Starting phenix.real_space_refine on Tue Feb 20 09:34:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7k_29814/02_2024/8g7k_29814.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7k_29814/02_2024/8g7k_29814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7k_29814/02_2024/8g7k_29814.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7k_29814/02_2024/8g7k_29814.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7k_29814/02_2024/8g7k_29814.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7k_29814/02_2024/8g7k_29814.pdb" } resolution = 3.8 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= -0.001 sd= 0.082 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 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 213": "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 "C PHE 213": "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 "D PHE 213": "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" Residue "G PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 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: 13.85, per 1000 atoms: 0.50 Number of scatterers: 27461 At special positions: 0 Unit cell: (164.079, 161.298, 91.773, 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: 10.03 Conformation dependent library (CDL) restraints added in 5.2 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 31 sheets defined 58.4% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.905A pdb=" N LEU A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.747A 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 64 through 77 removed outlier: 3.574A pdb=" N ILE A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 107 removed outlier: 4.520A pdb=" N THR A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 3.889A 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 removed outlier: 3.517A pdb=" N LEU A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) 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: 3.595A pdb=" N LEU A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 409 removed outlier: 4.036A pdb=" N GLU A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 4.106A 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 Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.502A pdb=" N GLU A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) 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: 3.971A pdb=" N LEU B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.768A 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 62 through 77 removed outlier: 3.569A pdb=" N ILE B 67 " --> pdb=" O LYS B 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 107 removed outlier: 4.512A pdb=" N THR B 88 " --> pdb=" O GLY B 84 " (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 280 through 295 Processing helix chain 'B' and resid 337 through 355 Processing helix chain 'B' and resid 357 through 373 removed outlier: 3.511A pdb=" N LEU B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 409 removed outlier: 3.681A pdb=" N GLU B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 4.023A 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: 3.510A 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 removed outlier: 3.521A pdb=" N GLU B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) 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: 3.876A pdb=" N LEU C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.780A 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: 3.920A pdb=" N ILE C 67 " --> pdb=" O LYS C 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 72 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 107 removed outlier: 4.558A pdb=" N THR C 88 " --> pdb=" O GLY C 84 " (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 removed outlier: 3.512A pdb=" N LEU C 235 " --> pdb=" O ILE C 231 " (cutoff:3.500A) 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: 3.554A pdb=" N LEU C 371 " --> pdb=" O ARG C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 409 removed outlier: 4.061A pdb=" N GLU C 390 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 3.843A 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 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: 3.909A pdb=" N LEU D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 3.744A 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: 3.762A pdb=" N ILE D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE D 72 " --> pdb=" O GLY D 68 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 107 removed outlier: 4.350A 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 removed outlier: 4.239A pdb=" N LEU D 235 " --> pdb=" O ILE D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 267 Processing helix chain 'D' and resid 280 through 295 Processing helix chain 'D' and resid 337 through 355 Processing helix chain 'D' and resid 357 through 373 Processing helix chain 'D' and resid 384 through 409 removed outlier: 4.031A pdb=" N GLU D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.854A 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: 3.945A pdb=" N LEU E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.797A 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: 3.897A pdb=" N ILE E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE E 72 " --> pdb=" O GLY E 68 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 107 removed outlier: 4.002A pdb=" N THR E 88 " --> pdb=" O GLY E 84 " (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 removed outlier: 3.575A pdb=" N LEU E 235 " --> pdb=" O ILE E 231 " (cutoff:3.500A) 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: 3.647A pdb=" N LEU E 371 " --> pdb=" O ARG E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 409 removed outlier: 4.119A pdb=" N GLU E 390 " --> pdb=" O VAL E 386 " (cutoff:3.500A) removed outlier: 3.949A 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 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: 3.900A pdb=" N LEU F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.782A 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: 3.808A pdb=" N ILE F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE F 72 " --> pdb=" O GLY F 68 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 