Starting phenix.real_space_refine on Fri Mar 15 03:14:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayg_7020/03_2024/6ayg_7020.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayg_7020/03_2024/6ayg_7020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayg_7020/03_2024/6ayg_7020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayg_7020/03_2024/6ayg_7020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayg_7020/03_2024/6ayg_7020.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ayg_7020/03_2024/6ayg_7020.pdb" } resolution = 4.65 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= 0.010 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 36 5.16 5 C 6648 2.51 5 N 1896 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10456 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 2614 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 308} Link IDs: {'PTRANS': 8, 'TRANS': 430} Chain breaks: 5 Unresolved non-hydrogen bonds: 1021 Unresolved non-hydrogen angles: 1300 Unresolved non-hydrogen dihedrals: 808 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 12, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 462 Chain: "B" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 2614 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 308} Link IDs: {'PTRANS': 8, 'TRANS': 430} Chain breaks: 5 Unresolved non-hydrogen bonds: 1021 Unresolved non-hydrogen angles: 1300 Unresolved non-hydrogen dihedrals: 808 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 12, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 462 Chain: "C" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 2614 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 308} Link IDs: {'PTRANS': 8, 'TRANS': 430} Chain breaks: 5 Unresolved non-hydrogen bonds: 1021 Unresolved non-hydrogen angles: 1300 Unresolved non-hydrogen dihedrals: 808 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 12, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 462 Chain: "D" Number of atoms: 2614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 2614 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 308} Link IDs: {'PTRANS': 8, 'TRANS': 430} Chain breaks: 5 Unresolved non-hydrogen bonds: 1021 Unresolved non-hydrogen angles: 1300 Unresolved non-hydrogen dihedrals: 808 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 12, 'GLU:plan': 15, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 462 Time building chain proxies: 6.62, per 1000 atoms: 0.63 Number of scatterers: 10456 At special positions: 0 Unit cell: (100.35, 100.35, 105.702, 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 36 16.00 O 1876 8.00 N 1896 7.00 C 6648 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: 4.37 Conformation dependent library (CDL) restraints added in 2.5 seconds 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3376 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 66.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 40 through 47 Processing helix chain 'A' and resid 49 through 54 Processing helix chain 'A' and resid 60 through 103 removed outlier: 3.613A pdb=" N ALA A 64 " --> pdb=" O PRO A 60 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 99 " --> pdb=" O THR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 140 removed outlier: 5.014A pdb=" N TYR A 137 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.508A pdb=" N VAL A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 302 Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 341 through 352 Processing helix chain 'A' and resid 352 through 366 Processing helix chain 'A' and resid 370 through 397 removed outlier: 3.905A pdb=" N SER A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 433 Proline residue: A 410 - end of helix removed outlier: 3.815A pdb=" N MET A 421 " --> pdb=" O CYS A 417 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 439 removed outlier: 4.629A pdb=" N TYR A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.536A pdb=" N ALA A 465 " --> pdb=" O PHE A 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 491 removed outlier: 3.524A pdb=" N ILE A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 513 removed outlier: 3.577A pdb=" N PHE A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 526 Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 60 through 103 removed outlier: 3.613A pdb=" N ALA B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS B 99 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 140 removed outlier: 5.014A pdb=" N TYR B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.508A