Starting phenix.real_space_refine on Sun Aug 24 20:37:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sk8_40558/08_2025/8sk8_40558.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sk8_40558/08_2025/8sk8_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 { model { file = "/net/cci-nas-00/data/ceres_data/8sk8_40558/08_2025/8sk8_40558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sk8_40558/08_2025/8sk8_40558.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sk8_40558/08_2025/8sk8_40558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sk8_40558/08_2025/8sk8_40558.map" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} 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: {'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} 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: {'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} 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: {'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} 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: {'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} 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: {'ASP:plan': 4, 'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 4.21, per 1000 atoms: 0.18 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 - 3.00 Amino acid : True - 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: 2.00 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.93 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: 3.99 Time building geometry restraints manager: 2.50 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: 0.00 - 1.05: 30478 1.05 - 2.11: 956 2.11 - 3.16: 155 3.16 - 4.22: 49 4.22 - 5.27: 18 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 3.040 nonbonded pdb=" OG SER E 153 " pdb=" OD1 ASP E 155 " model vdw 2.173 3.040 nonbonded pdb=" OG SER A 153 " pdb=" OD1 ASP A 155 " model vdw 2.174 3.040 nonbonded pdb=" OG SER C 153 " pdb=" OD1 ASP C 155 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR E 528 " pdb=" OE2 GLU E 544 " model vdw 2.184 3.040 ... (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 Time spend for trying shortcut: 0.05 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: 2.200 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.340 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.000 ------------------------------------------------------------------------------- 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= 0.186 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG D 453 TYR 0.014 0.001 TYR C 170 PHE 0.011 0.001 PHE A 304 TRP 0.010 0.001 TRP C 442 HIS 0.003 0.001 HIS F 315 Details of bonding type rmsd covalent geometry : bond 0.00435 (23424) covalent geometry : angle 0.46920 (31656) hydrogen bonds : bond 0.20595 ( 1337) hydrogen bonds : angle 5.91518 ( 3789) *********************** 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 to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 0.563 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: 0.6157 time to fit residues: 162.7699 Evaluate side-chains 175 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.071867 restraints weight = 38259.264| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.46 r_work: 0.2705 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1348 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= 0.143 Angle : 0.521 7.606 31656 Z= 0.269 Chirality : 0.042 0.144 3444 Planarity : 0.004 0.034 4128 Dihedral : 4.444 55.021 3256 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.54 % Allowed : 7.87 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.16), residues: 2964 helix: 2.55 (0.13), residues: 1578 sheet: -0.21 (0.29), residues: 336 loop : -0.00 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.009 0.001 TYR A 170 PHE 0.020 0.001 PHE F 66 TRP 0.011 0.001 TRP A 442 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00332 (23424) covalent geometry : angle 0.52069 (31656) hydrogen bonds : bond 0.04273 ( 1337) hydrogen bonds : angle 3.95311 ( 3789) *********************** 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 210 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.682 Fit side-chains REVERT: A 67 PHE cc_start: 0.8630 (t80) cc_final: 0.8388 (m-80) REVERT: B 67 PHE cc_start: 0.8457 (t80) cc_final: 0.8228 (m-80) REVERT: B 307 GLN cc_start: 0.8689 (tm-30) cc_final: 0.7734 (tm-30) REVERT: B 