107 removed outlier: 4.552A pdb=" N THR F 88 " --> pdb=" O GLY F 84 " (cutoff:3.500A) removed outlier: 3.534A 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 removed outlier: 3.563A pdb=" N LEU F 235 " --> pdb=" O ILE F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 267 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 337 through 355 Processing helix chain 'F' and resid 357 through 373 removed outlier: 3.599A pdb=" N LEU F 371 " --> pdb=" O ARG F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 409 removed outlier: 3.576A pdb=" N GLU F 390 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 4.174A 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 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: 3.941A pdb=" N LEU G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.846A pdb=" N ILE G 67 " --> pdb=" O LYS G 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE G 72 " --> pdb=" O GLY G 68 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL G 75 " --> pdb=" O LEU G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 107 removed outlier: 4.530A pdb=" N THR G 88 " --> pdb=" O GLY G 84 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 89 " --> pdb=" O ASP G 85 " (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 removed outlier: 3.550A pdb=" N LEU G 235 " --> pdb=" O ILE G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 267 Processing helix chain 'G' and resid 280 through 295 Processing helix chain 'G' and resid 337 through 355 Processing helix chain 'G' and resid 357 through 373 Processing helix chain 'G' and resid 384 through 409 removed outlier: 4.042A pdb=" N GLU G 390 " --> pdb=" O VAL G 386 " (cutoff:3.500A) removed outlier: 3.966A 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: 3.512A 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: 6.538A pdb=" N ILE A 37 " --> pdb=" O VAL G 520 " (cutoff:3.500A) removed outlier: 8.239A 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: 6.621A pdb=" N THR A 174 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N VAL A 380 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS A 176 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 190 through 193 removed outlier: 6.356A pdb=" N GLY A 334 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 319 " --> pdb=" O GLY A 334 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS A 318 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR A 217 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY A 320 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL A 246 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR A 217 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 248 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU A 219 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.497A 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: 6.076A pdb=" N ILE A 247 " --> pdb=" O VAL A 274 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA6, first strand: chain 'A' and resid 475 through 478 Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 6 Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 177 removed outlier: 8.030A pdb=" N GLU B 189 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY B 334 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 319 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU B 321 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN B 214 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 323 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU B 212 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 245 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL B 274 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE B 247 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 177 removed outlier: 8.030A pdb=" N GLU B 189 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLY B 334 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 319 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N GLU B 321 " --> pdb=" O GLN B 214 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN B 214 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 323 " --> pdb=" O GLU B 212 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU B 212 " --> pdb=" O ILE B 323 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N PHE B 299 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N LEU B 220 " --> pdb=" O PHE B 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB2, first strand: chain 'B' and resid 475 through 478 Processing sheet with id=AB3, first strand: chain 'C' and resid 2 through 6 Processing sheet with id=AB4, first strand: chain 'C' and resid 173 through 177 removed outlier: 6.544A pdb=" N THR C 174 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL C 380 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS C 176 " --> pdb=" O VAL C 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 190 through 193 removed outlier: 6.387A pdb=" N GLY C 334 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 319 " --> pdb=" O GLY C 334 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 7.066A 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: 6.634A pdb=" N LEU C 245 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL C 274 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE C 247 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AB7, first strand: chain 'C' and resid 475 through 478 Processing sheet with id=AB8, first strand: chain 'D' and resid 2 through 6 Processing sheet with id=AB9, first strand: chain 'D' and resid 173 through 177 removed outlier: 8.069A pdb=" N GLU D 189 " --> pdb=" O LYS D 333 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY D 334 " --> pdb=" O VAL D 319 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL D 319 " --> pdb=" O GLY D 334 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU D 321 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLN D 214 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE D 323 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU D 212 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU D 245 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N VAL D 274 " --> pdb=" O LEU D 245 