Starting phenix.real_space_refine on Tue Mar 19 02:34:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk8_40558/03_2024/8sk8_40558.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk8_40558/03_2024/8sk8_40558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk8_40558/03_2024/8sk8_40558.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk8_40558/03_2024/8sk8_40558.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk8_40558/03_2024/8sk8_40558.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sk8_40558/03_2024/8sk8_40558.pdb" } resolution = 2.31 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 14538 2.51 5 N 4020 2.21 5 O 4254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22920 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3820 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3820 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3820 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3820 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3820 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3820 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 12.14, per 1000 atoms: 0.53 Number of scatterers: 22920 At special positions: 0 Unit cell: (117.975, 110.55, 164.175, 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 108 16.00 O 4254 8.00 N 4020 7.00 C 14538 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: 8.76 Conformation dependent library (CDL) restraints added in 4.3 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5388 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 9 sheets defined 58.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 67 through 88 removed outlier: 3.959A pdb=" N GLU A 71 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 157 through 175 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.581A pdb=" N MET A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 255 removed outlier: 4.372A pdb=" N HIS A 252 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 255 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.519A pdb=" N PHE A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.676A pdb=" N GLN A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 410 through 420 removed outlier: 3.551A pdb=" N LYS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 455 through 479 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 501 through 528 removed outlier: 3.750A pdb=" N ILE A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 Processing helix chain 'B' and resid 67 through 88 removed outlier: 3.962A pdb=" N GLU B 71 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.525A pdb=" N LYS B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 244 removed outlier: 3.541A pdb=" N MET B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 255 removed outlier: 4.328A pdb=" N HIS B 252 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 255 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.512A pdb=" N PHE B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.671A pdb=" N GLN B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.560A pdb=" N LYS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 432 through 448 Processing helix chain 'B' and resid 455 through 479 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 501 through 528 removed outlier: 3.757A pdb=" N ILE B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 552 Processing helix chain 'C' and resid 67 through 88 removed outlier: 3.960A pdb=" N GLU C 71 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 110 Processing helix chain 'C' and resid 157 through 175 Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 194 through 212 Processing helix chain 'C' and resid 229 through 244 removed outlier: 3.582A pdb=" N MET C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 255 removed outlier: 4.373A pdb=" N HIS C 252 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL C 255 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 270 through 285 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.520A pdb=" N PHE C 323 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.671A pdb=" N GLN C 354 " --> pdb=" O ASP C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 410 through 420 removed outlier: 3.553A pdb=" N LYS C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 432 through 448 Processing helix chain 'C' and resid 455 through 479 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 501 through 528 removed outlier: 3.751A pdb=" N ILE C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 Processing helix chain 'D' and resid 67 through 88 removed outlier: 3.962A pdb=" N GLU D 71 " --> pdb=" O PHE D 67 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 110 Processing helix chain 'D' and resid 157 through 175 Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 194 through 212 removed outlier: 3.531A pdb=" N LYS D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 244 removed outlier: 3.541A pdb=" N MET D 233 " --> pdb=" O GLY D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 255 removed outlier: 4.328A pdb=" N HIS D 252 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL D 255 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 270 through 285 removed outlier: 3.500A pdb=" N PHE D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.512A pdb=" N PHE D 323 " --> pdb=" O TYR D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 356 removed outlier: 3.671A