0.8478 (p) REVERT: A 391 MET cc_start: 0.9581 (tpp) cc_final: 0.9370 (tpp) REVERT: B 47 ASP cc_start: 0.8600 (t0) cc_final: 0.8300 (t0) REVERT: B 61 LYS cc_start: 0.9645 (mttt) cc_final: 0.9285 (mttm) REVERT: B 240 MET cc_start: 0.9378 (tpp) cc_final: 0.9110 (mmp) REVERT: B 415 LEU cc_start: 0.9127 (tp) cc_final: 0.8861 (tp) REVERT: C 54 ASP cc_start: 0.8496 (m-30) cc_final: 0.7813 (p0) REVERT: C 314 ILE cc_start: 0.9061 (tt) cc_final: 0.8712 (pt) REVERT: C 323 MET cc_start: 0.7653 (mmm) cc_final: 0.7390 (mmm) REVERT: C 393 MET cc_start: 0.8694 (mmm) cc_final: 0.8400 (mmm) REVERT: D 91 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8655 (m) REVERT: D 126 GLU cc_start: 0.8707 (pt0) cc_final: 0.8369 (pt0) REVERT: D 323 MET cc_start: 0.7630 (mmm) cc_final: 0.7283 (mmm) REVERT: D 383 ASP cc_start: 0.7589 (t0) cc_final: 0.7212 (t0) REVERT: D 385 SER cc_start: 0.8911 (t) cc_final: 0.8464 (p) REVERT: E 47 ASP cc_start: 0.8591 (t0) cc_final: 0.8295 (t0) REVERT: E 61 LYS cc_start: 0.9634 (mttt) cc_final: 0.9256 (mttm) REVERT: E 415 LEU cc_start: 0.9132 (tp) cc_final: 0.8866 (tp) REVERT: F 54 ASP cc_start: 0.8494 (m-30) cc_final: 0.7825 (p0) REVERT: F 314 ILE cc_start: 0.9054 (tt) cc_final: 0.8711 (pt) REVERT: F 323 MET cc_start: 0.7665 (mmm) cc_final: 0.7399 (mmm) REVERT: F 393 MET cc_start: 0.8695 (mmm) cc_final: 0.8400 (mmm) REVERT: G 91 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8660 (m) REVERT: G 126 GLU cc_start: 0.8713 (pt0) cc_final: 0.8369 (pt0) REVERT: G 323 MET cc_start: 0.7638 (mmm) cc_final: 0.7294 (mmm) REVERT: G 383 ASP cc_start: 0.7609 (t0) cc_final: 0.7220 (t0) REVERT: G 385 SER cc_start: 0.8912 (t) cc_final: 0.8465 (p) REVERT: H 47 ASP cc_start: 0.8602 (t0) cc_final: 0.8305 (t0) REVERT: H 61 LYS cc_start: 0.9631 (mttt) cc_final: 0.9255 (mttm) REVERT: H 415 LEU cc_start: 0.9125 (tp) cc_final: 0.8856 (tp) REVERT: I 54 ASP cc_start: 0.8487 (m-30) cc_final: 0.7814 (p0) REVERT: I 314 ILE cc_start: 0.9063 (tt) cc_final: 0.8713 (pt) REVERT: I 323 MET cc_start: 0.7668 (mmm) cc_final: 0.7407 (mmm) REVERT: I 393 MET cc_start: 0.8695 (mmm) cc_final: 0.8403 (mmm) REVERT: J 91 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8662 (m) REVERT: J 126 GLU cc_start: 0.8711 (pt0) cc_final: 0.8372 (pt0) REVERT: J 323 MET cc_start: 0.7632 (mmm) cc_final: 0.7283 (mmm) REVERT: J 383 ASP cc_start: 0.7604 (t0) cc_final: 0.7218 (t0) REVERT: J 385 SER cc_start: 0.8911 (t) cc_final: 0.8462 (p) REVERT: K 47 ASP cc_start: 0.8588 (t0) cc_final: 0.8297 (t0) REVERT: K 61 LYS cc_start: 0.9632 (mttt) cc_final: 0.9253 (mttm) REVERT: K 393 MET cc_start: 0.8763 (mmm) cc_final: 0.8399 (mtp) REVERT: L 54 ASP cc_start: 0.8492 (m-30) cc_final: 0.7809 (p0) REVERT: L 314 ILE cc_start: 0.9067 (tt) cc_final: 0.8713 (pt) REVERT: L 323 MET cc_start: 0.7667 (mmm) cc_final: 0.7401 (mmm) REVERT: L 391 MET cc_start: 0.9410 (tpp) cc_final: 0.9050 (tpt) REVERT: L 393 MET cc_start: 0.8708 (mmm) cc_final: 0.8325 (mmm) outliers start: 193 outliers final: 170 residues processed: 530 average time/residue: 0.4217 time to fit residues: 394.2651 Evaluate side-chains 544 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 370 time to evaluate : 4.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 301 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 419 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 229 ILE Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 298 ILE Chi-restraints excluded: chain G residue 301 LEU Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 337 THR Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 312 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 344 LEU Chi-restraints excluded: chain H residue 401 SER Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 289 