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE D 247 " --> pdb=" O VAL D 274 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AC2, first strand: chain 'D' and resid 475 through 478 Processing sheet with id=AC3, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AC4, first strand: chain 'E' and resid 173 through 177 removed outlier: 6.667A pdb=" N THR E 174 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL E 380 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS E 176 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N GLU E 189 " --> pdb=" O LYS E 333 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY E 334 " --> pdb=" O VAL E 319 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL E 319 " --> pdb=" O GLY E 334 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS E 318 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N TYR E 217 " --> pdb=" O LYS E 318 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY E 320 " --> pdb=" O ASP E 215 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 410 through 412 Processing sheet with id=AC6, first strand: chain 'E' and resid 475 through 478 Processing sheet with id=AC7, first strand: chain 'F' and resid 2 through 6 Processing sheet with id=AC8, first strand: chain 'F' and resid 173 through 177 removed outlier: 6.648A pdb=" N THR F 174 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL F 380 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS F 176 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N GLU F 189 " --> pdb=" O LYS F 333 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY F 334 " --> pdb=" O VAL F 319 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL F 319 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU F 321 " --> pdb=" O GLN F 214 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLN F 214 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE F 323 " --> pdb=" O GLU F 212 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU F 212 " --> pdb=" O ILE F 323 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU F 245 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL F 274 " --> pdb=" O LEU F 245 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE F 247 " --> pdb=" O VAL F 274 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 410 through 412 Processing sheet with id=AD1, first strand: chain 'F' and resid 475 through 478 Processing sheet with id=AD2, first strand: chain 'G' and resid 173 through 177 removed outlier: 6.720A pdb=" N THR G 174 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL G 380 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYS G 176 " --> pdb=" O VAL G 380 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N GLU G 189 " --> pdb=" O LYS G 333 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY G 334 " --> pdb=" O VAL G 319 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL G 319 " --> pdb=" O GLY G 334 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU G 321 " --> pdb=" O GLN G 214 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLN G 214 " --> pdb=" O GLU G 321 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE G 323 " --> pdb=" O GLU G 212 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLU G 212 " --> pdb=" O ILE G 323 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N VAL G 246 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR G 217 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE G 248 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU G 219 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU G 245 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL G 274 " --> pdb=" O LEU G 245 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE G 247 " --> pdb=" O VAL G 274 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 410 through 412 Processing sheet with id=AD4, first strand: chain 'G' and resid 475 through 478 1807 hydrogen bonds defined for protein. 5184 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: 10.57 Time building geometry restraints manager: 10.86 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: 5476 1.31 - 1.44: 5180 1.44 - 1.56: 16810 1.56 - 1.69: 44 1.69 - 1.81: 175 Bond restraints: 27685 Sorted by residual: bond pdb=" N ILE B 448 " pdb=" CA ILE B 448 " ideal model delta sigma weight residual 1.461 1.505 -0.044 1.23e-02 6.61e+03 1.27e+01 bond pdb=" N ILE G 448 " pdb=" CA ILE G 448 " ideal model delta sigma weight residual 1.461 1.505 -0.044 1.23e-02 6.61e+03 1.27e+01 bond pdb=" N ILE D 448 " pdb=" CA ILE D 448 " ideal model delta sigma weight residual 1.461 1.504 -0.043 1.23e-02 6.61e+03 1.23e+01 bond pdb=" N ILE C 448 " pdb=" CA ILE C 448 " ideal model delta sigma weight residual 1.461 1.504 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" N ILE A 448 " pdb=" CA ILE A 448 " ideal model delta sigma weight residual 1.461 1.504 -0.043 1.23e-02 6.61e+03 1.21e+01 ... (remaining 27680 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.89: 614 106.89 - 113.62: 15597 113.62 - 120.34: 12243 120.34 - 127.06: 8818 127.06 - 133.78: 73 Bond angle restraints: 37345 Sorted by residual: angle pdb=" N ILE D 231 " pdb=" CA ILE D 231 " pdb=" C ILE D 231 " ideal model delta sigma weight residual 112.90 103.43 9.47 9.60e-01 1.09e+00 9.72e+01 angle pdb=" N ILE B 231 " pdb=" CA ILE B 231 " pdb=" C ILE B 231 " ideal model delta sigma weight residual 113.43 103.36 10.07 1.09e+00 8.42e-01 8.54e+01 angle pdb=" N ILE C 231 " pdb=" CA ILE C 231 " pdb=" C ILE C 231 " ideal model delta sigma weight residual 113.43 103.36 10.07 1.09e+00 8.42e-01 8.53e+01 angle pdb=" N ILE G 231 " pdb=" CA ILE G 231 " pdb=" C ILE G 231 " ideal model delta sigma weight residual 113.43 103.38 10.05 1.09e+00 8.42e-01 8.51e+01 angle pdb=" C ALA F 276 " pdb=" N PRO F 277 " pdb=" CA PRO F 277 " ideal model delta sigma weight residual 119.56 128.47 -8.91 1.01e+00 9.80e-01 7.79e+01 ... (remaining 37340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 16746 15.67 - 31.33: 369 31.33 - 47.00: 85 47.00 - 62.67: 41 62.67 - 78.33: 28 Dihedral angle restraints: 17269 sinusoidal: 6832 harmonic: 10437 Sorted by residual: dihedral pdb=" CA THR C 205 " pdb=" C THR C 205 " pdb=" N SER C 206 " pdb=" CA SER C 206 " ideal model