Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 24 11:31:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjt_4567/08_2023/6qjt_4567.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjt_4567/08_2023/6qjt_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_4567/08_2023/6qjt_4567.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjt_4567/08_2023/6qjt_4567.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjt_4567/08_2023/6qjt_4567.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjt_4567/08_2023/6qjt_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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 17.77, per 1000 atoms: 0.46 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: 14.11 Conformation dependent library (CDL) restraints added in 5.8 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: 3.62 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: 12.09 Time building geometry restraints manager: 15.19 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: 0.140 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: 0.040 Extract box with map and model: 4.320 Check model and map are aligned: 0.570 Set scattering table: 0.340 Process input model: 89.020 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.230 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:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.240 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 4.374 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 outliers start: 0 outliers final: 0 residues processed: 919 average time/residue: 0.5343 time to fit residues: 787.6661 Evaluate side-chains 412 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 4.067 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4381 ------------------------------------------------------------------------------- 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: 6.9990 chunk 206 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 251 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 385 optimal weight: 0.0570 chunk 149 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 287 optimal weight: 30.0000 chunk 446 optimal weight: 6.9990 overall best weight: 2.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 ASN A 320 GLN ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN C 320 GLN D 160 ASN D 320 GLN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 GLN F 320 GLN G 160 ASN G 320 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 320 GLN I 320 GLN J 160 ASN 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2353 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= 0.202 Angle : 0.606 10.115 53400 Z= 0.300 Chirality : 0.043 0.144 6060 Planarity : 0.005 0.064 6888 Dihedral : 4.702 21.606 5280 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer Outliers : 3.40 % 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 *********************** 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 662 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 523 time to evaluate : 4.637 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 outliers start: 139 outliers final: 95 residues processed: 618 average time/residue: 0.4737 time to fit residues: 493.5611 Evaluate side-chains 460 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 365 time to evaluate : 4.415 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 0 residues processed: 95 average time/residue: 0.3330 time to fit residues: 66.4162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 371 optimal weight: 7.9990 chunk 304 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 447 optimal weight: 2.9990 chunk 483 optimal weight: 10.0000 chunk 398 optimal weight: 6.9990 chunk 443 optimal weight: 0.6980 chunk 152 optimal weight: 6.9990 chunk 359 optimal weight: 4.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN D 127 ASN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN G 127 ASN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 127 ASN J 127 ASN ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 127 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2908 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= 0.254 Angle : 0.610 9.161 53400 Z= 0.300 Chirality : 0.043 0.135 6060 Planarity : 0.005 0.069 6888 Dihedral : 4.500 19.766 5280 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 2.22 % 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: -0.22 (0.12), residues: 4908 helix: 1.03 (0.11), residues: 2232 sheet: -1.64 (0.18), residues: 660 loop : -0.88 (0.15), residues: 2016 *********************** 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 495 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 404 time to evaluate : 4.987 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 outliers start: 91 outliers final: 55 residues processed: 479 average time/residue: 0.4527 time to fit residues: 372.2797 Evaluate side-chains 420 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 365 time to evaluate : 4.384 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.3320 time to fit residues: 40.7152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 49 optimal weight: 30.0000 chunk 213 optimal weight: 30.0000 chunk 300 optimal weight: 10.0000 chunk 449 optimal weight: 7.9990 chunk 475 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 425 optimal weight: 20.0000 chunk 128 optimal weight: 0.6980 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 ASN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 127 ASN ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 39312 Z= 0.317 Angle : 0.637 10.155 53400 Z= 0.312 Chirality : 0.043 0.134 6060 Planarity : 0.004 0.067 6888 Dihedral : 4.440 18.778 5280 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 4908 helix: 1.39 (0.11), residues: 2244 sheet: -1.42 (0.18), residues: 660 loop : -0.65 (0.15), residues: 2004 *********************** 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 460 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 399 time to evaluate : 4.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 37 residues processed: 436 average time/residue: 0.4531 time to fit residues: 336.5035 Evaluate side-chains 385 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 348 time to evaluate : 4.182 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.3342 time to fit residues: 29.3695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 6 optimal weight: 30.0000 chunk 354 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 405 optimal weight: 5.9990 chunk 328 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 chunk 426 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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** ** C 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 203 HIS ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 ASN G 203 HIS ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 160 ASN J 203 HIS ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.041 39312 Z= 0.392 Angle : 0.689 10.562 53400 Z= 0.337 Chirality : 0.044 0.140 6060 Planarity : 0.004 0.063 6888 Dihedral : 4.510 19.398 5280 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 2.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 4908 helix: 1.46 (0.11), residues: 2256 sheet: -1.31 (0.18), residues: 660 loop : -0.75 (0.15), residues: 1992 *********************** 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 435 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 351 time to evaluate : 4.