pdb=" N GLN D 354 " --> pdb=" O ASP D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 410 through 420 removed outlier: 3.555A pdb=" N LYS D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 431 Processing helix chain 'D' and resid 432 through 448 Processing helix chain 'D' and resid 455 through 479 Processing helix chain 'D' and resid 490 through 499 Processing helix chain 'D' and resid 501 through 528 removed outlier: 3.758A pdb=" N ILE D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 552 Processing helix chain 'E' and resid 67 through 88 removed outlier: 4.024A pdb=" N GLU E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 110 Processing helix chain 'E' and resid 157 through 175 Processing helix chain 'E' and resid 189 through 193 Processing helix chain 'E' and resid 194 through 212 removed outlier: 3.538A pdb=" N LYS E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 removed outlier: 3.561A pdb=" N MET E 233 " --> pdb=" O GLY E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 255 removed outlier: 4.337A pdb=" N HIS E 252 " --> pdb=" O ILE E 249 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL E 255 " --> pdb=" O HIS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 270 through 285 Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 344 through 356 removed outlier: 3.666A pdb=" N GLN E 354 " --> pdb=" O ASP E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'E' and resid 392 through 396 Processing helix chain 'E' and resid 410 through 420 removed outlier: 3.537A pdb=" N LYS E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 416 " --> pdb=" O GLU E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 431 Processing helix chain 'E' and resid 432 through 448 Processing helix chain 'E' and resid 455 through 479 Processing helix chain 'E' and resid 490 through 499 Processing helix chain 'E' and resid 501 through 528 removed outlier: 3.728A pdb=" N ILE E 505 " --> pdb=" O SER E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 552 Processing helix chain 'F' and resid 67 through 88 removed outlier: 4.026A pdb=" N GLU F 71 " --> pdb=" O PHE F 67 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 110 Processing helix chain 'F' and resid 157 through 175 Processing helix chain 'F' and resid 189 through 193 Processing helix chain 'F' and resid 194 through 212 removed outlier: 3.536A pdb=" N LYS F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 244 removed outlier: 3.562A pdb=" N MET F 233 " --> pdb=" O GLY F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 255 removed outlier: 4.338A pdb=" N HIS F 252 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL F 255 " --> pdb=" O HIS F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 270 through 285 Processing helix chain 'F' and resid 286 through 294 Processing helix chain 'F' and resid 310 through 323 Processing helix chain 'F' and resid 344 through 356 removed outlier: 3.670A pdb=" N GLN F 354 " --> pdb=" O ASP F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 374 Processing helix chain 'F' and resid 392 through 396 Processing helix chain 'F' and resid 410 through 420 removed outlier: 3.537A pdb=" N LYS F 415 " --> pdb=" O PRO F 411 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE F 416 " --> pdb=" O GLU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 431 Processing helix chain 'F' and resid 432 through 448 Processing helix chain 'F' and resid 455 through 479 Processing helix chain 'F' and resid 490 through 499 Processing helix chain 'F' and resid 501 through 528 removed outlier: 3.727A pdb=" N ILE F 505 " --> pdb=" O SER F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 552 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 6.566A pdb=" N CYS A 146 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ALA A 223 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY A 148 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS A 147 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA A 184 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY A 149 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL A 186 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 151 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS E 147 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA E 184 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY E 149 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL E 186 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG E 151 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS E 146 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA E 223 " --> pdb=" O CYS E 146 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLY E 148 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 6.754A pdb=" N PHE A 304 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLY A 331 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 306 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A 303 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE A 380 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 305 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 379 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 220 through 223 removed outlier: 6.575A pdb=" N CYS B 146 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA B 223 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 148 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LYS B 147 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA B 184 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY B 149 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL B 186 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG B 151 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS D 147 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA D 184 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY D 149 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL D 186 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG D 151 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS D 146 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA D 223 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY D 148 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 365 through 366 removed outlier: 6.761A pdb=" N PHE B 304 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLY B 331 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 306 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR B 303 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE B 380 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 305 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 379 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 220 through 223 removed outlier: 6.566A pdb=" N CYS C 146 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA C 223 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY C 148 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS C 147 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA C 184 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY C 149 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL C 186 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG C 151 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS F 147 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ALA F 184 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY F 149 " --> pdb=" O ALA F 184 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL F 186 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG F 151 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS F 146 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA F 223 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLY F 148 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.759A pdb=" N PHE C 304 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY C 331 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 306 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR C 303 " --> pdb=" O ILE C 378 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE C 380 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C 305 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 379 " --> pdb=" O ALA C 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 365 through 366 removed outlier: 6.763A pdb=" N PHE D 304 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLY D 331 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL D 306 " --> pdb=" O GLY D 331 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR D 303 " --> pdb=" O ILE D 378 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE D 380 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL D 305 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU D 379 " --> pdb=" O ALA D 402 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 365 through 366 removed outlier: 6.781A pdb=" N PHE E 304 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLY E 331 " --> pdb=" O PHE E 304 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL E 306 " --> pdb=" O GLY E 331 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR E 303 " --> pdb=" O ILE E 378 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE E 380 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL E 305 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 379 " --> pdb=" O ALA E 402 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 365 through 366 removed outlier: 6.762A pdb=" N PHE F 304 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY F 331 " --> pdb=" O PHE F 304 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL F 306 " --> pdb=" O GLY F 331 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR F 303 " --> pdb=" O ILE F 378 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE F 380 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL F 305 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU F 379 " --> pdb=" O ALA F 402 " (cutoff:3.500A) 1337 hydrogen bonds defined for protein. 3789 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: 7.70 Time building geometry restraints manager: 9.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7614 1.34 - 1.45: 3188 1.45 - 1.57: 12442 1.57 - 1.69: 0 1.69 - 1.80: 180 Bond restraints: 23424 Sorted by residual: bond pdb=" C GLY D 180 " pdb=" N GLY D 181 " ideal model delta sigma weight residual 1.331 1.322 0.008 1.00e-02 1.00e+04 7.22e-01 bond pdb=" C GLY B 180 " pdb=" N GLY B 181 " ideal model delta sigma weight residual 1.331 1.322 0.008 1.00e-02 1.00e+04 7.04e-01 bond pdb=" CA ILE D 219 " pdb=" CB ILE D 219 " ideal model delta sigma weight residual 1.545 1.538 0.008 9.10e-03 1.21e+04 6.86e-01 bond pdb=" CA ILE C 219 " pdb=" CB ILE C 219 " ideal model delta sigma weight residual 1.545 1.538 0.007 9.10e-03 1.21e+04 6.54e-01 bond pdb=" N ASP B 220 " pdb=" CA ASP B 220 " ideal model delta sigma weight residual 1.461 1.452 0.010 1.20e-02 6.94e+03 6.33e-01 ... (remaining 23419 