delta harmonic sigma weight residual 180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA THR A 205 " pdb=" C THR A 205 " pdb=" N SER A 206 " pdb=" CA SER A 206 " ideal model delta harmonic sigma weight residual 180.00 -161.96 -18.04 0 5.00e+00 4.00e-02 1.30e+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 -162.19 -17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 17266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2448 0.052 - 0.104: 1523 0.104 - 0.156: 408 0.156 - 0.208: 167 0.208 - 0.260: 25 Chirality restraints: 4571 Sorted by residual: chirality pdb=" CA PRO A 277 " pdb=" N PRO A 277 " pdb=" C PRO A 277 " pdb=" CB PRO A 277 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA GLU A 408 " pdb=" N GLU A 408 " pdb=" C GLU A 408 " pdb=" CB GLU A 408 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA GLU D 408 " pdb=" N GLU D 408 " pdb=" C GLU D 408 " pdb=" CB GLU D 408 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4568 not shown) Planarity restraints: 4809 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 73 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C GLN C 73 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN C 73 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP C 74 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 73 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C GLN D 73 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN D 73 " 0.017 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 A 73 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" C GLN A 73 " 0.044 2.00e-02 2.50e+03 pdb=" O GLN A 73 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 74 " -0.015 2.00e-02 2.50e+03 ... (remaining 4806 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 9755 2.87 - 3.38: 27152 3.38 - 3.88: 44041 3.88 - 4.39: 50232 4.39 - 4.90: 82929 Nonbonded interactions: 214109 Sorted by model distance: nonbonded pdb=" NZ LYS C 176 " pdb=" OE1 GLU C 321 " model vdw 2.362 2.520 nonbonded pdb=" N ASP C 281 " pdb=" OD1 ASP C 281 " model vdw 2.386 2.520 nonbonded pdb=" NZ LYS B 192 " pdb=" OD1 ASP B 328 " model vdw 2.386 2.520 nonbonded pdb=" OD2 ASP F 183 " pdb=" NZ LYS F 391 " model vdw 2.386 2.520 nonbonded pdb=" NZ LYS D 192 " pdb=" OD1 ASP D 328 " model vdw 2.390 2.520 ... (remaining 214104 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 10.800 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 69.390 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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= 0.968 Angle : 1.439 10.074 37345 Z= 1.052 Chirality : 0.072 0.260 4571 Planarity : 0.007 0.026 4809 Dihedral : 9.236 78.332 10549 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 0.82 % Favored : 98.99 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 0.30 (0.12), residues: 3668 helix: 0.21 (0.10), residues: 2023 sheet: 0.99 (0.21), residues: 553 loop : 0.08 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP G 42 HIS 0.003 0.001 HIS A 241 PHE 0.012 0.001 PHE F 213 TYR 0.028 0.002 TYR E 217 ARG 0.004 0.001 ARG E 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 805 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 805 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7009 (t70) cc_final: 0.6743 (t0) REVERT: A 244 PRO cc_start: 0.7107 (Cg_exo) cc_final: 0.6868 (Cg_endo) REVERT: A 308 LEU cc_start: 0.7617 (mt) cc_final: 0.6966 (pt) REVERT: A 464 ILE cc_start: 0.8416 (mm) cc_final: 0.8194 (mm) REVERT: A 487 MET cc_start: 0.7500 (mmt) cc_final: 0.7280 (tpp) REVERT: B 231 ILE cc_start: 0.7117 (pt) cc_final: 0.6830 (pt) REVERT: B 464 ILE cc_start: 0.8734 (mm) cc_final: 0.8522 (mm) REVERT: C 211 CYS cc_start: 0.8635 (t) cc_final: 0.8043 (m) REVERT: C 228 ILE cc_start: 0.7825 (mm) cc_final: 0.7607 (mm) REVERT: C 304 LEU cc_start: 0.8789 (tp) cc_final: 0.7961 (pt) REVERT: C 487 MET cc_start: 0.7723 (mmt) cc_final: 0.6919 (mmm) REVERT: D 213 PHE cc_start: 0.8618 (m-80) cc_final: 0.8306 (m-10) REVERT: D 279 PHE cc_start: 0.6549 (t80) cc_final: 0.6004 (t80) REVERT: E 338 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7452 (ttmt) REVERT: E 385 ASP cc_start: 0.6998 (p0) cc_final: 0.6651 (m-30) REVERT: E 523 ILE cc_start: 0.8370 (mt) cc_final: 0.8043 (tt) outliers start: 0 outliers final: 0 residues processed: 805 average time/residue: 0.4147 time to fit residues: 507.2552 Evaluate side-chains 336 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 3.284 ------------------------------------------------------------------------------- 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: 3.9990 chunk 275 optimal weight: 0.9980 chunk 153 optimal weight: 0.0050 chunk 94 optimal weight: 0.0470 chunk 186 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 212 optimal weight: 4.9990 chunk 330 optimal weight: 1.9990 overall best weight: 0.5692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 340 GLN A 346 GLN B 77 ASN B 282 ASN C 77 ASN D 214 GLN D 282 ASN ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 GLN F 78 ASN F 340 GLN G 204 ASN G 229 GLN G 282 ASN G 351 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27685 Z= 0.193 Angle : 0.557 7.130 37345 Z= 0.312 Chirality : 0.044 0.282 4571 Planarity : 0.004 0.042 4809 Dihedral : 4.247 31.016 3836 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.05 % Allowed : 8.84 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.13), residues: 3668 helix: 2.13 (0.11), residues: 1972 sheet: 1.05 (0.21), residues: 569 loop : -0.25 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 42 HIS 0.002 0.000 HIS E 314 PHE 0.023 0.002 PHE A 484 TYR 0.015 0.002 TYR A 477 ARG 0.007 0.001 ARG C 169 *********************** 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 462 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 401 time to evaluate : 3.