ASP Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 64 SER Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 298 ILE Chi-restraints excluded: chain J residue 301 LEU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 337 THR Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 378 MET Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain K residue 419 MET Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 312 LEU Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 2.9990 chunk 454 optimal weight: 9.9990 chunk 414 optimal weight: 0.9980 chunk 441 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 chunk 346 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 399 optimal weight: 4.9990 chunk 417 optimal weight: 9.9990 chunk 440 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39312 Z= 0.193 Angle : 0.621 15.049 53400 Z= 0.291 Chirality : 0.043 0.161 6060 Planarity : 0.004 0.053 6888 Dihedral : 4.277 17.386 5280 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.25 % Allowed : 15.42 % Favored : 80.33 % 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: 0.69 (0.13), residues: 4908 helix: 1.93 (0.12), residues: 2244 sheet: -1.00 (0.19), residues: 660 loop : -0.68 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 259 HIS 0.003 0.001 HIS D 60 PHE 0.027 0.001 PHE K 76 TYR 0.011 0.001 TYR E 125 ARG 0.002 0.000 ARG F 381 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 400 time to evaluate : 4.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8658 (m) REVERT: A 126 GLU cc_start: 0.8690 (pt0) cc_final: 0.8348 (pt0) REVERT: A 323 MET cc_start: 0.7629 (mmm) cc_final: 0.7288 (mmm) REVERT: A 383 ASP cc_start: 0.7599 (t0) cc_final: 0.7316 (t0) REVERT: A 385 SER cc_start: 0.8890 (t) cc_final: 0.8422 (p) REVERT: A 391 MET cc_start: 0.9572 (tpp) cc_final: 0.9362 (tpp) REVERT: B 47 ASP cc_start: 0.8579 (t0) cc_final: 0.8272 (t0) REVERT: B 61 LYS cc_start: 0.9643 (mttt) cc_final: 0.9267 (mttm) REVERT: B 240 MET cc_start: 0.9440 (tpp) cc_final: 0.9162 (mmp) REVERT: B 321 LEU cc_start: 0.9192 (tp) cc_final: 0.8833 (tp) REVERT: B 323 MET cc_start: 0.7857 (mmm) cc_final: 0.7614 (mmm) REVERT: C 54 ASP cc_start: 0.8475 (m-30) cc_final: 0.7795 (p0) REVERT: C 314 ILE cc_start: 0.9014 (tt) cc_final: 0.8656 (pt) REVERT: C 393 MET cc_start: 0.8576 (mmm) cc_final: 0.8309 (mmm) REVERT: D 91 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8659 (m) REVERT: D 126 GLU cc_start: 0.8692 (pt0) cc_final: 0.8389 (pt0) REVERT: D 323 MET cc_start: 0.7615 (mmm) cc_final: 0.7273 (mmm) REVERT: D 383 ASP cc_start: 0.7554 (t0) cc_final: 0.7284 (t0) REVERT: D 385 SER cc_start: 0.8883 (t) cc_final: 0.8409 (p) REVERT: E 47 ASP cc_start: 0.8569 (t0) cc_final: 0.8263 (t0) REVERT: E 61 LYS cc_start: 0.9644 (mttt) cc_final: 0.9269 (mttm) REVERT: E 321 LEU cc_start: 0.9199 (tp) cc_final: 0.8825 (tp) REVERT: E 323 MET cc_start: 0.7869 (mmm) cc_final: 0.7626 (mmm) REVERT: F 54 ASP cc_start: 0.8512 (m-30) cc_final: 0.7900 (p0) REVERT: F 314 ILE cc_start: 0.8994 (tt) cc_final: 0.8645 (pt) REVERT: F 393 MET cc_start: 0.8573 (mmm) cc_final: 0.8302 (mmm) REVERT: G 91 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8659 (m) REVERT: G 126 GLU cc_start: 0.8697 (pt0) cc_final: 0.8391 (pt0) REVERT: G 323 MET cc_start: 0.7623 (mmm) cc_final: 0.7283 (mmm) REVERT: G 383 ASP cc_start: 0.7576 (t0) cc_final: 0.7296 (t0) REVERT: G 385 SER cc_start: 0.8886 (t) cc_final: 0.8408 (p) REVERT: H 47 ASP cc_start: 0.8578 (t0) cc_final: 0.8272 (t0) REVERT: H 61 LYS cc_start: 0.9643 (mttt) cc_final: 0.9266 (mttm) REVERT: H 321 LEU cc_start: 0.9201 (tp) cc_final: 0.8839 (tp) REVERT: H 323 MET cc_start: 0.7871 (mmm) cc_final: 0.7627 (mmm) REVERT: I 54 ASP cc_start: 0.8466 (m-30) cc_final: 0.7794 (p0) REVERT: I 314 ILE cc_start: 