Starting phenix.real_space_refine on Wed Mar 20 13:17:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7j_29813/03_2024/8g7j_29813.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7j_29813/03_2024/8g7j_29813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7j_29813/03_2024/8g7j_29813.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7j_29813/03_2024/8g7j_29813.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7j_29813/03_2024/8g7j_29813.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7j_29813/03_2024/8g7j_29813.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.134 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 98 5.16 5 C 17227 2.51 5 N 4690 2.21 5 O 5446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27461 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain: "B" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain: "C" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain: "E" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain: "F" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Chain: "G" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3923 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 15, 'TRANS': 510} Time building chain proxies: 14.19, per 1000 atoms: 0.52 Number of scatterers: 27461 At special positions: 0 Unit cell: (165.933, 160.371, 89.919, 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 98 16.00 O 5446 8.00 N 4690 7.00 C 17227 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: 10.29 Conformation dependent library (CDL) restraints added in 5.5 seconds 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6720 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 28 sheets defined 58.4% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.987A pdb=" N LEU A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 62 through 77 removed outlier: 3.840A pdb=" N ILE A 67 " --> pdb=" O LYS A 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 107 removed outlier: 4.297A pdb=" N THR A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 133 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 254 through 267 Processing helix chain 'A' and resid 279 through 295 Processing helix chain 'A' and resid 337 through 355 Processing helix chain 'A' and resid 357 through 373 removed outlier: 3.578A pdb=" N LEU A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 409 removed outlier: 4.026A pdb=" N GLU A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'A' and resid 432 through 446 removed outlier: 3.503A pdb=" N ILE A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'A' and resid 496 through 516 Processing helix chain 'B' and resid 7 through 27 removed outlier: 3.982A pdb=" N LEU B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL B 27 " --> pdb=" O ASP B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.527A pdb=" N ILE B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 107 removed outlier: 4.406A pdb=" N THR B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 89 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 231 through 241 Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 279 through 295 Processing helix chain 'B' and resid 337 through 355 Processing helix chain 'B' and resid 357 through 373 removed outlier: 3.555A pdb=" N LEU B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 409 removed outlier: 4.118A pdb=" N GLU B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 421 through 426 Processing helix chain 'B' and resid 432 through 446 removed outlier: 3.505A pdb=" N ILE B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 496 through 516 Processing helix chain 'C' and resid 7 through 27 removed outlier: 3.988A pdb=" N LEU C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 58 Processing helix chain 'C' and resid 62 through 77 removed outlier: 3.794A pdb=" N ILE C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 107 removed outlier: 4.308A pdb=" N THR C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 133 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 153 through 168 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 231 through 241 Processing helix chain 'C' and resid 254 through 267 Processing helix chain 'C' and resid 279 through 295 Processing helix chain 'C' and resid 337 through 355 Processing helix chain 'C' and resid 357 through 373 removed outlier: 3.595A pdb=" N LEU C 371 " --> pdb=" O ARG C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 409 removed outlier: 4.078A pdb=" N GLU C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 421 through 426 Processing helix chain 'C' and resid 432 through 446 removed outlier: 3.504A pdb=" N ILE C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 460 through 470 Processing helix chain 'C' and resid 487 through 491 Processing helix chain 'C' and resid 496 through 516 Processing helix chain 'D' and resid 7 through 27 removed outlier: 3.980A pdb=" N LEU D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 58 Processing helix chain 'D' and resid 62 through 77 removed outlier: 3.817A pdb=" N ILE D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 107 removed outlier: 4.303A pdb=" N THR D 88 " --> pdb=" O GLY D 84 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR D 89 " --> pdb=" O ASP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 133 Processing helix chain 'D' and resid 138 through 150 Processing helix chain 'D' and resid 153 through 168 Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 231 through 241 Processing helix chain 'D' and resid 254 through 267 Processing helix chain 'D' and resid 279 through 295 Processing helix chain 'D' and resid 337 through 355 Processing helix chain 'D' and resid 357 through 373 removed outlier: 3.551A pdb=" N LEU D 371 " --> pdb=" O ARG D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 409 removed outlier: 4.099A pdb=" N GLU D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP D 393 " --> pdb=" O ASN D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 421 through 426 Processing helix chain 'D' and resid 432 through 446 Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 460 through 470 Processing helix chain 'D' and resid 487 through 491 Processing helix chain 'D' and resid 496 through 516 Processing helix chain 'E' and resid 7 through 27 removed outlier: 3.975A pdb=" N LEU E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 58 Processing helix chain 'E' and resid 62 through 77 removed outlier: 3.828A pdb=" N ILE E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE E 72 " --> pdb=" O GLY E 68 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 107 removed outlier: 4.373A pdb=" N THR E 88 " --> pdb=" O GLY E 84 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR E 89 " --> pdb=" O ASP E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 133 Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 153 through 168 Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 231 through 241 Processing helix chain 'E' and resid 254 through 267 Processing helix chain 'E' and resid 279 through 295 Processing helix chain 'E' and resid 337 through 355 Processing helix chain 'E' and resid 357 through 373 removed outlier: 3.570A pdb=" N LEU E 371 " --> pdb=" O ARG E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 409 removed outlier: 4.046A pdb=" N GLU E 390 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP E 393 " --> pdb=" O ASN E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 420 Processing helix chain 'E' and resid 421 through 426 Processing helix chain 'E' and resid 432 through 446 removed outlier: 3.984A pdb=" N ILE E 442 " --> pdb=" O GLY E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 458 Processing helix chain 'E' and resid 460 through 470 Processing helix chain 'E' and resid 487 through 491 Processing helix chain 'E' and resid 496 through 516 Processing helix chain 'F' and resid 7 through 27 removed outlier: 3.971A pdb=" N LEU F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 58 Processing helix chain 'F' and resid 62 through 77 removed outlier: 3.835A pdb=" N ILE F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE F 72 " --> pdb=" O GLY F 68 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 107 removed outlier: 3.837A pdb=" N THR F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 133 Processing helix chain 'F' and resid 138 through 150 Processing helix chain 'F' and resid 153 through 168 Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 231 through 241 Processing helix chain 'F' and resid 254 through 267 Processing helix chain 'F' and resid 279 through 295 Processing helix chain 'F' and resid 337 through 355 Processing helix chain 'F' and resid 357 through 373 removed outlier: 3.595A pdb=" N LEU F 371 " --> pdb=" O ARG F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 409 removed outlier: 4.100A pdb=" N GLU F 390 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP F 393 " --> pdb=" O ASN F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 Processing helix chain 'F' and resid 421 through 426 Processing helix chain 'F' and resid 432 through 446 removed outlier: 3.500A pdb=" N ILE F 442 " --> pdb=" O GLY F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 458 Processing helix chain 'F' and resid 460 through 470 Processing helix chain 'F' and resid 487 through 491 Processing helix chain 'F' and resid 496 through 516 Processing helix chain 'G' and resid 7 through 27 removed outlier: 3.978A pdb=" N LEU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 58 Processing helix chain 'G' and resid 62 through 77 removed outlier: 3.811A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 72 " --> pdb=" O GLY G 68 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 107 removed outlier: 4.310A pdb=" N THR G 88 " --> pdb=" O GLY G 84 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR G 89 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 133 Processing helix chain 'G' and resid 138 through 150 Processing helix chain 'G' and resid 153 through 168 Processing helix chain 'G' and resid 199 through 203 Processing helix chain 'G' and resid 231 through 241 Processing helix chain 'G' and resid 254 through 267 Processing helix chain 'G' and resid 279 through 295 Processing helix chain 'G' and resid 337 through 355 Processing helix chain 'G' and resid 357 through 373 removed outlier: 3.586A pdb=" N LEU G 371 " --> pdb=" O ARG G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 384 through 409 removed outlier: 4.148A pdb=" N GLU G 390 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP G 393 " --> pdb=" O ASN G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 420 Processing helix chain 'G' and resid 421 through 426 Processing helix chain 'G' and resid 432 through 446 removed outlier: 3.508A pdb=" N ILE G 442 " --> pdb=" O GLY G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 458 Processing helix chain 'G' and resid 460 through 470 Processing helix chain 'G' and resid 487 through 491 Processing helix chain 'G' and resid 496 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48 removed outlier: 6.540A pdb=" N ILE A 37 " --> pdb=" O VAL G 520 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLU G 522 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 173 through 177 removed outlier: 6.535A pdb=" N THR A 174 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL A 380 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS A 176 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLU A 189 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY A 334 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 319 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS A 318 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR A 217 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY A 320 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N VAL A 246 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR A 217 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE A 248 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU A 219 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 245 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N VAL A 274 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE A 247 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 478 Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 6 Processing sheet with id=AA7, first strand: chain 'B' and resid 173 through 177 removed outlier: 6.674A pdb=" N THR B 174 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL B 380 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS B 176 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLU B 189 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLY B 334 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 319 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS B 318 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR B 217 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY B 320 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 245 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL B 274 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE B 247 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA9, first strand: chain 'B' and resid 475 through 478 Processing sheet with id=AB1, first strand: chain 'C' and resid 2 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 173 through 177 removed outlier: 6.545A pdb=" N THR C 174 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL C 380 