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PRO cc_start: 0.7018 (Cg_exo) cc_final: 0.6647 (Cg_endo) REVERT: A 308 LEU cc_start: 0.7619 (mt) cc_final: 0.7097 (pt) REVERT: B 321 GLU cc_start: 0.7418 (tt0) cc_final: 0.7033 (tt0) REVERT: B 464 ILE cc_start: 0.8972 (mm) cc_final: 0.8711 (mm) REVERT: B 487 MET cc_start: 0.8198 (mmt) cc_final: 0.7596 (mmm) REVERT: C 61 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6671 (ptmt) REVERT: C 228 ILE cc_start: 0.8076 (mm) cc_final: 0.7844 (mm) REVERT: C 304 LEU cc_start: 0.8805 (tp) cc_final: 0.7919 (pt) REVERT: C 397 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: D 213 PHE cc_start: 0.8653 (m-80) cc_final: 0.8334 (m-10) REVERT: E 191 MET cc_start: 0.7240 (ptm) cc_final: 0.6889 (ptp) REVERT: E 215 ASP cc_start: 0.6656 (t0) cc_final: 0.6230 (t0) REVERT: E 523 ILE cc_start: 0.8371 (mt) cc_final: 0.8116 (tt) REVERT: F 153 ASP cc_start: 0.7747 (t0) cc_final: 0.7528 (t0) REVERT: F 345 ILE cc_start: 0.8944 (mt) cc_final: 0.8662 (mm) REVERT: G 263 ASN cc_start: 0.6875 (m-40) cc_final: 0.6671 (t0) REVERT: G 282 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.7114 (m-40) REVERT: G 284 LYS cc_start: 0.8220 (mttt) cc_final: 0.7680 (mtmm) REVERT: G 351 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7171 (mp10) outliers start: 61 outliers final: 32 residues processed: 446 average time/residue: 0.3680 time to fit residues: 266.3021 Evaluate side-chains 284 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 248 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 61 LYS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 282 ASN Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 228 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 282 ASN Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 351 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 183 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 331 optimal weight: 9.9990 chunk 357 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 chunk 328 optimal weight: 1.9990 chunk 112 optimal weight: 0.3980 chunk 265 optimal weight: 0.4980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN B 282 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 ASN E 282 ASN G 282 ASN G 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27685 Z= 0.177 Angle : 0.499 6.657 37345 Z= 0.278 Chirality : 0.042 0.203 4571 Planarity : 0.004 0.040 4809 Dihedral : 3.975 30.715 3836 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.39 % Allowed : 10.79 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.94 (0.14), residues: 3668 helix: 2.41 (0.11), residues: 1998 sheet: 1.09 (0.20), residues: 616 loop : -0.84 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 42 HIS 0.001 0.000 HIS E 314 PHE 0.024 0.002 PHE C 102 TYR 0.012 0.001 TYR G 359 ARG 0.005 0.000 ARG B 367 *********************** 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 365 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 294 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LYS cc_start: 0.8033 (tttt) cc_final: 0.7815 (ptpp) REVERT: A 244 PRO cc_start: 0.7069 (Cg_exo) cc_final: 0.6673 (Cg_endo) REVERT: A 308 LEU cc_start: 0.7581 (mt) cc_final: 0.7086 (pt) REVERT: B 321 GLU cc_start: 0.7504 (tt0) cc_final: 0.7125 (tt0) REVERT: B 464 ILE cc_start: 0.9052 (mm) cc_final: 0.8684 (mm) REVERT: C 201 TYR cc_start: 0.7897 (m-80) cc_final: 0.7649 (m-10) REVERT: C 304 LEU cc_start: 0.8806 (tp) cc_final: 0.7900 (pt) REVERT: C 487 MET cc_start: 0.7768 (mmt) cc_final: 0.7040 (mmm) REVERT: D 213 PHE cc_start: 0.8765 (m-80) cc_final: 0.8481 (m-10) REVERT: D 223 LYS cc_start: 0.8694 (tttt) cc_final: 0.8339 (mtmm) REVERT: D 230 SER cc_start: 0.7624 (m) cc_final: 0.7361 (p) REVERT: E 215 ASP cc_start: 0.6834 (t0) cc_final: 0.6521 (t0) REVERT: E 290 MET cc_start: 0.7297 (mmt) cc_final: 0.6941 (mmt) REVERT: E 385 ASP cc_start: 0.6773 (p0) cc_final: 0.6092 (p0) REVERT: F 153 ASP cc_start: 0.8009 (t0) cc_final: 0.7739 (t0) REVERT: F 202 PHE cc_start: 0.7758 (m-80) cc_final: 0.7446 (m-80) REVERT: F 345 ILE cc_start: 0.9026 (mt) cc_final: 0.8783 (mm) REVERT: G 284 LYS cc_start: 0.8336 (mttt) cc_final: 0.7769 (mttt) outliers start: 71 outliers final: 45 residues processed: 354 average time/residue: 0.3541 time to fit residues: 206.5827 Evaluate side-chains 286 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 241 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 282 ASN Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 351 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 327 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 332 optimal weight: 6.9990 chunk 351 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27685 Z= 0.226 Angle : 0.521 6.917 37345 Z= 0.286 Chirality : 0.043 0.183 4571 Planarity : 0.004 0.062 4809 Dihedral : 4.035 28.632 3836 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.36 % Allowed : 11.23 % Favored : 85.41 % 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: 1.82 (0.14), residues: 3668 helix: 2.45 (0.12), residues: 1965 sheet: 1.15 (0.20), residues: 580 loop : -1.09 (0.16), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 42 HIS 0.002 0.001 HIS E 314 PHE 0.022 0.002 PHE E 279 TYR 0.008 0.001 TYR A 64 ARG 0.011 0.001 ARG E 283 *********************** 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 363 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 263 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LYS cc_start: 0.8319 (tttt) cc_final: 0.7988 (ptpp) REVERT: A 244 PRO cc_start: 0.7413 (Cg_exo) cc_final: 0.7075 (Cg_endo) REVERT: A 290 MET cc_start: 0.5972 (mtt) cc_final: 0.5700 (mtt) REVERT: B 469 MET cc_start: 0.8237 (mtp) cc_final: 0.8006 (tpp) REVERT: C 224 LYS cc_start: 0.8715 (tttt) cc_final: 0.8421 (tttm) REVERT: C 290 MET cc_start: 0.6969 (mtt) cc_final: 0.6682 (mtt) REVERT: C 304 LEU cc_start: 0.8895 (tp) cc_final: 0.7997 (pt) REVERT: C 307 ASN cc_start: 0.7330 (p0) cc_final: 0.7106 (p0) REVERT: C 487 MET cc_start: 0.7768 (mmt) cc_final: 0.7154 (mmm) REVERT: D 215 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7004 (t0) REVERT: D 223 LYS cc_start: 0.8758 (tttt) cc_final: 0.8448 (ptpp) REVERT: D 230 SER cc_start: 0.7774 (m) cc_final: 0.7513 (p) REVERT: D 269 LEU cc_start: 0.8510 (mp) cc_final: 0.7938 (tp) REVERT: E 385 ASP cc_start: 0.6862 (p0) cc_final: 0.6157 (m-30) REVERT: F 153 ASP cc_start: 0.8032 (t0) cc_final: 0.7781 (t0) REVERT: F 202 PHE cc_start: 0.7935 (m-80) cc_final: 0.7377 (m-80) REVERT: F 345 ILE cc_start: 0.9069 (mt) cc_final: 0.8832 (mm) REVERT: F 487 MET cc_start: 0.8298 (tpp) cc_final: 0.7168 (mpp) REVERT: G 9 ASP cc_start: 0.7020 (t0) cc_final: 