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.94: 717 106.94 - 113.70: 12993 113.70 - 120.47: 8677 120.47 - 127.23: 9028 127.23 - 133.99: 241 Bond angle restraints: 31656 Sorted by residual: angle pdb=" N THR D 144 " pdb=" CA THR D 144 " pdb=" C THR D 144 " ideal model delta sigma weight residual 109.58 104.31 5.27 1.63e+00 3.76e-01 1.05e+01 angle pdb=" N THR B 144 " pdb=" CA THR B 144 " pdb=" C THR B 144 " ideal model delta sigma weight residual 109.58 104.31 5.27 1.63e+00 3.76e-01 1.05e+01 angle pdb=" N THR F 144 " pdb=" CA THR F 144 " pdb=" C THR F 144 " ideal model delta sigma weight residual 109.58 104.48 5.10 1.63e+00 3.76e-01 9.79e+00 angle pdb=" N THR E 144 " pdb=" CA THR E 144 " pdb=" C THR E 144 " ideal model delta sigma weight residual 109.58 104.48 5.10 1.63e+00 3.76e-01 9.79e+00 angle pdb=" N THR C 144 " pdb=" CA THR C 144 " pdb=" C THR C 144 " ideal model delta sigma weight residual 109.58 104.63 4.95 1.63e+00 3.76e-01 9.23e+00 ... (remaining 31651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 13190 15.91 - 31.82: 634 31.82 - 47.74: 86 47.74 - 63.65: 64 63.65 - 79.56: 12 Dihedral angle restraints: 13986 sinusoidal: 5520 harmonic: 8466 Sorted by residual: dihedral pdb=" CA PHE C 179 " pdb=" C PHE C 179 " pdb=" N GLY C 180 " pdb=" CA GLY C 180 " ideal model delta harmonic sigma weight residual 180.00 163.75 16.25 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PHE A 179 " pdb=" C PHE A 179 " pdb=" N GLY A 180 " pdb=" CA GLY A 180 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PHE F 179 " pdb=" C PHE F 179 " pdb=" N GLY F 180 " pdb=" CA GLY F 180 " ideal model delta harmonic sigma weight residual 180.00 164.71 15.29 0 5.00e+00 4.00e-02 9.36e+00 ... (remaining 13983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1851 0.026 - 0.053: 997 0.053 - 0.079: 356 0.079 - 0.106: 158 0.106 - 0.132: 82 Chirality restraints: 3444 Sorted by residual: chirality pdb=" CA ILE A 337 " pdb=" N ILE A 337 " pdb=" C ILE A 337 " pdb=" CB ILE A 337 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE F 337 " pdb=" N ILE F 337 " pdb=" C ILE F 337 " pdb=" CB ILE F 337 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE C 337 " pdb=" N ILE C 337 " pdb=" C ILE C 337 " pdb=" CB ILE C 337 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 3441 not shown) Planarity restraints: 4128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 63 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO A 64 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 63 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO C 64 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 63 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO F 64 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO F 64 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 64 " -0.021 5.00e-02 4.00e+02 ... (remaining 4125 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 831 2.72 - 3.26: 23847 3.26 - 3.81: 39031 3.81 - 4.35: 48670 4.35 - 4.90: 83519 Nonbonded interactions: 195898 Sorted by model distance: nonbonded pdb=" OG SER F 153 " pdb=" OD1 ASP F 155 " model vdw 2.172 2.440 nonbonded pdb=" OG SER E 153 " pdb=" OD1 ASP E 155 " model vdw 2.173 2.440 nonbonded pdb=" OG SER A 153 " pdb=" OD1 ASP A 155 " model vdw 2.174 2.440 nonbonded pdb=" OG SER C 153 " pdb=" OD1 ASP C 155 " model vdw 2.174 2.440 nonbonded pdb=" OH TYR E 528 " pdb=" OE2 GLU E 544 " model vdw 2.184 2.440 ... (remaining 195893 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 6.980 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 59.900 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.130 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:11.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 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 : 0.004 0.032 23424 Z= 0.290 Angle : 0.469 5.273 31656 Z= 0.263 Chirality : 0.041 0.132 3444 Planarity : 0.004 0.039 4128 Dihedral : 10.312 79.562 8598 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.54 % Allowed : 4.02 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.44 (0.15), residues: 2964 helix: 1.94 (0.12), residues: 1548 sheet: -0.16 (0.31), residues: 306 loop : -0.04 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 442 HIS 0.003 0.001 HIS F 315 PHE 0.011 0.001 PHE A 304 TYR 0.014 0.001 TYR C 170 ARG 0.003 0.000 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 222 time to evaluate : 2.748 Fit side-chains REVERT: A 67 PHE cc_start: 0.8117 (t80) cc_final: 0.7771 (m-80) REVERT: B 67 PHE cc_start: 0.8060 (t80) cc_final: 0.7727 (m-80) REVERT: B 338 TRP cc_start: 0.8803 (t60) cc_final: 0.8368 (t60) REVERT: B 387 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8767 (mp10) REVERT: B 548 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8689 (ttmm) REVERT: C 67 PHE cc_start: 0.8110 (t80) cc_final: 0.7767 (m-80) REVERT: D 67 PHE cc_start: 0.8062 (t80) cc_final: 0.7729 (m-80) REVERT: D 338 TRP cc_start: 0.8804 (t60) cc_final: 0.8361 (t60) REVERT: D 387 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8765 (mp10) REVERT: D 548 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8692 (ttmm) REVERT: E 67 PHE cc_start: 0.8235 (t80) cc_final: 0.7908 (m-80) REVERT: E 307 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8068 (tm-30) REVERT: E 338 TRP cc_start: 0.8882 (t60) cc_final: 0.8491 (t60) REVERT: E 387 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8967 (mp10) REVERT: E 548 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8635 (ttmm) REVERT: F 67 PHE cc_start: 0.8246 (t80) cc_final: 0.7897 (m-80) REVERT: F 307 GLN cc_start: 0.8318 (tm-30) cc_final: 0.8065 (tm-30) REVERT: F 338 TRP cc_start: 0.8874 (t60) cc_final: 0.8496 (t60) REVERT: F 387 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8896 (mp10) REVERT: F 548 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8635 (ttmm) outliers start: 13 outliers final: 8 residues processed: 235 average time/residue: 1.4800 time to fit residues: 393.4383 Evaluate side-chains 175 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 2.