338 TRP cc_start: 0.8714 (t60) cc_final: 0.8153 (t60) REVERT: B 387 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8782 (mp10) REVERT: B 548 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8854 (ttmm) REVERT: C 67 PHE cc_start: 0.8635 (t80) cc_final: 0.8396 (m-80) REVERT: D 67 PHE cc_start: 0.8465 (t80) cc_final: 0.8236 (m-80) REVERT: D 307 GLN cc_start: 0.8707 (tm-30) cc_final: 0.7757 (tm-30) REVERT: D 338 TRP cc_start: 0.8719 (t60) cc_final: 0.8160 (t60) REVERT: D 387 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8775 (mp10) REVERT: E 307 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8072 (tm-30) REVERT: E 338 TRP cc_start: 0.8795 (t60) cc_final: 0.8314 (t60) REVERT: E 387 GLN cc_start: 0.9195 (mm110) cc_final: 0.8754 (mp10) REVERT: E 548 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8769 (ttmm) REVERT: F 307 GLN cc_start: 0.8313 (tm-30) cc_final: 0.8030 (tm-30) REVERT: F 338 TRP cc_start: 0.8776 (t60) cc_final: 0.8295 (t60) REVERT: F 387 GLN cc_start: 0.9186 (mm110) cc_final: 0.8747 (mp10) REVERT: F 548 LYS cc_start: 0.8985 (ttmm) cc_final: 0.8761 (ttmm) outliers start: 13 outliers final: 13 residues processed: 210 average time/residue: 0.5275 time to fit residues: 127.6460 Evaluate side-chains 188 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 296 THR 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 F residue 66 PHE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 454 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 204 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 209 optimal weight: 0.8980 chunk 240 optimal weight: 2.9990 chunk 269 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 268 optimal weight: 0.0980 chunk 258 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS C 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.100186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.070029 restraints weight = 38206.584| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.38 r_work: 0.2782 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23424 Z= 0.110 Angle : 0.479 8.052 31656 Z= 0.245 Chirality : 0.041 0.144 3444 Planarity : 0.004 0.039 4128 Dihedral : 4.299 54.547 3252 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.68 % Allowed : 7.54 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.16), residues: 2964 helix: 2.82 (0.13), residues: 1566 sheet: -0.06 (0.32), residues: 282 loop : 0.02 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 151 TYR 0.008 0.001 TYR A 240 PHE 0.028 0.001 PHE A 66 TRP 0.014 0.001 TRP A 338 HIS 0.004 0.001 HIS D 315 Details of bonding type rmsd covalent geometry : bond 0.00251 (23424) covalent geometry : angle 0.47947 (31656) hydrogen bonds : bond 0.03547 ( 1337) hydrogen bonds : angle 3.67443 ( 3789) *********************** 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 258 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 218 time to evaluate : 0.956 Fit side-chains REVERT: A 67 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: A 68 LYS cc_start: 0.8895 (mtmm) cc_final: 0.8572 (mmpt) REVERT: B 67 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: B 68 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8597 (mmpt) REVERT: B 307 GLN cc_start: 0.8855 (tm-30) cc_final: 0.7873 (tm-30) REVERT: B 387 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8851 (mp10) REVERT: C 67 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: C 68 LYS cc_start: 0.8898 (mtmm) cc_final: 0.8572 (mmpt) REVERT: D 67 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: D 68 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8594 (mmpt) REVERT: D 307 GLN cc_start: 0.8842 (tm-30) cc_final: 0.7853 (tm-30) REVERT: D 387 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8838 (mp10) REVERT: E 67 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: E 123 ARG cc_start: 0.8930 (ttt180) cc_final: 0.8729 (tpt-90) REVERT: E 307 GLN cc_start: 0.8427 (tm-30) cc_final: 0.8121 (tm-30) REVERT: E 338 TRP cc_start: 0.8740 (t60) cc_final: 0.8316 (t60) REVERT: E 354 GLN cc_start: 0.9213 (pp30) cc_final: 0.8848 (pp30) REVERT: E 387 GLN cc_start: 0.9202 (mm110) cc_final: 0.8811 (mp10) REVERT: E 548 LYS cc_start: 0.9043 (ttmm) cc_final: 0.8839 (ttmm) REVERT: F 67 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: F 123 ARG cc_start: 0.8922 (ttt180) cc_final: 0.8715 (tpt-90) REVERT: F 307 