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS C 176 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLU C 189 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY C 334 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 319 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TYR C 217 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY C 320 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL C 246 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR C 217 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE C 248 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU C 219 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU C 245 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL C 274 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE C 247 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AB4, first strand: chain 'C' and resid 475 through 478 Processing sheet with id=AB5, first strand: chain 'D' and resid 2 through 6 Processing sheet with id=AB6, first strand: chain 'D' and resid 173 through 177 removed outlier: 6.551A pdb=" N THR D 174 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL D 380 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LYS D 176 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLU D 189 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLY D 334 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 319 " --> pdb=" O GLY D 334 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS D 318 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR D 217 " --> pdb=" O LYS D 318 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY D 320 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N VAL D 246 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR D 217 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE D 248 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU D 219 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU D 245 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL D 274 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE D 247 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AB8, first strand: chain 'D' and resid 475 through 478 Processing sheet with id=AB9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AC1, first strand: chain 'E' and resid 173 through 177 removed outlier: 6.517A pdb=" N THR E 174 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL E 380 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS E 176 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N GLU E 189 " --> pdb=" O LYS E 333 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY E 334 " --> pdb=" O VAL E 319 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL E 319 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS E 318 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR E 217 " --> pdb=" O LYS E 318 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY E 320 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N VAL E 246 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR E 217 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE E 248 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU E 219 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU E 245 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL E 274 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE E 247 " --> pdb=" O VAL E 274 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 410 through 412 Processing sheet with id=AC3, first strand: chain 'E' and resid 475 through 478 Processing sheet with id=AC4, first strand: chain 'F' and resid 2 through 6 Processing sheet with id=AC5, first strand: chain 'F' and resid 173 through 177 removed outlier: 6.527A pdb=" N THR F 174 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL F 380 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS F 176 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLU F 189 " --> pdb=" O LYS F 333 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY F 334 " --> pdb=" O VAL F 319 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL F 319 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS F 318 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR F 217 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY F 320 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL F 246 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TYR F 217 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE F 248 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU F 219 " --> pdb=" O ILE F 248 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU F 245 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL F 274 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE F 247 " --> pdb=" O VAL F 274 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 410 through 412 Processing sheet with id=AC7, first strand: chain 'F' and resid 475 through 478 Processing sheet with id=AC8, first strand: chain 'G' and resid 173 through 177 removed outlier: 6.580A pdb=" N THR G 174 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL G 380 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS G 176 " --> pdb=" O VAL G 380 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLU G 189 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY G 334 " --> pdb=" O VAL G 319 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL G 319 " --> pdb=" O GLY G 334 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLU G 321 " --> pdb=" O GLN G 214 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLN G 214 " --> pdb=" O GLU G 321 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE G 323 " --> pdb=" O GLU G 212 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU G 212 " --> pdb=" O ILE G 323 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL G 246 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR G 217 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE G 248 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU G 219 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU G 245 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL G 274 " --> pdb=" O LEU G 245 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE G 247 " --> pdb=" O VAL G 274 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 410 through 412 Processing sheet with id=AD1, first strand: chain 'G' and resid 475 through 478 1757 hydrogen bonds defined for protein. 5058 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: 9.41 Time building geometry restraints manager: 11.