0.9017 (tt) cc_final: 0.8661 (pt) REVERT: I 393 MET cc_start: 0.8530 (mmm) cc_final: 0.8158 (mmm) REVERT: J 91 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8664 (m) REVERT: J 126 GLU cc_start: 0.8694 (pt0) cc_final: 0.8392 (pt0) REVERT: J 323 MET cc_start: 0.7613 (mmm) cc_final: 0.7271 (mmm) REVERT: J 383 ASP cc_start: 0.7573 (t0) cc_final: 0.7298 (t0) REVERT: J 385 SER cc_start: 0.8886 (t) cc_final: 0.8412 (p) REVERT: K 47 ASP cc_start: 0.8570 (t0) cc_final: 0.8262 (t0) REVERT: K 61 LYS cc_start: 0.9642 (mttt) cc_final: 0.9264 (mttm) REVERT: K 321 LEU cc_start: 0.9200 (tp) cc_final: 0.8839 (tp) REVERT: K 323 MET cc_start: 0.7871 (mmm) cc_final: 0.7627 (mmm) REVERT: K 393 MET cc_start: 0.8754 (mmm) cc_final: 0.8400 (mtp) REVERT: L 54 ASP cc_start: 0.8467 (m-30) cc_final: 0.7791 (p0) REVERT: L 314 ILE cc_start: 0.9024 (tt) cc_final: 0.8658 (pt) REVERT: L 393 MET cc_start: 0.8586 (mmm) cc_final: 0.8115 (mmm) outliers start: 174 outliers final: 152 residues processed: 512 average time/residue: 0.4137 time to fit residues: 373.9026 Evaluate side-chains 540 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 384 time to evaluate : 4.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 344 LEU Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain E residue 419 MET Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ASP Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 289 ASP Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 79 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 243 VAL Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 344 LEU Chi-restraints excluded: chain H residue 401 SER Chi-restraints excluded: chain H residue 419 MET Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 64 SER Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 281 ASP Chi-restraints excluded: chain I residue 289 ASP Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 344 LEU Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain I residue 433 VAL Chi-restraints excluded: chain J residue 67 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 270 VAL Chi-restraints excluded: chain J residue 289 ASP Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 344 LEU Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain J residue 408 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 230 LEU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 243 VAL Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain K residue 425 VAL Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 243 VAL Chi-restraints excluded: chain L residue 270 VAL Chi-restraints excluded: chain L residue 281 ASP Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 344 LEU Chi-restraints excluded: chain L residue 385 SER Chi-restraints excluded: chain L residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 290 optimal weight: 1.9990 chunk 467 optimal weight: 8.9990 chunk 285 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 324 optimal weight: 3.9990 chunk 490 optimal weight: 0.9990 chunk 451 optimal weight: 0.2980 chunk 390 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 301 optimal weight: 2.9990 chunk 239 optimal weight: 0.0370 overall best weight: 1.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 39312 Z= 0.156 Angle : 0.624 15.444 53400 Z= 0.286 Chirality : 0.042 0.147 6060 Planarity : 0.004 0.061 6888 Dihedral : 4.169 18.035 5280 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.98 % Allowed : 16.98 % Favored : 80.03 % 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 (0.13), residues: 4908 helix: 2.07 (0.12), residues: 2220 sheet: -0.80 (0.19), residues: 660 loop : -0.70 (0.15), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 222 HIS 0.003 0.001 HIS C 103 PHE 0.023 0.001 PHE H 76 TYR 0.009 0.001 TYR G 303 ARG 0.003 0.000 ARG B 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9816 Ramachandran restraints generated. 