pdb=" N VAL B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS B 232 " --> pdb=" O GLN B 228 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN B 233 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 302 Processing helix chain 'B' and resid 306 through 318 Processing helix chain 'B' and resid 341 through 352 Processing helix chain 'B' and resid 352 through 366 Processing helix chain 'B' and resid 370 through 397 removed outlier: 3.905A pdb=" N SER B 380 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 433 Proline residue: B 410 - end of helix removed outlier: 3.814A pdb=" N MET B 421 " --> pdb=" O CYS B 417 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE B 422 " --> pdb=" O CYS B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 439 removed outlier: 4.629A pdb=" N TYR B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 456 Processing helix chain 'B' and resid 459 through 466 removed outlier: 3.537A pdb=" N ALA B 465 " --> pdb=" O PHE B 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 466 " --> pdb=" O ALA B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 491 removed outlier: 3.524A pdb=" N ILE B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 513 removed outlier: 3.577A pdb=" N PHE B 497 " --> pdb=" O ILE B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 526 Processing helix chain 'C' and resid 41 through 47 Processing helix chain 'C' and resid 49 through 54 Processing helix chain 'C' and resid 60 through 103 removed outlier: 3.612A pdb=" N ALA C 64 " --> pdb=" O PRO C 60 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 140 removed outlier: 5.014A pdb=" N TYR C 137 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.508A pdb=" N VAL C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N HIS C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 302 Processing helix chain 'C' and resid 306 through 318 Processing helix chain 'C' and resid 341 through 352 Processing helix chain 'C' and resid 352 through 366 Processing helix chain 'C' and resid 370 through 397 removed outlier: 3.905A pdb=" N SER C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 433 Proline residue: C 410 - end of helix removed outlier: 3.815A pdb=" N MET C 421 " --> pdb=" O CYS C 417 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 439 removed outlier: 4.629A pdb=" N TYR C 437 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP C 439 " --> pdb=" O GLY C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 456 Processing helix chain 'C' and resid 459 through 466 removed outlier: 3.537A pdb=" N ALA C 465 " --> pdb=" O PHE C 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 491 removed outlier: 3.524A pdb=" N ILE C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 513 removed outlier: 3.578A pdb=" N PHE C 497 " --> pdb=" O ILE C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 526 Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 49 through 54 Processing helix chain 'D' and resid 60 through 103 removed outlier: 3.612A pdb=" N ALA D 64 " --> pdb=" O PRO D 60 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 140 removed outlier: 5.014A pdb=" N TYR D 137 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.508A pdb=" N VAL D 230 " --> pdb=" O ASN D 226 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS D 232 " --> pdb=" O GLN D 228 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 302 Processing helix chain 'D' and resid 306 through 318 Processing helix chain 'D' and resid 341 through 352 Processing helix chain 'D' and resid 352 through 366 Processing helix chain 'D' and resid 370 through 397 removed outlier: 3.904A pdb=" N SER D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 433 Proline residue: D 410 - end of helix removed outlier: 3.815A pdb=" N MET D 421 " --> pdb=" O CYS D 417 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE D 422 " --> pdb=" O CYS D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 439 removed outlier: 4.630A pdb=" N TYR D 437 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP D 439 " --> pdb=" O GLY D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 456 Processing helix chain 'D' and resid 459 through 466 removed outlier: 3.537A pdb=" N ALA D 465 " --> pdb=" O PHE D 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 466 " --> pdb=" O ALA D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 491 removed outlier: 3.524A pdb=" N ILE D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 513 removed outlier: 3.577A pdb=" N PHE D 497 " --> pdb=" O ILE