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 60 residues processed: 418 average time/residue: 0.4506 time to fit residues: 328.1196 Evaluate side-chains 402 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 342 time to evaluate : 4.385 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.3405 time to fit residues: 45.0002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 10.0000 chunk 428 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 chunk 117 optimal weight: 30.0000 chunk 476 optimal weight: 8.9990 chunk 395 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 157 optimal weight: 6.9990 chunk 249 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** 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: 0.3736 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= 0.365 Angle : 0.676 10.673 53400 Z= 0.329 Chirality : 0.045 0.185 6060 Planarity : 0.004 0.060 6888 Dihedral : 4.519 19.032 5280 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 0.81 % 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: 0.28 (0.13), residues: 4908 helix: 1.46 (0.11), residues: 2256 sheet: -1.23 (0.18), residues: 660 loop : -0.73 (0.15), residues: 1992 *********************** 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 397 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 364 time to evaluate : 4.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 13 residues processed: 385 average time/residue: 0.4477 time to fit residues: 298.8389 Evaluate side-chains 346 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 333 time to evaluate : 4.249 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3400 time to fit residues: 14.1125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 271 optimal weight: 8.9990 chunk 347 optimal weight: 6.9990 chunk 269 optimal weight: 10.0000 chunk 400 optimal weight: 6.9990 chunk 265 optimal weight: 5.9990 chunk 474 optimal weight: 7.9990 chunk 296 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 339 GLN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 339 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 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: 0.8585 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 39312 Z= 0.248 Angle : 0.624 10.446 53400 Z= 0.300 Chirality : 0.043 0.169 6060 Planarity : 0.004 0.057 6888 Dihedral : 4.405 17.828 5280 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4908 helix: 1.65 (0.11), residues: 2256 sheet: -1.11 (0.19), residues: 660 loop : -0.67 (0.15), residues: 1992 *********************** 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 429 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 393 time to evaluate : 4.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 415 average time/residue: 0.4441 time to fit residues: 318.9579 Evaluate side-chains 371 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 350 time to evaluate : 4.648 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.3376 time to fit residues: 19.4262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 30.0000 chunk 189 optimal weight: 0.6980 chunk 283 optimal weight: 8.9990 chunk 142 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 301 optimal weight: 0.1980 chunk 323 optimal weight: 9.9990 chunk 234 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 372 optimal weight: 1.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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: 0.8550 moved from start: 0.3883 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= 0.173 Angle : 0.626 10.629 53400 Z= 0.292 Chirality : 0.042 0.154 6060 Planarity : 0.004 0.055 6888 Dihedral : 4.287 16.429 5280 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer Outliers : 0.66 % 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: 0.64 (0.13), residues: 4908 helix: 1.79 (0.12), residues: 2232 sheet: -0.94 (0.19), residues: 660 loop : -0.60 (0.15), residues: 2016 *********************** 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 417 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 390 time to evaluate : 4.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 401 average time/residue: 0.4476 time to fit residues: 313.7455 Evaluate side-chains 379 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 364 time to evaluate : 4.059 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3237 time to fit residues: 14.7958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 3.9990 chunk 454 optimal weight: 1.9990 chunk 414 optimal weight: 7.9990 chunk 441 optimal weight: 7.9990 chunk 265 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 346 optimal weight: 20.0000 chunk 135 optimal weight: 9.9990 chunk 399 optimal weight: 7.9990 chunk 417 optimal weight: 5.9990 chunk 440 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 39312 Z= 0.234 Angle : 0.637 14.736 53400 Z= 0.300 Chirality : 0.043 0.151 6060 Planarity : 0.004 0.056 6888 Dihedral : 4.234 16.854 5280 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.13), residues: 4908 helix: 1.80 (0.12), residues: 2232 sheet: -0.86 (0.21), residues: 516 loop : -0.57 (0.15), residues: 2160 *********************** 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 380 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 360 time to evaluate : 4.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 370 average time/residue: 0.4493 time to fit residues: 291.1640 Evaluate side-chains 353 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 344 time to evaluate : 4.453 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3326 time to fit residues: 11.6818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 290 optimal weight: 9.9990 chunk 467 optimal weight: 8.9990 chunk 285 optimal weight: 20.0000 chunk 221 optimal weight: 8.9990 chunk 324 optimal weight: 7.9990 chunk 490 optimal weight: 7.9990 chunk 451 optimal weight: 7.9990 chunk 390 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 301 optimal weight: 0.0670 chunk 239 optimal weight: 1.9990 overall best weight: 5.2126 ------------------------------------------------------------------------------- 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: 0.8581 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 39312 Z= 0.277 Angle : 0.674 16.220 53400 Z= 0.316 Chirality : 0.044 0.154 6060 Planarity : 0.004 0.057 6888 Dihedral : 4.277 17.184 5280 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 0.12 % 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: 0.76 (0.13), residues: 4908 helix: 1.88 (0.12), residues: 2232 sheet: -0.88 (0.21), residues: 516 loop : -0.58 (0.14), residues: 2160 ********************** 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 357 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 352 time to evaluate : 5.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 357 average time/residue: 0.4599 time to fit residues: 287.8100 Evaluate side-chains 347 residues out of total 4092 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 344 time to evaluate : 4.415 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3290 time to fit residues: 7.8612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 8.9990 chunk 415 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 359 optimal weight: 3.9990 chunk 57 optimal weight: 0.1980 chunk 108 optimal weight: 0.0980 chunk 390 optimal weight: 8.9990 chunk 163 optimal weight: 20.0000 chunk 401 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.082104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.062648 restraints weight = 107544.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.064966 restraints weight = 54477.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.066476 restraints weight = 35827.217| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.056 39312 Z= 0.165 Angle : 0.652 17.702 53400 Z= 0.298 Chirality : 0.042 0.134 6060 Planarity : 0.004 0.053 6888 Dihedral : 4.152 17.968 5280 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer Outliers : 0.17 % 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: 0.86 (0.13), residues: 4908 helix: 1.97 (0.12), residues: 2220 sheet: -0.51 (0.22), residues: 492 loop : -0.62 (0.15), residues: 2196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6904.84 seconds wall clock time: 127 minutes 2.69 seconds (7622.69 seconds total)