4908 Oldfield, 0 Emsley, 4908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 428 time to evaluate : 4.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8664 (m) REVERT: A 125 TYR cc_start: 0.9231 (t80) cc_final: 0.8709 (t80) REVERT: A 126 GLU cc_start: 0.8658 (pt0) cc_final: 0.8417 (pt0) REVERT: A 323 MET cc_start: 0.7580 (mmm) cc_final: 0.7241 (mmm) REVERT: A 383 ASP cc_start: 0.7447 (t0) cc_final: 0.7106 (t0) REVERT: A 385 SER cc_start: 0.8843 (t) cc_final: 0.8392 (p) REVERT: A 391 MET cc_start: 0.9580 (tpp) cc_final: 0.9357 (tpp) REVERT: B 47 ASP cc_start: 0.8519 (t0) cc_final: 0.8092 (t0) REVERT: B 125 TYR cc_start: 0.9107 (t80) cc_final: 0.8745 (t80) REVERT: B 240 MET cc_start: 0.9447 (tpp) cc_final: 0.9196 (mmp) REVERT: B 321 LEU cc_start: 0.9146 (tp) cc_final: 0.8790 (tp) REVERT: B 323 MET cc_start: 0.8243 (mmm) cc_final: 0.7724 (mmm) REVERT: C 54 ASP cc_start: 0.8478 (m-30) cc_final: 0.7848 (p0) REVERT: C 125 TYR cc_start: 0.9303 (t80) cc_final: 0.8627 (t80) REVERT: C 270 VAL cc_start: 0.9002 (t) cc_final: 0.8586 (p) REVERT: C 314 ILE cc_start: 0.8984 (tt) cc_final: 0.8597 (pt) REVERT: C 393 MET cc_start: 0.8353 (mmm) cc_final: 0.8060 (mmm) REVERT: D 91 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8661 (m) REVERT: D 125 TYR cc_start: 0.9262 (t80) cc_final: 0.8739 (t80) REVERT: D 126 GLU cc_start: 0.8659 (pt0) cc_final: 0.8391 (pt0) REVERT: D 323 MET cc_start: 0.7560 (mmm) cc_final: 0.7217 (mmm) REVERT: D 383 ASP cc_start: 0.7419 (t0) cc_final: 0.7089 (t0) REVERT: D 385 SER cc_start: 0.8835 (t) cc_final: 0.8390 (p) REVERT: E 47 ASP cc_start: 0.8505 (t0) cc_final: 0.8081 (t0) REVERT: E 125 TYR cc_start: 0.9109 (t80) cc_final: 0.8749 (t80) REVERT: E 289 ASP cc_start: 0.8096 (t0) cc_final: 0.7864 (p0) REVERT: E 321 LEU cc_start: 0.9161 (tp) cc_final: 0.8787 (tp) REVERT: E 323 MET cc_start: 0.8241 (mmm) cc_final: 0.7725 (mmm) REVERT: F 54 ASP cc_start: 0.8491 (m-30) cc_final: 0.7868 (p0) REVERT: F 125 TYR cc_start: 0.9302 (t80) cc_final: 0.8631 (t80) REVERT: F 270 VAL cc_start: 0.8991 (t) cc_final: 0.8577 (p) REVERT: F 314 ILE cc_start: 0.8956 (tt) cc_final: 0.8581 (pt) REVERT: G 91 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8666 (m) REVERT: G 125 TYR cc_start: 0.9263 (t80) cc_final: 0.8741 (t80) REVERT: G 126 GLU cc_start: 0.8665 (pt0) cc_final: 0.8393 (pt0) REVERT: G 323 MET cc_start: 0.7578 (mmm) cc_final: 0.7230 (mmm) REVERT: G 383 ASP cc_start: 0.7437 (t0) cc_final: 0.7103 (t0) REVERT: G 385 SER cc_start: 0.8835 (t) cc_final: 0.8387 (p) REVERT: H 47 ASP cc_start: 0.8517 (t0) cc_final: 0.8093 (t0) REVERT: H 125 TYR cc_start: 0.9104 (t80) cc_final: 0.8710 (t80) REVERT: H 289 ASP cc_start: 0.8095 (t0) cc_final: 0.7862 (p0) REVERT: H 321 LEU cc_start: 0.9163 (tp) cc_final: 0.8802 (tp) REVERT: H 323 MET cc_start: 0.8327 (mmm) cc_final: 0.7793 (mmm) REVERT: I 54 ASP cc_start: 0.8484 (m-30) cc_final: 0.7852 (p0) REVERT: I 125 TYR cc_start: 0.9303 (t80) cc_final: 0.8625 (t80) REVERT: I 270 VAL cc_start: 0.8990 (t) cc_final: 0.8581 (p) REVERT: I 314 ILE cc_start: 0.8978 (tt) cc_final: 0.8590 (pt) REVERT: J 91 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8668 (m) REVERT: J 125 TYR cc_start: 0.9266 (t80) cc_final: 0.8744 (t80) REVERT: J 126 GLU cc_start: 0.8661 (pt0) cc_final: 0.8393 (pt0) REVERT: J 323 MET cc_start: 0.7565 (mmm) cc_final: 0.7228 (mmm) REVERT: J 383 ASP cc_start: 0.7437 (t0) cc_final: 0.7105 (t0) REVERT: J 385 SER cc_start: 0.8829 (t) cc_final: 0.8385 (p) REVERT: K 47 ASP cc_start: 0.8502 (t0) cc_final: 0.8172 (t0) REVERT: K 125 TYR cc_start: 0.9101 (t80) cc_final: 0.8711 (t80) REVERT: K 321 