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 5415 1.31 - 1.44: 5220 1.44 - 1.56: 16830 1.56 - 1.69: 45 1.69 - 1.81: 175 Bond restraints: 27685 Sorted by residual: bond pdb=" CA ILE G 126 " pdb=" CB ILE G 126 " ideal model delta sigma weight residual 1.540 1.493 0.048 1.25e-02 6.40e+03 1.46e+01 bond pdb=" CA ILE B 126 " pdb=" CB ILE B 126 " ideal model delta sigma weight residual 1.540 1.493 0.048 1.25e-02 6.40e+03 1.45e+01 bond pdb=" CA ILE E 126 " pdb=" CB ILE E 126 " ideal model delta sigma weight residual 1.540 1.493 0.047 1.25e-02 6.40e+03 1.44e+01 bond pdb=" CA ILE F 126 " pdb=" CB ILE F 126 " ideal model delta sigma weight residual 1.540 1.493 0.047 1.25e-02 6.40e+03 1.44e+01 bond pdb=" CA ILE C 126 " pdb=" CB ILE C 126 " ideal model delta sigma weight residual 1.540 1.493 0.047 1.25e-02 6.40e+03 1.43e+01 ... (remaining 27680 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.07: 695 107.07 - 113.71: 15585 113.71 - 120.35: 12239 120.35 - 127.00: 8749 127.00 - 133.64: 77 Bond angle restraints: 37345 Sorted by residual: angle pdb=" N ILE E 231 " pdb=" CA ILE E 231 " pdb=" C ILE E 231 " ideal model delta sigma weight residual 113.43 103.34 10.09 1.09e+00 8.42e-01 8.57e+01 angle pdb=" N ILE G 231 " pdb=" CA ILE G 231 " pdb=" C ILE G 231 " ideal model delta sigma weight residual 113.43 103.34 10.09 1.09e+00 8.42e-01 8.57e+01 angle pdb=" N ILE B 231 " pdb=" CA ILE B 231 " pdb=" C ILE B 231 " ideal model delta sigma weight residual 113.43 103.34 10.09 1.09e+00 8.42e-01 8.56e+01 angle pdb=" N ILE C 231 " pdb=" CA ILE C 231 " pdb=" C ILE C 231 " ideal model delta sigma weight residual 113.43 103.35 10.08 1.09e+00 8.42e-01 8.55e+01 angle pdb=" N ILE A 231 " pdb=" CA ILE A 231 " pdb=" C ILE A 231 " ideal model delta sigma weight residual 113.43 103.35 10.08 1.09e+00 8.42e-01 8.55e+01 ... (remaining 37340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 16718 15.32 - 30.63: 387 30.63 - 45.95: 78 45.95 - 61.26: 54 61.26 - 76.58: 32 Dihedral angle restraints: 17269 sinusoidal: 6832 harmonic: 10437 Sorted by residual: dihedral pdb=" CA THR D 205 " pdb=" C THR D 205 " pdb=" N SER D 206 " pdb=" CA SER D 206 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA THR E 205 " pdb=" C THR E 205 " pdb=" N SER E 206 " pdb=" CA SER E 206 " ideal model delta harmonic sigma weight residual 180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" C ILE E 422 " pdb=" N ILE E 422 " pdb=" CA ILE E 422 " pdb=" CB ILE E 422 " ideal model delta harmonic sigma weight residual -122.00 -130.47 8.47 0 2.50e+00 1.60e-01 1.15e+01 ... (remaining 17266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2967 0.069 - 0.138: 1266 0.138 - 0.207: 289 0.207 - 0.276: 38 0.276 - 0.345: 11 Chirality restraints: 4571 Sorted by residual: chirality pdb=" CA ILE E 126 " pdb=" N ILE E 126 " pdb=" C ILE E 126 " pdb=" CB ILE E 126 " both_signs ideal model delta sigma weight residual False 2.43 2.09 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA ILE F 126 " pdb=" N ILE F 126 " pdb=" C ILE F 126 " pdb=" CB ILE F 126 " both_signs ideal model delta sigma weight residual False 2.43 2.09 0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" CA ILE D 126 " pdb=" N ILE D 126 " pdb=" C ILE D 126 " pdb=" CB ILE D 126 " both_signs ideal model delta sigma weight residual False 2.43 2.09 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 4568 not shown) Planarity restraints: 4809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 73 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.65e+00 pdb=" C GLN D 73 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN D 73 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP D 74 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 73 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C GLN E 73 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN E 73 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP E 74 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 73 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C GLN G 73 " -0.044 2.00e-02 2.50e+03 pdb=" O GLN G 73 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP G 74 " 0.015 2.00e-02 2.50e+03 ... (remaining 4806 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 9942 2.88 - 3.38: 27147 3.38 - 3.89: 44301 3.89 - 4.39: 50346 4.39 - 4.90: 82812 Nonbonded interactions: 214548 Sorted by model distance: nonbonded pdb=" NZ LYS E 176 " pdb=" OE1 GLU E 321 " model vdw 2.369 2.520 nonbonded pdb=" O ASN F 204 " pdb=" C THR F 205 " model vdw 2.402 3.270 nonbonded pdb=" OD2 ASP E 183 " pdb=" NZ LYS E 391 " model vdw 2.403 2.520 nonbonded pdb=" OD2 ASP A 215 " pdb=" NZ LYS A 243 " model vdw 2.403 2.520 nonbonded pdb=" NZ LYS G 170 " pdb=" OE1 GLU G 407 " model vdw 2.404 2.520 ... (remaining 214543 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.830 Check model and map are aligned: 0.370 Set scattering table: 0.260 Process input model: 70.570 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 89.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 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 : 0.015 0.084 27685 Z= 1.005 Angle : 1.457 10.093 37345 Z= 1.059 Chirality : 0.076 0.345 4571 Planarity : 0.007 0.027 4809 Dihedral : 9.299 76.575 10549 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 0.68 % Favored : 99.24 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 3668 helix: 0.11 (0.10), residues: 2065 sheet: 0.98 (0.21), residues: 553 loop : 0.11 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.006 TRP E 42 HIS 0.003 0.001 HIS F 241 PHE 0.012 0.002 PHE D 213 TYR 0.029 0.003 TYR B 217 ARG 0.004 0.000 ARG D 500 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 527 time to evaluate : 3.389 Fit side-chains REVERT: A 322 VAL cc_start: 0.7001 (t) cc_final: 0.6650 (p) REVERT: A 360 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7116 (mm-30) REVERT: A 487 MET cc_start: 0.7402 (mmt) cc_final: 0.7177 (mpp) REVERT: A 492 ILE cc_start: 0.7573 (mt) cc_final: 0.7318 (mt) REVERT: B 218 VAL cc_start: 0.6822 (t) cc_final: 0.6404 (p) REVERT: B 360 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7075 (mm-30) REVERT: B 464 ILE cc_start: 0.7224 (mm) cc_final: 0.7003 (mm) REVERT: C 218 VAL cc_start: 0.6690 (t) cc_final: 0.6434 (p) REVERT: C 360 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6787 (mm-30) REVERT: D 218 VAL cc_start: 0.6832 (t) cc_final: 0.6486 (p) REVERT: D 285 ASN cc_start: 0.6014 (m-40) cc_final: 0.5259 (t0) REVERT: D 360 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6762 (mm-30) REVERT: E 285 ASN cc_start: 0.5828 (m-40) cc_final: 0.5222 (t0) REVERT: E 307 ASN cc_start: 0.5077 (t0) cc_final: 0.4386 (m-40) REVERT: E 328 ASP cc_start: 0.6777 (t70) cc_final: 0.6506 (t70) REVERT: E 330 MET cc_start: 0.7502 (ttm) cc_final: 0.6991 (ttt) REVERT: E 360 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7152 (mm-30) REVERT: E 464 ILE cc_start: 0.7417 (mm) cc_final: 0.7160 (mm) REVERT: F 218 VAL cc_start: 0.6808 (t) cc_final: 0.6485 (p) REVERT: F 307 ASN cc_start: 0.5239 (t0) cc_final: 0.4653 (m-40) REVERT: F 322 VAL cc_start: 0.6998 (t) cc_final: 0.6795 (p) REVERT: F 330 MET cc_start: 0.7426 (ttm) cc_final: 0.6893 (ttt) REVERT: G 285 ASN cc_start: 0.5887 (m-40) cc_final: 0.5201 (t0) REVERT: G 328 ASP cc_start: 0.6970 (t70) cc_final: 0.6616 (t70) REVERT: G 464 ILE cc_start: 0.7455 (mm) cc_final: 0.7236 (mm) REVERT: G 487 MET cc_start: 0.7405 (mmt) cc_final: 0.7048 (mpp) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.4270 time to fit residues: 338.1025 Evaluate side-chains 245 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 3.