0.6812 (t0) REVERT: G 263 ASN cc_start: 0.7241 (m-40) cc_final: 0.6417 (t0) outliers start: 100 outliers final: 73 residues processed: 351 average time/residue: 0.3396 time to fit residues: 199.0489 Evaluate side-chains 306 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 232 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 515 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 310 ASP Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 386 VAL Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 515 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 293 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 315 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 282 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27685 Z= 0.207 Angle : 0.500 9.178 37345 Z= 0.273 Chirality : 0.042 0.196 4571 Planarity : 0.004 0.043 4809 Dihedral : 3.978 28.073 3836 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.03 % Allowed : 11.90 % Favored : 85.08 % 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: 1.78 (0.14), residues: 3668 helix: 2.49 (0.12), residues: 1980 sheet: 1.06 (0.20), residues: 580 loop : -1.29 (0.16), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 42 HIS 0.002 0.001 HIS E 314 PHE 0.026 0.002 PHE D 213 TYR 0.009 0.001 TYR G 359 ARG 0.004 0.000 ARG B 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 347 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 257 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LYS cc_start: 0.8465 (tttt) cc_final: 0.8125 (ptpp) REVERT: A 244 PRO cc_start: 0.7536 (Cg_exo) cc_final: 0.7191 (Cg_endo) REVERT: A 290 MET cc_start: 0.6019 (mtt) cc_final: 0.5769 (mtt) REVERT: B 321 GLU cc_start: 0.7577 (tt0) cc_final: 0.7263 (tt0) REVERT: C 224 LYS cc_start: 0.8728 (tttt) cc_final: 0.8371 (tttm) REVERT: C 304 LEU cc_start: 0.8939 (tp) cc_final: 0.8101 (pt) REVERT: C 307 ASN cc_start: 0.7595 (p0) cc_final: 0.7235 (p0) REVERT: C 487 MET cc_start: 0.7829 (mmt) cc_final: 0.7314 (mmm) REVERT: D 215 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7055 (t0) REVERT: D 223 LYS cc_start: 0.8807 (tttt) cc_final: 0.8549 (ptpp) REVERT: D 230 SER cc_start: 0.7872 (m) cc_final: 0.7648 (p) REVERT: D 269 LEU cc_start: 0.8449 (mp) cc_final: 0.7899 (tp) REVERT: E 223 LYS cc_start: 0.8696 (tttt) cc_final: 0.8354 (mtmt) REVERT: F 153 ASP cc_start: 0.8099 (t0) cc_final: 0.7861 (t0) REVERT: F 487 MET cc_start: 0.8286 (tpp) cc_final: 0.7236 (mpp) REVERT: G 9 ASP cc_start: 0.7015 (t0) cc_final: 0.6788 (t0) REVERT: G 119 MET cc_start: 0.7729 (tpp) cc_final: 0.7464 (tpp) outliers start: 90 outliers final: 68 residues processed: 331 average time/residue: 0.3546 time to fit residues: 194.0361 Evaluate side-chains 302 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 233 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 515 THR Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 459 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 515 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 118 optimal weight: 4.9990 chunk 316 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 206 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 352 optimal weight: 3.9990 chunk 292 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN D 229 GLN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 27685 Z= 0.166 Angle : 0.472 7.193 37345 Z= 0.257 Chirality : 0.041 0.172 4571 Planarity : 0.004 0.041 4809 Dihedral : 3.864 27.329 3836 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.72 % Allowed : 13.11 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.14), residues: 3668 helix: 2.54 (0.12), residues: 1998 sheet: 1.05 (0.21), residues: 580 loop : -1.37 (0.16), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 42 HIS 0.001 0.000 HIS B 241 PHE 0.021 0.001 PHE E 279 TYR 0.011 0.001 TYR E 217 ARG 0.004 0.000 ARG F 195 *********************** 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 325 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 244 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LYS cc_start: 0.8520 (tttt) cc_final: 0.8224 (ptpp) REVERT: A 244 PRO cc_start: 0.7465 (Cg_exo) cc_final: 0.7147 (Cg_endo) REVERT: A 290 MET cc_start: 0.6103 (mtt) cc_final: 0.5879 (mtt) REVERT: B 288 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8433 (tttm) REVERT: B 321 GLU cc_start: 0.7532 (tt0) cc_final: 0.7234 (tt0) REVERT: C 224 LYS cc_start: 0.8695 (tttt) cc_final: 0.8374 (tttm) REVERT: C 304 LEU cc_start: 0.8939 (tp) cc_final: 0.8052 (pt) REVERT: C 307 ASN cc_start: 0.7762 (p0) cc_final: 0.7377 (p0) REVERT: C 487 MET cc_start: 0.7863 (mmt) cc_final: 0.7378 (mmm) REVERT: D 215 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7201 (t0) REVERT: D 223 LYS cc_start: 0.8805 (tttt) cc_final: 0.8537 (ptpp) REVERT: D 230 SER cc_start: 0.7857 (m) cc_final: 0.7619 (p) REVERT: D 269 LEU cc_start: 0.8478 (mp) cc_final: 0.7955 (tp) REVERT: E 223 LYS cc_start: 0.8657 (tttt) cc_final: 0.8363 (mtmt) REVERT: E 290 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6672 (mtt) REVERT: F 153 ASP cc_start: 0.8051 (t0) cc_final: 0.7819 (t0) REVERT: F 224 LYS cc_start: 0.7806 (tttt) cc_final: 0.7531 (tmtt) REVERT: F 487 MET cc_start: 0.8238 (tpp) cc_final: 0.7161 (mpp) REVERT: G 9 ASP cc_start: 0.6907 (t0) cc_final: 0.6669 (t0) REVERT: G 119 MET cc_start: 0.7668 (tpp) cc_final: 0.7441 (tpp) REVERT: G 223 LYS cc_start: 0.8323 (ptpt) cc_final: 0.8101 (pttm) REVERT: G 269 LEU cc_start: 0.6953 (mt) cc_final: 0.6660 (mt) REVERT: G 284 LYS cc_start: 0.8288 (mttt) cc_final: 0.7719 (mtmt) outliers start: 81 outliers final: 65 residues processed: 314 average time/residue: 0.3458 time to fit residues: 181.6357 Evaluate side-chains 300 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 232 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 515 THR Chi-restraints excluded: chain G residue 523 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 339 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 257 optimal weight: 0.0870 chunk 199 optimal weight: 0.9990 chunk 296 optimal weight: 4.9990 chunk 196 optimal weight: 0.9990 chunk 350 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 213 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN C 282 ASN