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8104 (tm-30) REVERT: F 338 TRP cc_start: 0.8716 (t60) cc_final: 0.8302 (t60) REVERT: F 354 GLN cc_start: 0.9217 (pp30) cc_final: 0.8871 (pp30) REVERT: F 387 GLN cc_start: 0.9204 (mm110) cc_final: 0.8813 (mp10) REVERT: F 548 LYS cc_start: 0.9042 (ttmm) cc_final: 0.8838 (ttmm) outliers start: 40 outliers final: 12 residues processed: 249 average time/residue: 0.4807 time to fit residues: 139.1675 Evaluate side-chains 212 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 67 PHE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 454 LEU 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 67 PHE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 67 PHE Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain F residue 67 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 84 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 264 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS B 278 HIS C 278 HIS C 355 HIS D 278 HIS E 278 HIS F 278 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.065771 restraints weight = 38235.466| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.39 r_work: 0.2712 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 23424 Z= 0.226 Angle : 0.550 7.536 31656 Z= 0.282 Chirality : 0.044 0.138 3444 Planarity : 0.004 0.038 4128 Dihedral : 4.389 56.367 3248 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.68 % Allowed : 9.30 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.16), residues: 2964 helix: 2.73 (0.13), residues: 1566 sheet: -0.25 (0.30), residues: 312 loop : -0.08 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 453 TYR 0.013 0.002 TYR F 170 PHE 0.021 0.002 PHE F 66 TRP 0.011 0.002 TRP A 338 HIS 0.005 0.001 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00538 (23424) covalent geometry : angle 0.55039 (31656) hydrogen bonds : bond 0.04440 ( 1337) hydrogen bonds : angle 3.72189 ( 3789) *********************** 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 232 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.716 Fit side-chains REVERT: A 67 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: A 307 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8498 (tm-30) REVERT: B 67 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7902 (m-80) REVERT: B 233 MET cc_start: 0.9156 (mmp) cc_final: 0.8912 (mmt) REVERT: B 307 GLN cc_start: 0.8734 (tm-30) cc_final: 0.7717 (tm-30) REVERT: B 387 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8849 (mp10) REVERT: C 67 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: C 307 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8477 (tm-30) REVERT: D 67 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: D 233 MET cc_start: 0.9165 (mmp) cc_final: 0.8922 (mmt) REVERT: D 307 GLN cc_start: 0.8773 (tm-30) cc_final: 0.7744 (tm-30) REVERT: D 387 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8855 (mp10) REVERT: E 151 ARG cc_start: 0.8623 (ttt180) cc_final: 0.8387 (ttt90) REVERT: E 307 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8170 (tm-30) REVERT: E 354 GLN cc_start: 0.9234 (pp30) cc_final: 0.8907 (pp30) REVERT: E 387 GLN cc_start: 0.9266 (mm110) cc_final: 0.8878 (mp10) REVERT: E 548 LYS cc_start: 0.9069 (ttmm) cc_final: 0.8828 (ttmm) REVERT: F 151 ARG cc_start: 0.8611 (ttt180) cc_final: 0.8376 (ttt90) REVERT: F 307 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8185 (tm-30) REVERT: F 354 GLN cc_start: 0.9230 (pp30) cc_final: 0.8916 (pp30) REVERT: F 387 GLN cc_start: 0.9253 (mm110) cc_final: 0.8860 (mp10) REVERT: F 548 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8831 (ttmm) outliers start: 40 outliers final: 25 residues processed: 219 average time/residue: 0.4674 time to fit residues: 119.0841 Evaluate side-chains 210 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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 244 ILE 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 378 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 244 ILE 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 378 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 244 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 199 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 290 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 274 optimal weight: 0.0020 chunk 278 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.104068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.073888 