D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 526 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 188 removed outlier: 4.244A pdb=" N THR A 215 " --> pdb=" O HIS A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 Processing sheet with id=AA3, first strand: chain 'B' and resid 181 through 188 removed outlier: 4.244A pdb=" N THR B 215 " --> pdb=" O HIS B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 167 through 168 Processing sheet with id=AA5, first strand: chain 'C' and resid 181 through 188 removed outlier: 4.244A pdb=" N THR C 215 " --> pdb=" O HIS C 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 167 through 168 Processing sheet with id=AA7, first strand: chain 'D' and resid 181 through 188 removed outlier: 4.244A pdb=" N THR D 215 " --> pdb=" O HIS D 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 167 through 168 949 hydrogen bonds defined for protein. 2799 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: 3.42 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3636 1.36 - 1.49: 3104 1.49 - 1.63: 3888 1.63 - 1.76: 0 1.76 - 1.89: 48 Bond restraints: 10676 Sorted by residual: bond pdb=" CB PHE D 102 " pdb=" CG PHE D 102 " ideal model delta sigma weight residual 1.502 1.428 0.074 2.30e-02 1.89e+03 1.02e+01 bond pdb=" CB PHE B 102 " pdb=" CG PHE B 102 " ideal model delta sigma weight residual 1.502 1.429 0.073 2.30e-02 1.89e+03 1.02e+01 bond pdb=" CB PHE C 102 " pdb=" CG PHE C 102 " ideal model delta sigma weight residual 1.502 1.429 0.073 2.30e-02 1.89e+03 1.02e+01 bond pdb=" CB PHE A 102 " pdb=" CG PHE A 102 " ideal model delta sigma weight residual 1.502 1.429 0.073 2.30e-02 1.89e+03 1.01e+01 bond pdb=" CB PHE B 288 " pdb=" CG PHE B 288 " ideal model delta sigma weight residual 1.502 1.575 -0.073 2.30e-02 1.89e+03 1.01e+01 ... (remaining 10671 not shown) Histogram of bond angle deviations from ideal: 96.00 - 103.65: 104 103.65 - 111.30: 4027 111.30 - 118.94: 4006 118.94 - 126.59: 6419 126.59 - 134.24: 196 Bond angle restraints: 14752 Sorted by residual: angle pdb=" N ILE B 493 " pdb=" CA ILE B 493 " pdb=" C ILE B 493 " ideal model delta sigma weight residual 110.42 122.48 -12.06 9.60e-01 1.09e+00 1.58e+02 angle pdb=" N ILE A 493 " pdb=" CA ILE A 493 " pdb=" C ILE A 493 " ideal model delta sigma weight residual 110.42 122.47 -12.05 9.60e-01 1.09e+00 1.58e+02 angle pdb=" N ILE C 493 " pdb=" CA ILE C 493 " pdb=" C ILE C 493 " ideal model delta sigma weight residual 110.42 122.47 -12.05 9.60e-01 1.09e+00 1.58e+02 angle pdb=" N ILE D 493 " pdb=" CA ILE D 493 " pdb=" C ILE D 493 " ideal model delta sigma weight residual 110.42 122.44 -12.02 9.60e-01 1.09e+00 1.57e+02 angle pdb=" N PHE A 210 " pdb=" CA PHE A 210 " pdb=" C PHE A 210 " ideal model delta sigma weight residual 111.07 121.28 -10.21 1.07e+00 8.73e-01 9.11e+01 ... (remaining 14747 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.26: 5477 13.26 - 26.52: 364 26.52 - 39.78: 107 39.78 - 53.04: 16 53.04 - 66.30: 8 Dihedral angle restraints: 5972 sinusoidal: 804 harmonic: 5168 Sorted by residual: dihedral pdb=" CA LYS C 466 " pdb=" C LYS C 466 " pdb=" N MET C 467 " pdb=" CA MET C 467 " ideal model delta harmonic sigma weight residual -180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LYS A 466 " pdb=" C LYS A 466 " pdb=" N MET A 467 " pdb=" CA MET A 467 " ideal model delta harmonic sigma weight residual -180.00 -156.72 -23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LYS D 466 " pdb=" C LYS D 466 " pdb=" N MET D 467 " pdb=" CA MET D 467 " ideal model delta harmonic sigma weight residual -180.00 -156.72 -23.28 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 5969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1352 0.076 - 0.152: 318 0.152 - 0.228: 50 0.228 - 0.304: 8 0.304 - 0.380: 16 Chirality restraints: 1744 Sorted by residual: chirality pdb=" CG LEU C 482 " pdb=" CB LEU C 482 " pdb=" CD1 LEU C 482 " pdb=" CD2 LEU C 482 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CG LEU B 482 " pdb=" CB LEU B 482 " pdb=" CD1 LEU B 482 " pdb=" CD2 LEU B 482 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CG LEU D 482 " pdb=" CB LEU D 482 " pdb=" CD1 LEU D 482 " pdb=" CD2 LEU D 482 " both_signs ideal model delta sigma weight residual False -2.59 -2.97 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 1741 not shown) Planarity restraints: 2004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 48 " -0.104 5.00e-02 4.00e+02 1.73e-01 4.81e+01 pdb=" N PRO B 49 " 0.300 5.00e-02 4.00e+02 pdb=" CA PRO B 49 " -0.103 5.00e-02 4.00e+02 pdb=" CD PRO B 49 " -0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 48 " 0.104 5.00e-02 4.00e+02 1.73e-01 4.80e+01 pdb=" N PRO A 49 " -0.300 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " 0.103 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " 0.093 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 48 " 0.104 5.00e-02 4.00e+02 1.73e-01 4.80e+01 pdb=" N PRO D 49 " -0.300 5.00e-02 4.00e+02 pdb=" CA PRO D 49 " 0.103 5.00e-02 4.00e+02 pdb=" CD PRO D 49 " 0.093 5.00e-02 4.00e+02 ... (remaining 2001 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 907 2.72 - 3.27: 11353 3.27 - 3.81: 15814 3.81 - 4.36: 18109 4.36 - 4.90: 28141 Nonbonded interactions: 74324 Sorted by model distance: nonbonded pdb=" O PHE D 489 " pdb=" N ILE D 493 " model vdw 2.180 2.520 nonbonded pdb=" O PHE C 489 " pdb=" N ILE C 493 " model vdw 2.204 2.520 nonbonded pdb=" O PHE B 489 " pdb=" N ILE B 493 " model vdw 2.204 2.520 nonbonded pdb=" O PHE A 489 " pdb=" N ILE A 493 " model vdw 2.205 2.520 nonbonded pdb=" O LEU A 488 " pdb=" CB MET A 492 " model vdw 2.252 3.440 ... (remaining 74319 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' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 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: 0.000 Extract box with map and model: 1.530 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 33.090 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.013 0.093 10676 Z= 0.887 Angle : 1.563 15.688 14752 Z= 1.006 Chirality : 0.073 0.380 1744 Planarity : 0.013 0.173 2004 Dihedral : 11.749 66.300 2596 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.67 % Favored : 91.86 % Rotamer: Outliers : 1.09 % Allowed : 15.22 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.16), residues: 1708 helix: -3.18 (0.12), residues: 996 sheet: -1.38 (0.27), residues: 264 loop : -2.32 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.006 TRP C 61 HIS 0.016 0.006 HIS C 252 PHE 0.045 0.005 PHE C 291 TYR 0.043 0.008 TYR D 481 ARG 0.016 0.004 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.1221 time to fit residues: 7.3935 Evaluate side-chains 39 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.0870 chunk 130 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 81 optimal weight: 40.0000 chunk 100 optimal weight: 7.9990 chunk 156 optimal weight: 5.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10676 Z= 0.245 Angle : 0.597 6.333 14752 Z= 0.356 Chirality : 0.041 0.162 1744 Planarity : 0.005 0.056 2004 Dihedral : 5.504 19.036 1808 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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: -2.14 (0.18), residues: 1708 helix: -1.05 (0.14), residues: 1052 sheet: -1.30 (0.26), residues: 276 loop : -1.91 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 475 HIS 0.004 0.001 HIS A 252 PHE 0.023 0.002 PHE B 489 TYR 0.018 0.003 TYR C 123 ARG 0.004 0.001 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.324 Fit side-chains REVERT: A 255 ARG cc_start: 0.8338 (ptt180) cc_final: 0.7218 (mmt90) REVERT: A 385 TRP cc_start: 0.9281 (m100) cc_final: 0.8935 (m-90) REVERT: A 452 PHE cc_start: 0.9207 (t80) cc_final: 0.8990 (t80) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0946 time to fit residues: 5.6021 Evaluate side-chains 37 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 30.0000 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 30.0000 chunk 106 optimal weight: 0.4980 chunk 43 optimal weight: 30.0000 chunk 156 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 53 optimal weight: 0.0010 chunk 125 optimal weight: 5.9990 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10676 Z= 0.142 Angle : 0.480 5.755 14752 Z= 0.272 Chirality : 0.039 0.120 1744 Planarity : 0.004 0.051 2004 Dihedral : 4.638 17.296 1808 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % 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: 0.18 (0.19), residues: 1708 helix: 0.96 (0.15), residues: 1076 sheet: -0.69 (0.27), residues: 268 loop : -1.54 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 431 HIS 0.004 0.001 HIS A 252 PHE 0.027 0.001 PHE C 489 TYR 0.011 0.001 TYR B 123 ARG 0.002 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.329 Fit side-chains REVERT: A 255 ARG cc_start: 0.8071 (ptt180) cc_final: 0.7225 (tpp-160) REVERT: A 385 TRP cc_start: 0.9164 (m100) cc_final: 0.8668 (m-10) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1020 time to fit residues: 5.8612 Evaluate side-chains 37 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 30.0000 chunk 117 optimal weight: 0.0370 chunk 81 optimal weight: 30.0000 chunk 17 optimal