D 78 ASN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27685 Z= 0.141 Angle : 0.451 8.270 37345 Z= 0.245 Chirality : 0.041 0.170 4571 Planarity : 0.004 0.041 4809 Dihedral : 3.721 21.294 3836 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.59 % Allowed : 13.75 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.14), residues: 3668 helix: 2.62 (0.12), residues: 2012 sheet: 1.05 (0.21), residues: 580 loop : -1.36 (0.16), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 42 HIS 0.001 0.000 HIS E 314 PHE 0.019 0.001 PHE E 279 TYR 0.010 0.001 TYR E 217 ARG 0.004 0.000 ARG F 195 *********************** 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 323 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 246 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 LYS cc_start: 0.8476 (tttt) cc_final: 0.8190 (ptpp) REVERT: A 244 PRO cc_start: 0.7399 (Cg_exo) cc_final: 0.7068 (Cg_endo) REVERT: B 288 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8406 (tttm) REVERT: B 321 GLU cc_start: 0.7479 (tt0) cc_final: 0.7193 (tt0) REVERT: C 224 LYS cc_start: 0.8698 (tttt) cc_final: 0.8389 (tttm) REVERT: C 304 LEU cc_start: 0.8940 (tp) cc_final: 0.8103 (pt) REVERT: C 307 ASN cc_start: 0.7869 (p0) cc_final: 0.7426 (p0) REVERT: C 487 MET cc_start: 0.7785 (mmt) cc_final: 0.7380 (mmm) REVERT: D 215 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7060 (t0) REVERT: D 230 SER cc_start: 0.7856 (m) cc_final: 0.7632 (p) REVERT: D 269 LEU cc_start: 0.8425 (mp) cc_final: 0.7879 (tp) REVERT: D 304 LEU cc_start: 0.8330 (tp) cc_final: 0.8107 (mp) REVERT: E 223 LYS cc_start: 0.8627 (tttt) cc_final: 0.8391 (mtmt) REVERT: E 290 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6987 (mmm) REVERT: F 153 ASP cc_start: 0.8014 (t0) cc_final: 0.7783 (t0) REVERT: G 119 MET cc_start: 0.7647 (tpp) cc_final: 0.7419 (tpp) REVERT: G 223 LYS cc_start: 0.8292 (ptpt) cc_final: 0.8087 (pttm) REVERT: G 284 LYS cc_start: 0.8287 (mttt) cc_final: 0.7711 (mtmt) outliers start: 77 outliers final: 60 residues processed: 313 average time/residue: 0.3419 time to fit residues: 178.9366 Evaluate side-chains 297 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 234 time to evaluate : 3.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 215 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 523 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 209 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 chunk 239 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27685 Z= 0.163 Angle : 0.466 8.186 37345 Z= 0.251 Chirality : 0.041 0.195 4571 Planarity : 0.004 0.041 4809 Dihedral : 3.725 22.752 3836 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.55 % Allowed : 14.05 % Favored : 83.39 % 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: 1.91 (0.14), residues: 3668 helix: 2.63 (0.12), residues: 2011 sheet: 1.07 (0.21), residues: 580 loop : -1.38 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 42 HIS 0.002 0.000 HIS D 241 PHE 0.017 0.001 PHE E 279 TYR 0.010 0.001 TYR E 217 ARG 0.005 0.000 ARG F 344 *********************** 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 310 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 234 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PRO cc_start: 0.7463 (Cg_exo) cc_final: 0.7120 (Cg_endo) REVERT: B 288 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8398 (tttm) REVERT: B 321 GLU cc_start: 0.7503 (tt0) cc_final: 0.7219 (tt0) REVERT: C 224 LYS cc_start: 0.8718 (tttt) cc_final: 0.8385 (tttm) REVERT: C 290 MET cc_start: 0.6905 (mtt) cc_final: 0.6592 (mtt) REVERT: C 304 LEU cc_start: 0.8952 (tp) cc_final: 0.8123 (pt) REVERT: C 307 ASN cc_start: 0.7964 (p0) cc_final: 0.7519 (p0) REVERT: C 487 MET cc_start: 0.7806 (mmt) cc_final: 0.7371 (mmm) REVERT: D 215 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7059 (t0) REVERT: D 230 SER cc_start: 0.7896 (m) cc_final: 0.7692 (p) REVERT: D 269 LEU cc_start: 0.8436 (mp) cc_final: 0.7697 (tp) REVERT: D 304 LEU cc_start: 0.8350 (tp) cc_final: 0.8131 (mp) REVERT: E 223 LYS cc_start: 0.8647 (tttt) cc_final: 0.8405 (mtmt) REVERT: E 290 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7063 (mmm) REVERT: F 153 ASP cc_start: 0.8066 (t0) cc_final: 0.7864 (t0) REVERT: F 487 MET cc_start: 0.8087 (tpp) cc_final: 0.7187 (mpp) REVERT: G 119 MET cc_start: 0.7695 (tpp) cc_final: 0.7486 (tpp) REVERT: G 223 LYS cc_start: 0.8282 (ptpt) cc_final: 0.8050 (pttm) outliers start: 76 outliers final: 65 residues processed: 298 average time/residue: 0.3306 time to fit residues: 166.5472 Evaluate side-chains 294 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 226 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 212 GLU Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 58 ILE Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 386 VAL Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain E residue 515 THR Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 287 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 523 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 319 optimal weight: 0.0470 chunk 336 optimal weight: 4.9990 chunk 306 optimal weight: 0.7980 chunk 326 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 256 optimal weight: 0.0970 chunk 100 optimal weight: 3.9990 chunk 295 optimal weight: 2.9990 chunk 309 optimal weight: 0.6980 chunk 325 optimal weight: 2.9990 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN C 78 ASN D 78 ASN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 27685 Z= 0.126 Angle : 0.452 9.216 37345 Z= 0.241 Chirality : 0.041 0.192 4571 Planarity : 0.004 0.042 4809 Dihedral : 3.602 21.021 3836 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.61 % Allowed : 15.26 % Favored : 83.13 % 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: 2.08 (0.14), residues: 3668 helix: 2.79 (0.12), residues: 1994 sheet: 0.94 (0.21), residues: 592 loop : -1.19 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 42 HIS 0.001 0.000 HIS B 314 PHE 0.021 0.001 PHE E 279 TYR 0.013 0.001 TYR A 477 ARG 0.004 0.000 ARG F 195 *********************** 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 297 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 249 