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 1.9990 chunk 275 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 186 optimal weight: 0.9980 chunk 147 optimal weight: 0.0050 chunk 285 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 173 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 330 optimal weight: 1.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27685 Z= 0.219 Angle : 0.574 12.237 37345 Z= 0.311 Chirality : 0.045 0.165 4571 Planarity : 0.004 0.036 4809 Dihedral : 4.356 29.640 3836 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.51 % Allowed : 5.95 % Favored : 92.54 % 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: 1.40 (0.13), residues: 3668 helix: 1.78 (0.11), residues: 1995 sheet: 0.89 (0.20), residues: 630 loop : -0.66 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 42 HIS 0.001 0.000 HIS A 314 PHE 0.015 0.002 PHE A 193 TYR 0.011 0.002 TYR G 64 ARG 0.005 0.001 ARG F 367 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 303 time to evaluate : 3.137 Fit side-chains REVERT: A 131 LYS cc_start: 0.7728 (ttmm) cc_final: 0.7332 (ttmt) REVERT: A 322 VAL cc_start: 0.6900 (t) cc_final: 0.6699 (p) REVERT: C 209 GLN cc_start: 0.6819 (mm-40) cc_final: 0.6568 (mt0) REVERT: D 330 MET cc_start: 0.7288 (ttp) cc_final: 0.6352 (ttt) REVERT: E 328 ASP cc_start: 0.6506 (t70) cc_final: 0.6126 (t0) REVERT: E 330 MET cc_start: 0.7497 (ttm) cc_final: 0.7057 (ttt) REVERT: E 360 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6911 (mm-30) REVERT: E 494 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7608 (t0) REVERT: F 131 LYS cc_start: 0.7585 (ttmm) cc_final: 0.7209 (ttmt) REVERT: F 223 LYS cc_start: 0.7123 (tttt) cc_final: 0.6678 (mtmm) REVERT: G 328 ASP cc_start: 0.6590 (t70) cc_final: 0.6256 (t0) REVERT: G 487 MET cc_start: 0.7676 (mmt) cc_final: 0.6930 (mpp) outliers start: 45 outliers final: 18 residues processed: 341 average time/residue: 0.4413 time to fit residues: 229.0659 Evaluate side-chains 220 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 3.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 192 LYS Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 275 optimal weight: 0.9990 chunk 225 optimal weight: 0.0570 chunk 91 optimal weight: 0.5980 chunk 331 optimal weight: 8.9990 chunk 357 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 328 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 265 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27685 Z= 0.166 Angle : 0.479 10.617 37345 Z= 0.264 Chirality : 0.042 0.172 4571 Planarity : 0.004 0.036 4809 Dihedral : 3.960 27.890 3836 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.75 % Allowed : 7.56 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.14), residues: 3668 helix: 2.20 (0.11), residues: 2009 sheet: 0.73 (0.20), residues: 630 loop : -0.84 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 42 HIS 0.001 0.000 HIS D 314 PHE 0.021 0.002 PHE E 202 TYR 0.010 0.001 TYR A 477 ARG 0.004 0.000 ARG C 344 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 242 time to evaluate : 3.221 Fit side-chains REVERT: A 131 LYS cc_start: 0.7651 (ttmm) cc_final: 0.7292 (ttmt) REVERT: A 185 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7062 (tt) REVERT: C 131 LYS cc_start: 0.7621 (ttmm) cc_final: 0.7336 (ttpt) REVERT: C 209 GLN cc_start: 0.6830 (mm-40) cc_final: 0.6597 (mt0) REVERT: D 131 LYS cc_start: 0.7678 (ttmm) cc_final: 0.7249 (ttmt) REVERT: D 330 MET cc_start: 0.7210 (ttp) cc_final: 0.6269 (ttt) REVERT: D 367 ARG cc_start: 0.6016 (mtp85) cc_final: 0.5054 (mtp85) REVERT: E 328 ASP cc_start: 0.6558 (t70) cc_final: 0.5516 (p0) REVERT: E 330 MET cc_start: 0.7508 (ttm) cc_final: 0.6699 (ttt) REVERT: E 360 GLU cc_start: 0.7388 (mt-10) cc_final: 0.6967 (mm-30) REVERT: E 494 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7644 (t0) REVERT: F 131 LYS cc_start: 0.7509 (ttmm) cc_final: 0.7176 (ttmt) REVERT: F 307 ASN cc_start: 0.5442 (t0) cc_final: 0.4713 (m-40) REVERT: G 328 ASP cc_start: 0.6654 (t70) cc_final: 0.6087 (t70) REVERT: G 487 MET cc_start: 0.7715 (mmt) cc_final: 0.7001 (mpp) outliers start: 52 outliers final: 23 residues processed: 286 average time/residue: 0.4044 time to fit residues: 182.5082 Evaluate side-chains 234 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 209 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 445 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 171 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 222 optimal weight: 0.7980 chunk 332 optimal weight: 20.0000 chunk 351 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 chunk 314 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27685 Z= 0.164 Angle : 0.464 10.128 37345 Z= 0.252 Chirality : 0.042 0.164 4571 Planarity : 0.004 0.035 4809 Dihedral : 3.864 28.108 3836 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.68 % Allowed : 8.44 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.14), residues: 3668 helix: 2.19 (0.12), residues: 2051 sheet: 0.65 (0.20), residues: 630 loop : -1.15 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 42 HIS 0.001 0.000 HIS C 314 PHE 0.019 0.002 PHE E 202 TYR 0.014 0.001 TYR E 477 ARG 0.003 0.000 ARG G 367 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 226 time to evaluate : 3.195 Fit side-chains REVERT: A 131 LYS cc_start: 0.7610 (ttmm) cc_final: 0.7215 (ttpt) REVERT: A 367 ARG cc_start: 0.5794 (mtp85) cc_final: 0.4855 (mtp85) REVERT: B 360 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6867 (mm-30) REVERT: B 367 ARG cc_start: 0.5845 (mtp85) cc_final: 0.5131 (mtp85) REVERT: C 131 LYS cc_start: 0.7602 (ttmm) cc_final: 0.7317 (ttpt) REVERT: C 209 GLN cc_start: 0.6902 (mm-40) cc_final: 0.6616 (mt0) REVERT: C 360 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6792 (mm-30) REVERT: D 131 LYS cc_start: 0.7668 (ttmm) cc_final: 0.7230 (ttmt) REVERT: E 328 ASP cc_start: 0.6480 (t70) cc_final: 0.5496 (p0) REVERT: E 330 MET cc_start: 0.7305 (ttm) cc_final: 0.6504 (ttt) REVERT: E 360 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6934 (mm-30) REVERT: E 367 ARG cc_start: 0.5886 (mtp85) cc_final: 0.5568 (mtp85) REVERT: E 494 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7647 (t0) REVERT: F 131 LYS cc_start: 0.7517 (ttmm) cc_final: 0.7172 (ttmt) REVERT: F 217 TYR cc_start: 0.5436 (m-80) cc_final: 0.4781 (m-80) REVERT: G 328 ASP cc_start: 0.6619 (t70) cc_final: 0.6117 (t70) REVERT: G 487 MET cc_start: 0.7718 (mmt) cc_final: 0.7000 (mpp) outliers start: 50 outliers final: 28 residues processed: 268 average time/residue: 0.4125 time to fit residues: 173.2487 Evaluate side-chains 238 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 325 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 5 optimal weight: 0.0970 chunk 261 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 300 optimal weight: 0.5980 chunk 243 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 179 optimal weight: 0.4980 chunk 315 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27685 Z= 0.134 Angle : 0.431 8.943 37345 Z= 0.235 Chirality : 0.040 0.152 4571 Planarity : 0.004 0.036 4809 Dihedral : 3.696 27.495 3836 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.02 % Allowed : 8.81 % Favored : 89.18 % 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: 1.81 (0.14), residues: 3668 helix: 2.42 (0.12), residues: 2030 sheet: 0.62 (0.20), residues: 630 loop : -1.02 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 42 HIS 0.001 0.000 HIS C 314 PHE 0.019 0.002 PHE E 202 TYR 0.013 0.001 TYR E 477 ARG 0.003 0.000 ARG F 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 226 time to evaluate : 3.259 Fit side-chains REVERT: A 131 LYS cc_start: 0.7590 (ttmm) cc_final: 0.7232 (ttpt) REVERT: A 367 ARG cc_start: 0.5818 (mtp85) cc_final: 0.5568 (mtp85) REVERT: B 154 LYS cc_start: 0.7259 (mttt) cc_final: 0.6908 (mmtt) REVERT: B 360 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6861 (mm-30) REVERT: B 367 ARG cc_start: 0.5883 (mtp85) cc_final: 0.5022 (mtp85) REVERT: C 131 LYS cc_start: 0.7552 (ttmm) cc_final: 0.7241 (ttpt) REVERT: D 131 LYS cc_start: 0.7614 (ttmm) cc_final: 0.7186 (ttmt) REVERT: D 217 TYR cc_start: 0.5257 (m-80) cc_final: 0.4549 (m-80) REVERT: D 360 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6637 (mm-30) REVERT: D 367 ARG cc_start: 0.6225 (mtm180) cc_final: 0.5854 (mtp85) REVERT: E 131 LYS cc_start: 0.7542 (ttmm) cc_final: 0.7270 (ttpt) REVERT: E 328 ASP cc_start: 0.6469 (t70) cc_final: 0.6089 (t70) REVERT: E 330 MET cc_start: 0.7330 (ttm) cc_final: 0.6552 (ttt) REVERT: E 360 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6938 (mm-30) REVERT: E 494 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7660 (t0) REVERT: F 131 LYS cc_start: 0.7453 (ttmm) cc_final: 0.7065 (ttmt) REVERT: F 217 TYR cc_start: 0.5313 (m-80) cc_final: 0.4701 (m-80) REVERT: F 408 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6403 (mm-30) REVERT: G 328 ASP cc_start: 0.6579 (t70) cc_final: 0.6098 (t0) REVERT: G 367 ARG cc_start: 0.5713 (mtp85) cc_final: 0.5370 (mtp85) REVERT: G 487 MET cc_start: 0.7713 (mmt) cc_final: 0.6995 (mpp) outliers start: 60 outliers final: 32 residues processed: 277 average time/residue: 0.4129 time to fit residues: 179.1330 Evaluate side-chains 248 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 214 time to evaluate : 2.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 222 GLU Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 408 GLU Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 170 LYS Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 464 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 0.7980 chunk 316 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 352 optimal weight: 2.9990 chunk 292 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 chunk 29 optimal weight: 0.0470 chunk 116 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27685 Z= 0.189 Angle : 0.485 9.675 37345 Z= 0.259 Chirality : 0.042 0.145 4571 Planarity : 0.004 0.037 4809 Dihedral : 3.809 27.283 3836 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.12 % Allowed : 9.48 % Favored : 88.40 % 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: 1.50 (0.14), residues: 3668 helix: 2.17 (0.12), residues: 2093 sheet: 0.53 (0.20), residues: 595 loop : -1.36 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 42 HIS 0.001 0.001 HIS E 314 PHE 0.015 0.002 PHE E 202 TYR 0.012 0.001 TYR E 477 ARG 0.004 0.000 ARG F 367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 242 time to evaluate : 3.164 Fit side-chains REVERT: A 131 LYS cc_start: 0.7664 (ttmm) cc_final: 0.7326 (ttpt) REVERT: A 367 ARG cc_start: 0.5804 (mtp85) cc_final: 0.5537 (mtp85) REVERT: B 154 LYS cc_start: 0.7521 (mttt) cc_final: 0.7172 (mmtt) REVERT: B 360 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6813 (mm-30) REVERT: C 131 LYS cc_start: 0.7621 (ttmm) cc_final: 0.7310 (ttpt) REVERT: C 360 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6924 (mm-30) REVERT: D 131 LYS cc_start: 0.7684 (ttmm) cc_final: 0.7239 (ttmt) REVERT: D 217 TYR cc_start: 0.5342 (m-80) cc_final: 0.4595 (m-80) REVERT: D 307 ASN cc_start: 0.5436 (t0) cc_final: 0.5181 (t0) REVERT: D 360 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6767 (mm-30) REVERT: E 131 LYS cc_start: 0.7583 (ttmm) cc_final: 0.7326 (ttpt) REVERT: E 328 ASP cc_start: 0.6508 (t70) cc_final: 0.6169 (t70) REVERT: E 330 MET cc_start: 0.7345 (ttm) cc_final: 0.6563 (ttt) REVERT: E 360 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7001 (mm-30) REVERT: E 367 ARG cc_start: 0.5836 (mtp85) cc_final: 0.5478 (mtp85) REVERT: E 494 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7604 (t0) REVERT: F 131 LYS cc_start: 0.7541 (ttmm) cc_final: 0.7149 (ttmt) REVERT: F 154 LYS cc_start: 0.7526 (mttt) cc_final: 0.7230 (tptt) REVERT: F 217 TYR cc_start: 0.5593 (m-80) cc_final: 0.4998 (m-80) REVERT: G 154 LYS cc_start: 0.7529 (mttt) cc_final: 0.7190 (mmtt) REVERT: G 328 ASP cc_start: 0.6600 (t70) cc_final: 0.6105 (t0) REVERT: G 367 ARG cc_start: 0.5802 (mtp85) cc_final: 0.5472 (mtp85) REVERT: G 487 MET cc_start: 0.7711 (mmt) cc_final: 0.7000 (mpp) outliers start: 63 outliers final: 50 residues processed: 289 average time/residue: 0.4110 time to fit residues: 186.7545 Evaluate side-chains 273 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 222 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 474 GLU Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain G residue 170 LYS Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 464 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 296 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 350 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 161 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 27685 Z= 0.164 Angle : 0.464 10.014 37345 Z= 0.247 Chirality : 0.041 0.146 4571 Planarity : 0.004 0.038 4809 Dihedral : 3.738 26.193 3836 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.85 % Allowed : 10.55 % Favored : 87.60 % 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: 1.60 (0.14), residues: 3668 helix: 2.25 (0.12), residues: 2072 sheet: 0.56 (0.20), residues: 595 loop : -1.23 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 42 HIS 0.001 0.000 HIS E 314 PHE 0.019 0.002 PHE F 202 TYR 0.013 0.001 TYR A 477 ARG 0.004 0.000 ARG F 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 240 time to evaluate : 3.523 Fit side-chains REVERT: A 70 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7526 (mtpt) REVERT: A 131 LYS cc_start: 0.7673 (ttmm) cc_final: 0.7330 (ttpt) REVERT: A 367 ARG cc_start: 0.5775 (mtp85) cc_final: 0.4787 (mtp85) REVERT: B 154 LYS cc_start: 0.7521 (mttt) cc_final: 0.7187 (mmtt) REVERT: B 360 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6817 (mm-30) REVERT: C 131 LYS cc_start: 0.7597 (ttmm) cc_final: 0.7305 (ttpt) REVERT: C 360 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6913 (mm-30) REVERT: D 131 LYS cc_start: 0.7685 (ttmm) cc_final: 0.7273 (ttmt) REVERT: D 217 TYR cc_start: 0.5329 (m-80) cc_final: 0.4642 (m-80) REVERT: D 360 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6842 (mm-30) REVERT: D 367 ARG cc_start: 0.6075 (mtm180) cc_final: 0.5511 (mtp85) REVERT: E 131 LYS cc_start: 0.7582 (ttmm) cc_final: 0.7332 (ttpt) REVERT: E 328 ASP cc_start: 0.6524 (t70) cc_final: 0.6176 (t0) REVERT: E 330 MET cc_start: 0.7348 (ttm) cc_final: 0.6556 (ttt) REVERT: E 360 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6995 (mm-30) REVERT: E 367 ARG cc_start: 0.5759 (mtp85) cc_final: 0.5373 (mtp85) REVERT: E 494 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7613 (t0) REVERT: F 131 LYS cc_start: 0.7571 (ttmm) cc_final: 0.7147 (ttmt) REVERT: F 154 LYS cc_start: 0.7510 (mttt) cc_final: 0.7156 (tptt) REVERT: F 217 TYR cc_start: 0.5573 (m-80) cc_final: 0.4991 (m-80) REVERT: F 367 ARG cc_start: 0.6142 (mtp85) cc_final: 0.5744 (mtp85) REVERT: G 154 LYS cc_start: 0.7536 (mttt) cc_final: 0.7206 (mmtt) REVERT: G 328 ASP cc_start: 0.6586 (t70) cc_final: 0.6066 (t0) REVERT: G 367 ARG cc_start: 0.5687 (mtp85) cc_final: 0.5344 (mtp85) REVERT: G 487 MET cc_start: 0.7698 (mmt) cc_final: 0.6980 (mpp) outliers start: 55 outliers final: 44 residues processed: 281 average time/residue: 0.4130 time to fit residues: 180.3535 Evaluate side-chains 271 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 226 time to evaluate : 3.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain G residue 170 LYS Chi-restraints excluded: chain G residue 247 ILE Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 464 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27685 Z= 0.172 Angle : 0.477 9.856 37345 Z= 0.252 Chirality : 0.042 0.152 4571 Planarity : 0.004 0.038 4809 Dihedral : 3.757 26.381 3836 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.98 % Allowed : 10.76 % Favored : 87.26 % 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: 1.58 (0.14), residues: 3668 helix: 2.25 (0.12), residues: 2072 sheet: 0.55 (0.20), residues: 595 loop : -1.27 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 42 HIS 0.001 0.000 HIS C 314 PHE 0.021 0.002 PHE A 299 TYR 0.014 0.001 TYR A 477 ARG 0.003 0.000 ARG F 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 245 time to evaluate : 3.092 Fit side-chains REVERT: A 70 LYS cc_start: 0.7817 (mmtt) cc_final: 0.7537 (mtpt) REVERT: A 131 LYS cc_start: 0.7705 (ttmm) cc_final: 0.7368 (ttpt) REVERT: A 154 LYS cc_start: 0.7300 (mttt) cc_final: 0.7060 (mmtt) REVERT: A 217 TYR cc_start: 0.5379 (m-80) cc_final: 0.4344 (m-80) REVERT: A 367 ARG cc_start: 0.5742 (mtp85) cc_final: 0.4830 (mtp85) REVERT: A 487 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6793 (tpp) REVERT: B 154 LYS cc_start: 0.7553 (mttt) cc_final: 0.7193 (tptt) REVERT: B 360 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6724 (mm-30) REVERT: C 217 TYR cc_start: 0.5512 (m-80) cc_final: 0.5057 (m-10) REVERT: C 360 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6936 (mm-30) REVERT: D 131 LYS cc_start: 0.7702 (ttmm) cc_final: 0.7273 (ttmt) REVERT: D 217 TYR cc_start: 0.5396 (m-80) cc_final: 0.4758 (m-80) REVERT: D 360 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6798 (mm-30) REVERT: D 367 ARG cc_start: 0.6218 (mtm180) cc_final: 0.5069 (mtp85) REVERT: E 131 LYS cc_start: 0.7635 (ttmm) cc_final: 0.7373 (ttpt) REVERT: E 154 LYS cc_start: 0.7491 (mttt) cc_final: 0.7271 (tptt) REVERT: E 328 ASP cc_start: 0.6510 (t70) cc_final: 0.6148 (t0) REVERT: E 330 MET cc_start: 0.7275 (ttm) cc_final: 0.6476 (ttt) REVERT: E 360 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6923 (mm-30) REVERT: F 131 LYS cc_start: 0.7605 (ttmm) cc_final: 0.7172 (ttmt) REVERT: F 154 LYS cc_start: 0.7538 (mttt) cc_final: 0.7166 (tptt) REVERT: F 217 TYR cc_start: 0.5622 (m-80) cc_final: 0.5009 (m-80) REVERT: F 367 ARG cc_start: 0.6153 (mtp85) cc_final: 0.5698 (mtp85) REVERT: G 154 LYS cc_start: 0.7641 (mttt) cc_final: 0.7264 (tptt) REVERT: G 307 ASN cc_start: 0.5506 (m-40) cc_final: 0.5302 (t0) REVERT: G 328 ASP cc_start: 0.6562 (t70) cc_final: 0.6062 (t0) REVERT: G 367 ARG cc_start: 0.5709 (mtp85) cc_final: 0.5331 (mtp85) REVERT: G 487 MET cc_start: 0.7699 (mmt) cc_final: 0.6953 (mpp) outliers start: 59 outliers final: 47 residues processed: 289 average time/residue: 0.4150 time to fit residues: 184.6522 Evaluate side-chains 282 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 234 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain G residue 170 LYS Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 464 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 3.9990 chunk 336 optimal weight: 0.6980 chunk 306 optimal weight: 2.9990 chunk 326 optimal weight: 0.9990 chunk 196 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 256 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 295 optimal weight: 8.9990 chunk 309 optimal weight: 0.7980 chunk 325 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27685 Z= 0.161 Angle : 0.476 10.037 37345 Z= 0.250 Chirality : 0.041 0.185 4571 Planarity : 0.004 0.038 4809 Dihedral : 3.732 26.011 3836 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.75 % Allowed : 11.26 % Favored : 86.99 % 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: 1.61 (0.14), residues: 3668 helix: 2.26 (0.12), residues: 2079 sheet: 0.58 (0.20), residues: 595 loop : -1.26 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 42 HIS 0.001 0.000 HIS F 314 PHE 0.022 0.002 PHE A 299 TYR 0.012 0.001 TYR A 477 ARG 0.006 0.000 ARG C 367 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 242 time to evaluate : 3.120 Fit side-chains REVERT: A 70 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7535 (mtpt) REVERT: A 131 LYS cc_start: 0.7696 (ttmm) cc_final: 0.7356 (ttpt) REVERT: A 217 TYR cc_start: 