restraints weight = 37722.432| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.38 r_work: 0.2749 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1838 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= 0.120 Angle : 0.519 12.107 31656 Z= 0.260 Chirality : 0.042 0.129 3444 Planarity : 0.004 0.039 4128 Dihedral : 4.217 54.947 3248 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.26 % Allowed : 10.13 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.16), residues: 2964 helix: 2.82 (0.13), residues: 1566 sheet: 0.06 (0.32), residues: 282 loop : -0.12 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 496 TYR 0.008 0.001 TYR C 240 PHE 0.023 0.001 PHE D 66 TRP 0.010 0.001 TRP A 442 HIS 0.004 0.001 HIS A 315 Details of bonding type rmsd covalent geometry : bond 0.00282 (23424) covalent geometry : angle 0.51925 (31656) hydrogen bonds : bond 0.03504 ( 1337) hydrogen bonds : angle 3.58444 ( 3789) *********************** 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 245 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 0.804 Fit side-chains REVERT: A 307 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8459 (tm-30) REVERT: B 67 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: B 307 GLN cc_start: 0.8819 (tm-30) cc_final: 0.7754 (tm-30) REVERT: B 387 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8773 (mp10) REVERT: C 307 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8438 (tm-30) REVERT: D 67 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: D 307 GLN cc_start: 0.8814 (tm-30) cc_final: 0.7773 (tm-30) REVERT: D 387 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8832 (mp10) REVERT: E 67 PHE cc_start: 0.8330 (m-80) cc_final: 0.8124 (m-80) REVERT: E 68 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8531 (mmmt) REVERT: E 151 ARG cc_start: 0.8567 (ttt180) cc_final: 0.8345 (ttt90) REVERT: E 307 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8236 (tm-30) REVERT: E 354 GLN cc_start: 0.9189 (pp30) cc_final: 0.8884 (pp30) REVERT: E 387 GLN cc_start: 0.9230 (mm110) cc_final: 0.8851 (mp10) REVERT: E 548 LYS cc_start: 0.9059 (ttmm) cc_final: 0.8858 (ttmm) REVERT: F 67 PHE cc_start: 0.8340 (m-80) cc_final: 0.8133 (m-80) REVERT: F 68 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8531 (mmmt) REVERT: F 151 ARG cc_start: 0.8546 (ttt180) cc_final: 0.8324 (ttt90) REVERT: F 307 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8199 (tm-30) REVERT: F 354 GLN cc_start: 0.9214 (pp30) cc_final: 0.8912 (pp30) REVERT: F 387 GLN cc_start: 0.9221 (mm110) cc_final: 0.8847 (mp10) outliers start: 30 outliers final: 21 residues processed: 237 average time/residue: 0.5728 time to fit residues: 155.9393 Evaluate side-chains 209 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 PHE 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 B residue 67 PHE Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 66 PHE 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 296 THR Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 454 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 2 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.067427 restraints weight = 38329.898| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.47 r_work: 0.2647 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 23424 Z= 0.249 Angle : 0.582 12.328 31656 Z= 0.297 Chirality : 0.046 0.160 3444 Planarity : 0.004 0.042 4128 Dihedral : 4.510 56.072 3248 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.93 % Allowed : 10.76 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.16), residues: 2964 helix: 2.71 (0.13), residues: 1560 sheet: -0.36 (0.30), residues: 312 loop : -0.20 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 453 TYR 0.015 0.002 TYR F 170 PHE 0.038 0.002 PHE C 67 TRP 0.017 0.002 TRP F 338 HIS 0.005 0.001 HIS A 355 Details of bonding type rmsd covalent geometry : bond 0.00594 (23424) covalent geometry : angle 0.58214 (31656) hydrogen bonds : bond 0.04551 ( 1337) hydrogen bonds : angle 3.68222 ( 3789) *********************** 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 243 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.809 Fit side-chains REVERT: A 151 ARG cc_start: 0.8545 (ttt180) cc_final: 0.8183 (ttt90) REVERT: A 307 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8405 (tm-30) REVERT: B 67 