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 PRO cc_start: 0.7534 (Cg_exo) cc_final: 0.7214 (Cg_endo) REVERT: B 288 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8382 (tttm) REVERT: B 321 GLU cc_start: 0.7430 (tt0) cc_final: 0.7152 (tt0) REVERT: C 224 LYS cc_start: 0.8775 (tttt) cc_final: 0.8505 (tttm) REVERT: C 275 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8137 (tttp) REVERT: C 290 MET cc_start: 0.6871 (mtt) cc_final: 0.6566 (mtt) REVERT: C 304 LEU cc_start: 0.8959 (tp) cc_final: 0.8167 (pt) REVERT: C 307 ASN cc_start: 0.8027 (p0) cc_final: 0.7555 (p0) REVERT: C 487 MET cc_start: 0.7767 (mmt) cc_final: 0.7381 (mmm) REVERT: D 215 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7095 (t0) REVERT: D 304 LEU cc_start: 0.8330 (tp) cc_final: 0.8081 (mp) REVERT: E 223 LYS cc_start: 0.8568 (tttt) cc_final: 0.8315 (mtmt) REVERT: E 290 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7040 (mmm) REVERT: E 385 ASP cc_start: 0.7193 (p0) cc_final: 0.6685 (m-30) REVERT: F 153 ASP cc_start: 0.8022 (t0) cc_final: 0.7786 (t0) REVERT: F 487 MET cc_start: 0.8121 (tpp) cc_final: 0.7836 (tpp) REVERT: G 119 MET cc_start: 0.7625 (tpp) cc_final: 0.7415 (tpp) REVERT: G 223 LYS cc_start: 0.8236 (ptpt) cc_final: 0.8013 (pttm) REVERT: G 284 LYS cc_start: 0.8274 (mttt) cc_final: 0.7702 (mtmt) outliers start: 48 outliers final: 39 residues processed: 291 average time/residue: 0.3367 time to fit residues: 164.9672 Evaluate side-chains 270 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 228 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 523 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 214 optimal weight: 0.6980 chunk 345 optimal weight: 4.9990 chunk 211 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 362 optimal weight: 0.7980 chunk 333 optimal weight: 0.9990 chunk 288 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN D 78 ASN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 27685 Z= 0.147 Angle : 0.463 9.280 37345 Z= 0.246 Chirality : 0.041 0.191 4571 Planarity : 0.004 0.041 4809 Dihedral : 3.593 21.506 3836 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.58 % Allowed : 15.73 % Favored : 82.69 % 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: 2.05 (0.14), residues: 3668 helix: 2.75 (0.12), residues: 2011 sheet: 1.12 (0.21), residues: 580 loop : -1.35 (0.17), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 42 HIS 0.001 0.000 HIS D 241 PHE 0.022 0.001 PHE E 279 TYR 0.010 0.001 TYR A 477 ARG 0.003 0.000 ARG F 195 ********************** 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 275 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 228 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 PHE cc_start: 0.7888 (m-80) cc_final: 0.7676 (m-80) REVERT: A 244 PRO cc_start: 0.7479 (Cg_exo) cc_final: 0.7143 (Cg_endo) REVERT: B 288 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8390 (tttm) REVERT: B 321 GLU cc_start: 0.7438 (tt0) cc_final: 0.7170 (tt0) REVERT: C 224 LYS cc_start: 0.8723 (tttt) cc_final: 0.8465 (tttm) REVERT: C 290 MET cc_start: 0.6915 (mtt) cc_final: 0.6646 (mtt) REVERT: C 304 LEU cc_start: 0.8947 (tp) cc_final: 0.8124 (pt) REVERT: C 307 ASN cc_start: 0.8061 (p0) cc_final: 0.7593 (p0) REVERT: C 487 MET cc_start: 0.7801 (mmt) cc_final: 0.7406 (mmm) REVERT: D 215 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7103 (t0) REVERT: D 269 LEU cc_start: 0.8102 (mp) cc_final: 0.7739 (tt) REVERT: D 304 LEU cc_start: 0.8304 (tp) cc_final: 0.8032 (mp) REVERT: E 223 LYS cc_start: 0.8589 (tttt) cc_final: 0.8315 (mtmt) REVERT: E 290 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.7085 (mmm) REVERT: E 385 ASP cc_start: 0.7289 (p0) cc_final: 0.6820 (m-30) REVERT: F 153 ASP cc_start: 0.8088 (t0) cc_final: 0.7863 (t0) REVERT: F 487 MET cc_start: 0.8101 (tpp) cc_final: 0.7818 (tpp) REVERT: G 223 LYS cc_start: 0.8258 (ptpt) cc_final: 0.8034 (pttm) outliers start: 47 outliers final: 43 residues processed: 268 average time/residue: 0.3426 time to fit residues: 155.3352 Evaluate side-chains 264 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 218 time to evaluate : 4.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 179 LYS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 288 LYS Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 72 ILE Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 215 ASP Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 58 ILE Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 393 ASP Chi-restraints excluded: chain E residue 445 THR Chi-restraints excluded: chain F residue 57 SER Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 445 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 511 SER Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 445 THR Chi-restraints excluded: chain G residue 475 VAL Chi-restraints excluded: chain G residue 523 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 229 optimal weight: 3.9990 chunk 307 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 42 optimal weight: 0.0020 chunk 80 optimal weight: 3.9990 chunk 289 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 296 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN C 78 ASN D 229 GLN ** D 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.140305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115884 restraints weight = 44819.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118490 restraints weight = 30759.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120311 restraints weight = 23617.881| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27685 Z= 0.198 Angle : 0.496 9.352 37345 Z= 0.265 Chirality : 0.042 0.171 4571 Planarity : 0.004 0.043 4809 Dihedral : 3.735 21.435 3836 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.85 % Allowed : 15.60 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.14), residues: 3668 helix: 2.60 (0.12), residues: 2032 sheet: 1.13 (0.21), residues: 561 loop : -1.41 (0.17), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 42 HIS 0.003 0.001 HIS D 241 PHE 0.022 0.002 PHE E 279 TYR 0.010 0.001 TYR A 477 ARG 0.004 0.000 ARG E 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4966.23 seconds wall clock time: 92 minutes 15.43 seconds (5535.43 seconds total)