weight: 50.0000 chunk 74 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 157 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10676 Z= 0.118 Angle : 0.454 7.111 14752 Z= 0.252 Chirality : 0.039 0.118 1744 Planarity : 0.003 0.049 2004 Dihedral : 4.304 17.673 1808 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % 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: 1.35 (0.20), residues: 1708 helix: 2.01 (0.15), residues: 1076 sheet: -0.33 (0.29), residues: 272 loop : -1.54 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 385 HIS 0.004 0.001 HIS D 252 PHE 0.014 0.001 PHE D 485 TYR 0.009 0.001 TYR A 123 ARG 0.002 0.000 ARG B 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.325 Fit side-chains REVERT: A 72 MET cc_start: 0.9604 (ttm) cc_final: 0.9270 (ttt) REVERT: A 255 ARG cc_start: 0.8039 (ptt180) cc_final: 0.7249 (tpp-160) REVERT: A 385 TRP cc_start: 0.9070 (m100) cc_final: 0.8464 (m-10) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1001 time to fit residues: 5.6850 Evaluate side-chains 39 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 30.0000 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10676 Z= 0.167 Angle : 0.468 5.949 14752 Z= 0.264 Chirality : 0.039 0.158 1744 Planarity : 0.003 0.047 2004 Dihedral : 4.092 17.202 1808 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.20), residues: 1708 helix: 2.47 (0.15), residues: 1072 sheet: -0.17 (0.29), residues: 272 loop : -1.42 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 431 HIS 0.004 0.001 HIS C 252 PHE 0.023 0.002 PHE B 489 TYR 0.007 0.001 TYR D 123 ARG 0.001 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.341 Fit side-chains REVERT: A 72 MET cc_start: 0.9616 (ttm) cc_final: 0.9327 (ttp) REVERT: A 385 TRP cc_start: 0.9043 (m100) cc_final: 0.8456 (m-10) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0787 time to fit residues: 4.7021 Evaluate side-chains 36 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 5.9990 chunk 149 optimal weight: 0.0470 chunk 32 optimal weight: 4.9990 chunk 97 optimal weight: 30.0000 chunk 41 optimal weight: 0.9980 chunk 166 optimal weight: 0.9980 chunk 138 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 overall best weight: 2.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10676 Z= 0.126 Angle : 0.441 6.424 14752 Z= 0.248 Chirality : 0.039 0.155 1744 Planarity : 0.003 0.045 2004 Dihedral : 3.879 17.099 1808 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.21), residues: 1708 helix: 2.88 (0.15), residues: 1068 sheet: 0.03 (0.30), residues: 272 loop : -1.33 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 385 HIS 0.003 0.001 HIS A 252 PHE 0.017 0.001 PHE C 489 TYR 0.007 0.001 TYR C 239 ARG 0.001 0.000 ARG C 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.308 Fit side-chains REVERT: A 72 MET cc_start: 0.9597 (ttm) cc_final: 0.9225 (ttp) REVERT: A 385 TRP cc_start: 0.9000 (m100) cc_final: 0.8534 (m-10) REVERT: A 431 TRP cc_start: 0.8919 (t60) cc_final: 0.8461 (t60) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0759 time to fit residues: 4.5143 Evaluate side-chains 35 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 140 optimal weight: 30.0000 chunk 92 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 103 optimal weight: 50.0000 chunk 101 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 102 optimal weight: 0.0270 chunk 66 optimal weight: 1.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 10676 Z= 0.133 Angle : 0.455 7.214 14752 Z= 0.251 Chirality : 0.039 0.140 1744 Planarity : 0.003 0.043 2004 Dihedral : 3.808 16.465 1808 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % 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: 2.61 (0.21), residues: 1708 helix: 3.11 (0.15), residues: 1076 sheet: 0.07 (0.30), residues: 272 loop : -1.45 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 385 HIS 0.002 0.001 HIS D 252 PHE 0.016 0.001 PHE D 489 TYR 0.007 0.001 TYR B 239 ARG 0.001 0.000 ARG D 479 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.290 Fit side-chains REVERT: A 72 MET cc_start: 0.9604 (ttm) cc_final: 0.9221 (ttp) REVERT: A 385 TRP cc_start: 0.8982 (m100) cc_final: 0.8490 (m-10) REVERT: A 431 TRP cc_start: 0.8933 (t60) cc_final: 0.8495 (t60) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0745 time to fit residues: 4.3807 Evaluate side-chains 34 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 105 optimal weight: 0.3980 chunk 112 optimal weight: 5.9990 chunk 81 optimal weight: 40.0000 chunk 15 optimal weight: 0.9980 chunk 130 optimal weight: 0.0770 chunk 150 optimal weight: 40.0000 chunk 158 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 overall best weight: 1.