0.5399 (m-80) cc_final: 0.4347 (m-80) REVERT: A 367 ARG cc_start: 0.5752 (mtp85) cc_final: 0.4910 (mtp85) REVERT: A 487 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6752 (tpp) REVERT: B 154 LYS cc_start: 0.7557 (mttt) cc_final: 0.7194 (tptt) REVERT: B 360 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6720 (mm-30) REVERT: B 367 ARG cc_start: 0.5922 (mtp85) cc_final: 0.5137 (mtp85) REVERT: C 131 LYS cc_start: 0.7617 (ttmm) cc_final: 0.7288 (ttpt) REVERT: C 154 LYS cc_start: 0.7166 (mttt) cc_final: 0.6922 (tptt) REVERT: C 217 TYR cc_start: 0.5571 (m-80) cc_final: 0.5170 (m-10) REVERT: C 360 GLU cc_start: 0.7162 (mt-10) cc_final: 0.6924 (mm-30) REVERT: D 131 LYS cc_start: 0.7685 (ttmm) cc_final: 0.7258 (ttmt) REVERT: D 217 TYR cc_start: 0.5376 (m-80) cc_final: 0.4736 (m-80) REVERT: D 360 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6812 (mm-30) REVERT: D 367 ARG cc_start: 0.6033 (mtm180) cc_final: 0.4945 (mtp85) REVERT: E 131 LYS cc_start: 0.7629 (ttmm) cc_final: 0.7369 (ttpt) REVERT: E 328 ASP cc_start: 0.6497 (t70) cc_final: 0.6127 (t0) REVERT: E 360 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6945 (mm-30) REVERT: E 367 ARG cc_start: 0.5746 (mtp85) cc_final: 0.5421 (mtp85) REVERT: F 131 LYS cc_start: 0.7597 (ttmm) cc_final: 0.7154 (ttmt) REVERT: F 154 LYS cc_start: 0.7494 (mttt) cc_final: 0.7123 (tptt) REVERT: F 217 TYR cc_start: 0.5503 (m-80) cc_final: 0.4944 (m-80) REVERT: G 154 LYS cc_start: 0.7617 (mttt) cc_final: 0.7249 (tptt) REVERT: G 328 ASP cc_start: 0.6558 (t70) cc_final: 0.6049 (t0) REVERT: G 487 MET cc_start: 0.7689 (mmt) cc_final: 0.6947 (mpp) outliers start: 52 outliers final: 48 residues processed: 279 average time/residue: 0.4194 time to fit residues: 180.6646 Evaluate side-chains 280 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 231 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain G residue 170 LYS Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 0.7980 chunk 345 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 362 optimal weight: 0.9990 chunk 333 optimal weight: 0.0870 chunk 288 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27685 Z= 0.222 Angle : 0.521 9.939 37345 Z= 0.275 Chirality : 0.043 0.226 4571 Planarity : 0.004 0.038 4809 Dihedral : 3.896 26.451 3836 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.95 % Allowed : 11.29 % Favored : 86.76 % 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: 1.42 (0.14), residues: 3668 helix: 2.19 (0.12), residues: 2058 sheet: 0.69 (0.22), residues: 497 loop : -1.40 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 42 HIS 0.001 0.001 HIS F 314 PHE 0.024 0.002 PHE A 299 TYR 0.012 0.002 TYR A 477 ARG 0.009 0.001 ARG A 420 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7336 Ramachandran restraints generated. 3668 Oldfield, 0 Emsley, 3668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 248 time to evaluate : 3.015 Fit side-chains REVERT: A 70 LYS cc_start: 0.7835 (mmtt) cc_final: 0.7531 (mtpt) REVERT: A 217 TYR cc_start: 0.5471 (m-80) cc_final: 0.4414 (m-80) REVERT: A 360 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7157 (mm-30) REVERT: A 487 MET cc_start: 0.7082 (OUTLIER) cc_final: 0.6513 (mpp) REVERT: B 131 LYS cc_start: 0.7957 (tmtt) cc_final: 0.7446 (ttmm) REVERT: B 154 LYS cc_start: 0.7639 (mttt) cc_final: 0.7260 (tptt) REVERT: B 360 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6867 (mm-30) REVERT: C 131 LYS cc_start: 0.7707 (ttmm) cc_final: 0.7345 (ttpt) REVERT: C 154 LYS cc_start: 0.7326 (mttt) cc_final: 0.7012 (tptt) REVERT: C 217 TYR cc_start: 0.5754 (m-80) cc_final: 0.5343 (m-10) REVERT: D 131 LYS cc_start: 0.7766 (ttmm) cc_final: 0.7326 (ttmt) REVERT: D 183 ASP cc_start: 0.6766 (p0) cc_final: 0.6547 (p0) REVERT: D 217 TYR cc_start: 0.5401 (m-80) cc_final: 0.4714 (m-80) REVERT: D 360 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6880 (mm-30) REVERT: D 367 ARG cc_start: 0.6039 (mtm180) cc_final: 0.4953 (mtp85) REVERT: E 131 LYS cc_start: 0.7680 (ttmm) cc_final: 0.7444 (ttpt) REVERT: E 328 ASP cc_start: 0.6594 (t70) cc_final: 0.6160 (t0) REVERT: E 360 GLU cc_start: 0.7326 (mt-10) cc_final: 0.7022 (mm-30) REVERT: E 367 ARG cc_start: 0.5710 (mtp85) cc_final: 0.5343 (mtp85) REVERT: E 494 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7556 (t0) REVERT: F 131 LYS cc_start: 0.7655 (ttmm) cc_final: 0.7223 (ttmt) REVERT: F 154 LYS cc_start: 0.7608 (mttt) cc_final: 0.7201 (tptt) REVERT: F 217 TYR cc_start: 0.5651 (m-80) cc_final: 0.5073 (m-80) REVERT: G 154 LYS cc_start: 0.7716 (mttt) cc_final: 0.7326 (tptt) REVERT: G 217 TYR cc_start: 0.5254 (m-80) cc_final: 0.4458 (m-80) REVERT: G 328 ASP cc_start: 0.6413 (t70) cc_final: 0.6134 (t0) REVERT: G 487 MET cc_start: 0.7711 (mmt) cc_final: 0.6885 (mpp) outliers start: 58 outliers final: 52 residues processed: 289 average time/residue: 0.4202 time to fit residues: 189.7027 Evaluate side-chains 290 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 236 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain A residue 494 ASP Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 494 ASP Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 494 ASP Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain D residue 494 ASP Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 464 ILE Chi-restraints excluded: chain E residue 494 ASP Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 204 ASN Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 464 ILE Chi-restraints excluded: chain F residue 494 ASP Chi-restraints excluded: chain G residue 170 LYS Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain G residue 325 THR Chi-restraints excluded: chain G residue 464 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 266 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 296 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.247618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.223906 restraints weight = 26938.162| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 1.02 r_work: 0.4248 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27685 Z= 0.222 Angle : 0.525 10.543 37345 Z= 0.277 Chirality : 0.043 0.207 4571 Planarity : 0.004 0.038 4809 Dihedral : 3.931 26.480 3836 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.88 % Allowed : 11.73 % Favored : 86.39 % 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: 1.36 (0.14), residues: 3668 helix: 2.19 (0.12), residues: 2030 sheet: 0.49 (0.21), residues: 497 loop : -1.35 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 42 HIS 0.001 0.001 HIS C 314 PHE 0.023 0.002 PHE A 299 TYR 0.013 0.002 TYR A 477 ARG 0.006 0.000 ARG F 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5249.97 seconds wall clock time: 95 minutes 48.89 seconds (5748.89 seconds total)