LEU cc_start: 0.9162 (tp) cc_final: 0.8807 (tp) REVERT: K 323 MET cc_start: 0.8327 (mmm) cc_final: 0.7788 (mmm) REVERT: K 393 MET cc_start: 0.8732 (mmm) cc_final: 0.8420 (mtp) REVERT: L 54 ASP cc_start: 0.8488 (m-30) cc_final: 0.7854 (p0) REVERT: L 125 TYR cc_start: 0.9295 (t80) cc_final: 0.8582 (t80) REVERT: L 270 VAL cc_start: 0.8991 (t) cc_final: 0.8590 (p) REVERT: L 314 ILE cc_start: 0.8992 (tt) cc_final: 0.8605 (pt) REVERT: L 393 MET cc_start: 0.8648 (mmm) cc_final: 0.8169 (mmm) outliers start: 122 outliers final: 80 residues processed: 518 average time/residue: 0.4438 time to fit residues: 407.1795 Evaluate side-chains 493 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 409 time to evaluate : 4.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 401 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 401 SER Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 341 ILE Chi-restraints excluded: chain E residue 344 LEU Chi-restraints excluded: chain E residue 401 SER Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 243 VAL Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain G residue 401 SER Chi-restraints excluded: chain H residue 62 MET Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 67 THR Chi-restraints excluded: chain H residue 164 VAL Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 231 LEU Chi-restraints excluded: chain H residue 337 THR Chi-restraints excluded: chain H residue 341 ILE Chi-restraints excluded: chain H residue 344 LEU Chi-restraints excluded: chain H residue 401 SER Chi-restraints excluded: chain I residue 50 LEU Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain I residue 337 THR Chi-restraints excluded: chain I residue 385 SER Chi-restraints excluded: chain I residue 390 LEU Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 243 VAL Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain J residue 401 SER Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 180 GLU Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 337 THR Chi-restraints excluded: chain K residue 341 ILE Chi-restraints excluded: chain K residue 344 LEU Chi-restraints excluded: chain K residue 401 SER Chi-restraints excluded: chain K residue 425 VAL Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 289 ASP Chi-restraints excluded: chain L residue 321 LEU Chi-restraints excluded: chain L residue 337 THR Chi-restraints excluded: chain L residue 385 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 1.9990 chunk 415 optimal weight: 5.9990 chunk 119 optimal weight: 0.0060 chunk 359 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 390 optimal weight: 1.9990 chunk 163 optimal weight: 20.0000 chunk 401 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.082539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.062412 restraints weight = 108299.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.064720 restraints weight = 56438.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.066227 restraints weight = 37771.436| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 39312 Z= 0.160 Angle : 0.628 15.884 53400 Z= 0.286 Chirality : 0.042 0.145 6060 Planarity : 0.004 0.056 6888 Dihedral : 4.095 16.651 5280 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.08 % Allowed : 18.13 % Favored : 79.79 % 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: 0.83 (0.13), residues: 4908 helix: 2.02 (0.12), residues: 2232 sheet: -0.71 (0.19), residues: 660 loop : -0.67 (0.15), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 196 HIS 0.002 0.001 HIS L 103 PHE 0.024 0.001 PHE K 76 TYR 0.009 0.001 TYR J 303 ARG 0.002 0.000 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7639.22 seconds wall clock time: 139 minutes 47.48 seconds (8387.48 seconds total)