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10676 Z= 0.112 Angle : 0.432 6.582 14752 Z= 0.236 Chirality : 0.039 0.151 1744 Planarity : 0.003 0.044 2004 Dihedral : 3.682 16.385 1808 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.21), residues: 1708 helix: 3.34 (0.15), residues: 1080 sheet: 0.13 (0.30), residues: 272 loop : -1.45 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 385 HIS 0.002 0.001 HIS C 252 PHE 0.015 0.001 PHE D 489 TYR 0.007 0.001 TYR D 106 ARG 0.001 0.000 ARG D 56 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.312 Fit side-chains REVERT: A 72 MET cc_start: 0.9617 (ttm) cc_final: 0.9233 (ttp) REVERT: A 385 TRP cc_start: 0.8938 (m100) cc_final: 0.8587 (m-10) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0754 time to fit residues: 4.4925 Evaluate side-chains 36 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 30.0000 chunk 158 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 67 optimal weight: 40.0000 chunk 121 optimal weight: 0.0000 chunk 47 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 146 optimal weight: 50.0000 chunk 153 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10676 Z= 0.253 Angle : 0.543 6.667 14752 Z= 0.317 Chirality : 0.040 0.122 1744 Planarity : 0.003 0.043 2004 Dihedral : 4.155 16.750 1808 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.21), residues: 1708 helix: 2.95 (0.15), residues: 1076 sheet: -0.12 (0.30), residues: 272 loop : -1.61 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 385 HIS 0.004 0.001 HIS A 100 PHE 0.026 0.002 PHE B 489 TYR 0.012 0.002 TYR B 106 ARG 0.003 0.001 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.295 Fit side-chains REVERT: D 72 MET cc_start: 0.9616 (ttm) cc_final: 0.9285 (ttp) REVERT: D 431 TRP cc_start: 0.8970 (t60) cc_final: 0.8430 (t60) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0767 time to fit residues: 4.5744 Evaluate side-chains 34 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 171 optimal weight: 9.9990 chunk 157 optimal weight: 0.0020 chunk 136 optimal weight: 20.0000 chunk 14 optimal weight: 0.0980 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 145 optimal weight: 0.0470 overall best weight: 0.3886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10676 Z= 0.115 Angle : 0.448 6.780 14752 Z= 0.242 Chirality : 0.039 0.121 1744 Planarity : 0.003 0.046 2004 Dihedral : 3.811 15.661 1808 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.54 (0.21), residues: 1708 helix: 3.05 (0.15), residues: 1084 sheet: 0.07 (0.31), residues: 272 loop : -1.58 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 385 HIS 0.002 0.001 HIS D 252 PHE 0.019 0.001 PHE C 489 TYR 0.008 0.001 TYR A 239 ARG 0.002 0.000 ARG C 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2562 Ramachandran restraints generated. 1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.293 Fit side-chains REVERT: D 72 MET cc_start: 0.9615 (ttm) cc_final: 0.9278 (ttp) REVERT: D 385 TRP cc_start: 0.9042 (m100) cc_final: 0.8514 (m-10) REVERT: D 431 TRP cc_start: 0.8714 (t60) cc_final: 0.8234 (t60) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.0807 time to fit residues: 4.7524 Evaluate side-chains 36 residues out of total 400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 6.9990 chunk 125 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 57 optimal weight: 0.5980 chunk 140 optimal weight: 30.0000 chunk 17 optimal weight: 50.0000 chunk 25 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.065739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.051946 restraints weight = 18832.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.052789 restraints weight = 14251.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.053395 restraints weight = 11586.188| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.6153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10676 Z= 0.166 Angle : 0.457 5.679 14752 Z= 0.259 Chirality : 0.039 0.118 1744 Planarity : 0.003 0.044 2004 Dihedral : 3.853 15.937 1808 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.21), residues: 1708 helix: 3.14 (0.15), residues: 1080 sheet: 0.04 (0.31), residues: 272 loop : -1.60 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 385 HIS 0.003 0.001 HIS C 100 PHE 0.015 0.002 PHE A 485 TYR 0.010 0.001 TYR A 106 ARG 0.001 0.000 ARG A 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1404.70 seconds wall clock time: 25 minutes 55.58 seconds (1555.58 seconds total)