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain F residue 454 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 6.9990 chunk 222 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 266 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 ASN C 282 ASN E 354 GLN E 355 HIS E 387 GLN F 354 GLN F 355 HIS F 387 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 23424 Z= 0.275 Angle : 0.526 7.554 31656 Z= 0.272 Chirality : 0.043 0.143 3444 Planarity : 0.004 0.035 4128 Dihedral : 4.487 55.020 3256 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.67 % Allowed : 8.17 % Favored : 91.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.06 (0.16), residues: 2964 helix: 2.55 (0.13), residues: 1578 sheet: -0.17 (0.30), residues: 306 loop : 0.09 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 442 HIS 0.004 0.001 HIS F 315 PHE 0.020 0.001 PHE F 66 TYR 0.011 0.002 TYR F 170 ARG 0.002 0.000 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 2.782 Fit side-chains REVERT: A 67 PHE cc_start: 0.8310 (t80) cc_final: 0.8021 (m-80) REVERT: B 67 PHE cc_start: 0.8220 (t80) cc_final: 0.7731 (m-80) REVERT: B 307 GLN cc_start: 0.8669 (tm-30) cc_final: 0.7679 (tm-30) REVERT: B 338 TRP cc_start: 0.8718 (t60) cc_final: 0.8254 (t60) REVERT: B 387 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8862 (mp10) REVERT: B 548 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8721 (ttmm) REVERT: C 67 PHE cc_start: 0.8304 (t80) cc_final: 0.8033 (m-80) REVERT: D 67 PHE cc_start: 0.8220 (t80) cc_final: 0.7732 (m-80) REVERT: D 307 GLN cc_start: 0.8676 (tm-30) cc_final: 0.7681 (tm-30) REVERT: D 338 TRP cc_start: 0.8717 (t60) cc_final: 0.8255 (t60) REVERT: D 387 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8862 (mp10) REVERT: D 548 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8722 (ttmm) REVERT: E 67 PHE cc_start: 0.8379 (t80) cc_final: 0.8048 (m-80) REVERT: E 307 GLN cc_start: 0.8357 (tm-30) cc_final: 0.8041 (tm-30) REVERT: E 338 TRP cc_start: 0.8795 (t60) cc_final: 0.8383 (t60) REVERT: E 387 GLN cc_start: 0.9227 (mm110) cc_final: 0.8933 (mp10) REVERT: E 548 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8655 (ttmm) REVERT: F 67 PHE cc_start: 0.8383 (t80) cc_final: 0.8046 (m-80) REVERT: F 307 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8034 (tm-30) REVERT: F 338 TRP cc_start: 0.8767 (t60) cc_final: 0.8348 (t60) REVERT: F 387 GLN cc_start: 0.9210 (mm110) cc_final: 0.8920 (mp10) REVERT: F 548 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8654 (ttmm) outliers start: 16 outliers final: 14 residues processed: 205 average time/residue: 1.2521 time to fit residues: 297.6582 Evaluate side-chains 196 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 182 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 556 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 222 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 267 optimal weight: 7.9990 chunk 288 optimal weight: 2.9990 chunk 238 optimal weight: 0.4980 chunk 265 optimal weight: 4.9990 chunk 91 optimal weight: 30.0000 chunk 214 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS C 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23424 Z= 0.304 Angle : 0.524 7.623 31656 Z= 0.270 Chirality : 0.043 0.144 3444 Planarity : 0.004 0.038 4128 Dihedral : 4.541 54.994 3252 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.68 % Allowed : 8.63 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.18 (0.16), residues: 2964 helix: 2.74 (0.13), residues: 1566 sheet: -0.03 (0.31), residues: 276 loop : -0.01 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 338 HIS 0.004 0.001 HIS F 315 PHE 0.025 0.002 PHE C 66 TYR 0.012 0.002 TYR E 170 ARG 0.002 0.000 ARG E 453 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 182 time to evaluate : 2.660 Fit side-chains REVERT: A 67 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: A 68 LYS cc_start: 0.8978 (mtmm) cc_final: 0.8771 (mmpt) REVERT: B 67 PHE cc_start: 0.8268 (t80) cc_final: 0.8031 (m-80) REVERT: B 233 MET cc_start: 0.9097 (mmp) cc_final: 0.8770 (mmt) REVERT: B 307 GLN cc_start: 0.8654 (tm-30) cc_final: 0.7610 (tm-30) REVERT: B 387 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8828 (mp10) REVERT: C 67 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7812 (m-80) REVERT: C 68 LYS cc_start: 0.8981 (mtmm) cc_final: 0.8771 (mmpt) REVERT: D 67 PHE cc_start: 0.8270 (t80) cc_final: 0.8031 (m-80) REVERT: D 233 MET cc_start: 0.9095 (mmp) cc_final: 0.8769 (mmt) REVERT: D 307 GLN cc_start: 0.8655 (tm-30) cc_final: 0.7611 (tm-30) REVERT: D 387 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8838 (mp10) REVERT: E 307 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8056 (tm-30) REVERT: E 387 GLN cc_start: 0.9271 (mm110) cc_final: 0.8985 (mp10) REVERT: E 548 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8649 (ttmm) REVERT: F 307 GLN cc_start: 0.8403 (tm-30) cc_final: 0.8044 (tm-30) REVERT: F 338 TRP cc_start: 0.8747 (t60) cc_final: 0.8378 (t60) REVERT: F 387 GLN cc_start: 0.9270 (mm110) cc_final: 0.8991 (mp10) REVERT: F 548 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8648 (ttmm) outliers start: 40 outliers final: 20 residues processed: 216 average time/residue: 1.2079 time to fit residues: 303.4398 Evaluate side-chains 203 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 556 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 0.0770 chunk 201 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 179 optimal weight: 20.0000 chunk 268 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 254 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS B 262 GLN C 355 HIS D 262 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 23424 Z= 0.233 Angle : 0.501 7.782 31656 Z= 0.255 Chirality : 0.042 0.128 3444 Planarity : 0.004 0.036 4128 Dihedral : 4.441 54.730 3252 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.68 % Allowed : 9.76 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.22 (0.16), residues: 2964 helix: 2.79 (0.13), residues: 1566 sheet: -0.03 (0.31), residues: 276 loop : -0.03 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 442 HIS 0.006 0.001 HIS E 355 PHE 0.016 0.001 PHE A 67 TYR 0.010 0.001 TYR E 170 ARG 0.002 0.000 ARG F 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 203 time to evaluate : 2.881 Fit side-chains REVERT: B 67 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: B 233 MET cc_start: 0.9103 (mmp) cc_final: 0.8845 (mmt) REVERT: B 307 GLN cc_start: 0.8679 (tm-30) cc_final: 0.7603 (tm-30) REVERT: B 387 GLN cc_start: 0.9167 (mm-40) cc_final: 0.8826 (mp10) REVERT: D 67 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7770 (m-80) REVERT: D 387 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8792 (mp10) REVERT: E 307 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8051 (tm-30) REVERT: E 338 TRP cc_start: 0.8754 (t60) cc_final: 0.8401 (t60) REVERT: E 387 GLN cc_start: 0.9235 (mm110) cc_final: 0.8974 (mp10) REVERT: E 548 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8633 (ttmm) REVERT: F 307 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8050 (tm-30) REVERT: F 338 TRP cc_start: 0.8711 (t60) cc_final: 0.8378 (t60) REVERT: F 387 GLN cc_start: 0.9239 (mm110) cc_final: 0.8976 (mp10) REVERT: F 548 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8636 (ttmm) outliers start: 40 outliers final: 20 residues processed: 233 average time/residue: 1.1681 time to fit residues: 317.7362 Evaluate side-chains 201 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 179 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 454 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 0.7980 chunk 161 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23424 Z= 0.292 Angle : 0.544 12.254 31656 Z= 0.275 Chirality : 0.043 0.139 3444 Planarity : 0.004 0.041 4128 Dihedral : 4.543 54.862 3252 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.76 % Allowed : 10.39 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.09 (0.16), residues: 2964 helix: 2.81 (0.13), residues: 1566 sheet: -0.45 (0.28), residues: 336 loop : -0.15 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 442 HIS 0.005 0.001 HIS E 355 PHE 0.026 0.002 PHE F 66 TYR 0.011 0.002 TYR F 170 ARG 0.002 0.000 ARG E 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 188 time to evaluate : 2.643 Fit side-chains REVERT: A 307 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8369 (tm-30) REVERT: B 67 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: B 233 MET cc_start: 0.9093 (mmp) cc_final: 0.8811 (mmt) REVERT: B 387 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8849 (mp10) REVERT: C 307 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8369 (tm-30) REVERT: D 67 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: D 233 MET cc_start: 0.9094 (mmp) cc_final: 0.8818 (mmt) REVERT: D 307 GLN cc_start: 0.8791 (tm-30) cc_final: 0.7882 (tm-30) REVERT: D 387 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8898 (mp10) REVERT: E 307 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8051 (tm-30) REVERT: E 387 GLN cc_start: 0.9247 (mm110) cc_final: 0.8959 (mp10) REVERT: E 548 LYS cc_start: 0.8919 (ttmm) cc_final: 0.8639 (ttmm) REVERT: F 307 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8048 (tm-30) REVERT: F 387 GLN cc_start: 0.9247 (mm110) cc_final: 0.8962 (mp10) REVERT: F 548 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8639 (ttmm) outliers start: 42 outliers final: 26 residues processed: 220 average time/residue: 1.2809 time to fit residues: 325.5060 Evaluate side-chains 209 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 556 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 0.7980 chunk 255 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 284 optimal weight: 0.6980 chunk 236 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23424 Z= 0.169 Angle : 0.492 8.768 31656 Z= 0.248 Chirality : 0.042 0.164 3444 Planarity : 0.003 0.038 4128 Dihedral : 4.309 54.284 3252 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.30 % Allowed : 11.52 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.21 (0.16), residues: 2964 helix: 2.90 (0.13), residues: 1566 sheet: -0.40 (0.28), residues: 336 loop : -0.08 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 338 HIS 0.005 0.001 HIS F 355 PHE 0.027 0.001 PHE A 66 TYR 0.009 0.001 TYR D 247 ARG 0.002 0.000 ARG A 496 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 2.596 Fit side-chains REVERT: B 67 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: B 387 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8824 (mp10) REVERT: D 67 PHE cc_start: 0.7964 (OUTLIER) cc_final: 0.7684 (m-80) REVERT: D 307 GLN cc_start: 0.8789 (tm-30) cc_final: 0.7897 (tm-30) REVERT: D 387 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8853 (mp10) REVERT: E 307 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8064 (tm-30) REVERT: E 387 GLN cc_start: 0.9203 (mm110) cc_final: 0.8850 (mp10) REVERT: E 548 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8707 (ttmm) REVERT: F 307 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8059 (tm-30) REVERT: F 387 GLN cc_start: 0.9204 (mm110) cc_final: 0.8880 (mp10) REVERT: F 548 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8702 (ttmm) outliers start: 31 outliers final: 25 residues processed: 238 average time/residue: 1.2515 time to fit residues: 344.5546 Evaluate side-chains 211 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain D residue 67 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain F residue 296 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 207 optimal weight: 0.4980 chunk 160 optimal weight: 5.9990 chunk 239 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23424 Z= 0.305 Angle : 0.562 11.755 31656 Z= 0.281 Chirality : 0.044 0.187 3444 Planarity : 0.004 0.042 4128 Dihedral : 4.292 54.845 3248 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.55 % Allowed : 12.06 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.15 (0.16), residues: 2964 helix: 2.86 (0.13), residues: 1566 sheet: -0.47 (0.28), residues: 336 loop : -0.12 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 338 HIS 0.006 0.001 HIS E 355 PHE 0.017 0.002 PHE F 66 TYR 0.012 0.002 TYR B 247 ARG 0.002 0.000 ARG F 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 2.858 Fit side-chains REVERT: B 233 MET cc_start: 0.9101 (mmp) cc_final: 0.8797 (mmt) REVERT: B 387 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8869 (mp10) REVERT: D 233 MET cc_start: 0.9105 (mmp) cc_final: 0.8808 (mmt) REVERT: D 387 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8881 (mp10) REVERT: E 307 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8061 (tm-30) REVERT: E 387 GLN cc_start: 0.9239 (mm110) cc_final: 0.8886 (mp10) REVERT: E 548 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8636 (ttmm) REVERT: F 387 GLN cc_start: 0.9229 (mm110) cc_final: 0.8929 (mp10) REVERT: F 548 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8639 (ttmm) outliers start: 37 outliers final: 25 residues processed: 217 average time/residue: 1.2533 time to fit residues: 316.2440 Evaluate side-chains 208 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 378 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 2.9990 chunk 113 optimal weight: 0.3980 chunk 169 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 180 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23424 Z= 0.224 Angle : 0.535 11.495 31656 Z= 0.268 Chirality : 0.043 0.208 3444 Planarity : 0.004 0.043 4128 Dihedral : 4.236 54.723 3248 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.09 % Allowed : 12.40 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.15 (0.16), residues: 2964 helix: 2.86 (0.13), residues: 1566 sheet: -0.46 (0.28), residues: 336 loop : -0.11 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 338 HIS 0.004 0.001 HIS E 355 PHE 0.031 0.001 PHE A 66 TYR 0.013 0.001 TYR B 247 ARG 0.001 0.000 ARG E 496 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 197 time to evaluate : 2.923 Fit side-chains REVERT: A 68 LYS cc_start: 0.8867 (mtmm) cc_final: 0.8661 (mmmt) REVERT: B 233 MET cc_start: 0.9109 (mmp) cc_final: 0.8829 (mmt) REVERT: B 387 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8875 (mp10) REVERT: B 476 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8600 (ptp90) REVERT: C 68 LYS cc_start: 0.8948 (mtmm) cc_final: 0.8681 (mmmt) REVERT: D 233 MET cc_start: 0.9100 (mmp) cc_final: 0.8831 (mmt) REVERT: D 387 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8888 (mp10) REVERT: D 476 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8599 (ptp90) REVERT: E 387 GLN cc_start: 0.9213 (mm110) cc_final: 0.8917 (mp10) REVERT: E 548 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8628 (ttmm) REVERT: F 68 LYS cc_start: 0.8856 (mtmm) cc_final: 0.8586 (mmmt) REVERT: F 387 GLN cc_start: 0.9194 (mm110) cc_final: 0.8911 (mp10) REVERT: F 548 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8629 (ttmm) outliers start: 26 outliers final: 27 residues processed: 219 average time/residue: 1.2229 time to fit residues: 311.2659 Evaluate side-chains 212 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 476 ARG Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain F residue 378 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 264 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 207 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 238 optimal weight: 10.0000 chunk 249 optimal weight: 0.9980 chunk 263 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23424 Z= 0.178 Angle : 0.548 11.557 31656 Z= 0.270 Chirality : 0.042 0.220 3444 Planarity : 0.003 0.041 4128 Dihedral : 4.161 54.263 3248 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.92 % Allowed : 12.98 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.20 (0.16), residues: 2964 helix: 2.89 (0.13), residues: 1566 sheet: -0.43 (0.28), residues: 336 loop : -0.09 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 338 HIS 0.004 0.001 HIS F 355 PHE 0.032 0.001 PHE C 66 TYR 0.013 0.001 TYR B 247 ARG 0.001 0.000 ARG C 496 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 209 time to evaluate : 2.658 Fit side-chains REVERT: A 67 PHE cc_start: 0.7759 (m-80) cc_final: 0.7521 (m-80) REVERT: A 476 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.7782 (ttp80) REVERT: B 387 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8837 (mp10) REVERT: B 476 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8598 (ptp90) REVERT: C 67 PHE cc_start: 0.7760 (m-80) cc_final: 0.7541 (m-80) REVERT: C 476 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.7783 (ttp80) REVERT: D 233 MET cc_start: 0.9098 (mmp) cc_final: 0.8837 (mmt) REVERT: D 387 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8832 (mp10) REVERT: D 476 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8598 (ptp90) REVERT: E 387 GLN cc_start: 0.9176 (mm110) cc_final: 0.8913 (mp10) REVERT: E 548 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8714 (ttmm) REVERT: F 68 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8574 (mmmt) REVERT: F 387 GLN cc_start: 0.9167 (mm110) cc_final: 0.8906 (mp10) REVERT: F 548 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8714 (ttmm) outliers start: 22 outliers final: 21 residues processed: 229 average time/residue: 1.2425 time to fit residues: 330.5614 Evaluate side-chains 220 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 195 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 244 ILE Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 476 ARG Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain F residue 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 8.9990 chunk 279 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 292 optimal weight: 2.9990 chunk 269 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 278 HIS D 278 HIS E 278 HIS ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 278 HIS ** F 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 23424 Z= 0.415 Angle : 0.625 11.078 31656 Z= 0.314 Chirality : 0.046 0.223 3444 Planarity : 0.004 0.037 4128 Dihedral : 4.488 55.790 3248 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.09 % Allowed : 13.07 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.10 (0.16), residues: 2964 helix: 2.77 (0.13), residues: 1566 sheet: -0.47 (0.29), residues: 306 loop : -0.07 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP F 338 HIS 0.005 0.001 HIS F 315 PHE 0.052 0.002 PHE A 66 TYR 0.014 0.002 TYR A 170 ARG 0.003 0.000 ARG E 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 2.683 Fit side-chains REVERT: A 68 LYS cc_start: 0.8325 (mmmt) cc_final: 0.8121 (mtmm) REVERT: A 476 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.7821 (ttp80) REVERT: B 233 MET cc_start: 0.9132 (mmp) cc_final: 0.8799 (mmt) REVERT: B 387 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8868 (mp10) REVERT: B 476 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8582 (ptp90) REVERT: C 68 LYS cc_start: 0.8292 (mmmt) cc_final: 0.8091 (mtmm) REVERT: C 307 GLN cc_start: 0.8580 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 476 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7751 (ttp80) REVERT: D 233 MET cc_start: 0.9128 (mmp) cc_final: 0.8803 (mmt) REVERT: D 387 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8873 (mp10) REVERT: D 476 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8581 (ptp90) REVERT: E 68 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8702 (mmmt) REVERT: E 387 GLN cc_start: 0.9250 (mm110) cc_final: 0.8958 (mp10) REVERT: E 548 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8640 (ttmm) REVERT: F 68 LYS cc_start: 0.8909 (mtmm) cc_final: 0.8668 (mmmt) REVERT: F 307 GLN cc_start: 0.8664 (tm-30) cc_final: 0.8110 (tm-30) REVERT: F 387 GLN cc_start: 0.9235 (mm110) cc_final: 0.8929 (mp10) REVERT: F 548 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8639 (ttmm) outliers start: 26 outliers final: 25 residues processed: 213 average time/residue: 1.3014 time to fit residues: 320.3454 Evaluate side-chains 212 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 476 ARG Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 476 ARG Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 233 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 239 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.072000 restraints weight = 37611.915| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.44 r_work: 0.2700 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23424 Z= 0.194 Angle : 0.567 11.578 31656 Z= 0.281 Chirality : 0.042 0.203 3444 Planarity : 0.004 0.034 4128 Dihedral : 4.287 55.038 3248 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.09 % Allowed : 13.32 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.11 (0.16), residues: 2964 helix: 2.83 (0.13), residues: 1566 sheet: -0.49 (0.28), residues: 336 loop : -0.14 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 338 HIS 0.004 0.001 HIS F 315 PHE 0.042 0.002 PHE A 66 TYR 0.012 0.001 TYR B 247 ARG 0.001 0.000 ARG C 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7289.13 seconds wall clock time: 130 minutes 43.83 seconds (7843.83 seconds total)