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: B 233 MET cc_start: 0.9078 (mmp) cc_final: 0.8836 (mmt) REVERT: B 307 GLN cc_start: 0.8683 (tm-30) cc_final: 0.7712 (tm-30) REVERT: B 387 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8796 (mp10) REVERT: C 66 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7552 (p90) REVERT: C 67 PHE cc_start: 0.8165 (m-80) cc_final: 0.7853 (m-80) REVERT: C 151 ARG cc_start: 0.8548 (ttt180) cc_final: 0.8191 (ttt90) REVERT: C 307 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8416 (tm-30) REVERT: D 67 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: D 233 MET cc_start: 0.9081 (mmp) cc_final: 0.8837 (mmt) REVERT: D 307 GLN cc_start: 0.8718 (tm-30) cc_final: 0.7760 (tm-30) REVERT: D 387 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8801 (mp10) REVERT: E 68 LYS cc_start: 0.8927 (mtmm) cc_final: 0.8637 (mmmt) REVERT: E 151 ARG cc_start: 0.8606 (ttt180) cc_final: 0.8390 (ttt90) REVERT: E 307 GLN cc_start: 0.8516 (tm-30) cc_final: 0.8169 (tm-30) REVERT: E 354 GLN cc_start: 0.9201 (pp30) cc_final: 0.8926 (pp30) REVERT: E 387 GLN cc_start: 0.9245 (mm110) cc_final: 0.8853 (mp10) REVERT: E 548 LYS cc_start: 0.9015 (ttmm) cc_final: 0.8788 (ttmm) REVERT: F 68 LYS cc_start: 0.8927 (mtmm) cc_final: 0.8637 (mmmt) REVERT: F 151 ARG cc_start: 0.8594 (ttt180) cc_final: 0.8378 (ttt90) REVERT: F 307 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8156 (tm-30) REVERT: F 354 GLN cc_start: 0.9222 (pp30) cc_final: 0.8937 (pp30) REVERT: F 387 GLN cc_start: 0.9233 (mm110) cc_final: 0.8839 (mp10) outliers start: 46 outliers final: 28 residues processed: 225 average time/residue: 0.5299 time to fit residues: 138.6974 Evaluate side-chains 218 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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 215 ILE Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 244 ILE 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 215 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 508 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 5 optimal weight: 0.9990 chunk 194 optimal weight: 0.8980 chunk 125 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 285 optimal weight: 0.9980 chunk 282 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN D 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.103706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.073020 restraints weight = 37795.753| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.45 r_work: 0.2732 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23424 Z= 0.109 Angle : 0.518 11.341 31656 Z= 0.259 Chirality : 0.042 0.179 3444 Planarity : 0.004 0.038 4128 Dihedral : 4.182 54.770 3248 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.09 % Allowed : 11.68 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.16), residues: 2964 helix: 2.83 (0.13), residues: 1566 sheet: -0.40 (0.28), residues: 342 loop : -0.19 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 496 TYR 0.009 0.001 TYR D 240 PHE 0.025 0.001 PHE C 66 TRP 0.018 0.001 TRP F 338 HIS 0.004 0.001 HIS D 315 Details of bonding type rmsd covalent geometry : bond 0.00249 (23424) covalent geometry : angle 0.51765 (31656) hydrogen bonds : bond 0.03268 ( 1337) hydrogen bonds : angle 3.50277 ( 3789) *********************** 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 243 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.919 Fit side-chains REVERT: A 67 PHE cc_start: 0.8080 (m-80) cc_final: 0.7734 (m-80) REVERT: A 68 LYS cc_start: 0.8741 (mtmm) cc_final: 0.8447 (mmmt) REVERT: A 307 GLN cc_start: 0.8675 (tm-30) cc_final: 0.7951 (tm-30) REVERT: B 67 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8280 (m-80) REVERT: B 307 GLN cc_start: 0.8808 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 387 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8826 (mp10) REVERT: C 67 PHE cc_start: 0.8149 (m-80) cc_final: 0.7750 (m-80) REVERT: C 68 LYS cc_start: 0.8748 (mtmm) cc_final: 0.8486 (mmmt) REVERT: C 307 GLN cc_start: 0.8669 (tm-30) cc_final: 0.7945 (tm-30) REVERT: D 67 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: D 307 GLN cc_start: 0.8808 (tm-30) cc_final: 0.7759 (tm-30) REVERT: D 387 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8819 (mp10) REVERT: E 67 PHE cc_start: 0.8353 (m-80) cc_final: 0.8129 (m-80) REVERT: E 68 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8538 (mmmt) REVERT: E 151 ARG cc_start: 0.8619 (ttt180) cc_final: 0.8401 (ttt90) REVERT: E 307 GLN cc_start: 0.8574 (tm-30) cc_final: 0.8205 (tm-30) REVERT: E 354 GLN cc_start: 0.9248 (pp30) cc_final: 0.8926 (pp30) REVERT: E 387 GLN cc_start: 0.9215 (mm110) cc_final: 0.8787 (mp10) REVERT: F 67 PHE cc_start: 0.8367 (m-80) cc_final: 0.8147 (m-80) REVERT: F 68 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8547 (mmmt) REVERT: F 151 ARG cc_start: 0.8604 (ttt180) cc_final: 0.8387 (ttt90) REVERT: F 307 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8180 (tm-30) REVERT: F 354 GLN cc_start: 0.9252 (pp30) cc_final: 0.8954 (pp30) REVERT: F 387 GLN cc_start: 0.9206 (mm110) cc_final: 0.8782 (mp10) outliers start: 26 outliers final: 21 residues processed: 238 average time/residue: 0.5371 time to fit residues: 149.5564 Evaluate side-chains 219 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 255 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 508 SER 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 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 378 ILE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 508 SER 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 28 optimal weight: 3.9990 chunk 292 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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** ** D 262 GLN ** 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 = 0.3418 r_free = 0.3418 target = 0.098310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.067231 restraints weight = 38010.321| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.44 r_work: 0.2692 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23424 Z= 0.159 Angle : 0.555 11.015 31656 Z= 0.277 Chirality : 0.044 0.198 3444 Planarity : 0.004 0.039 4128 Dihedral : 4.280 55.415 3248 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.26 % Allowed : 12.40 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.16), residues: 2964 helix: 2.83 (0.13), residues: 1566 sheet: -0.38 (0.28), residues: 342 loop : -0.21 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 136 TYR 0.010 0.001 TYR B 247 PHE 0.025 0.001 PHE F 66 TRP 0.021 0.002 TRP F 338 HIS 0.004 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00377 (23424) covalent geometry : angle 0.55544 (31656) hydrogen bonds : bond 0.03743 ( 1337) hydrogen bonds : angle 3.51273 ( 3789) *********************** 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 228 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.874 Fit side-chains REVERT: A 67 PHE cc_start: 0.8100 (m-80) cc_final: 0.7736 (m-80) REVERT: A 68 LYS cc_start: 0.8817 (mtmm) cc_final: 0.8464 (mmmt) REVERT: A 151 ARG cc_start: 0.8530 (ttt180) cc_final: 0.8255 (ttt90) REVERT: A 307 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8355 (tm-30) REVERT: B 67 PHE cc_start: 0.8455 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: B 68 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8502 (mmmt) REVERT: B 307 GLN cc_start: 0.8772 (tm-30) cc_final: 0.7699 (tm-30) REVERT: B 387 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8826 (mp10) REVERT: C 67 PHE cc_start: 0.8172 (m-80) cc_final: 0.7790 (m-80) REVERT: C 68 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8522 (mmmt) REVERT: C 307 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8363 (tm-30) REVERT: D 67 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: D 68 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8501 (mmmt) REVERT: D 233 MET cc_start: 0.9075 (mmp) cc_final: 0.8839 (mmt) REVERT: D 307 GLN cc_start: 0.8778 (tm-30) cc_final: 0.7706 (tm-30) REVERT: D 387 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8826 (mp10) REVERT: E 67 PHE cc_start: 0.8450 (m-80) cc_final: 0.8168 (m-80) REVERT: E 68 LYS cc_start: 0.8895 (mtmm) cc_final: 0.8567 (mmmt) REVERT: E 151 ARG cc_start: 0.8603 (ttt180) cc_final: 0.8383 (ttt90) REVERT: E 307 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8173 (tm-30) REVERT: E 354 GLN cc_start: 0.9279 (pp30) cc_final: 0.8931 (pp30) REVERT: E 387 GLN cc_start: 0.9221 (mm110) cc_final: 0.8773 (mp10) REVERT: F 67 PHE cc_start: 0.8453 (m-80) cc_final: 0.8172 (m-80) REVERT: F 68 LYS cc_start: 0.8907 (mtmm) cc_final: 0.8580 (mmmt) REVERT: F 151 ARG cc_start: 0.8585 (ttt180) cc_final: 0.8364 (ttt90) REVERT: F 307 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8161 (tm-30) REVERT: F 354 GLN cc_start: 0.9265 (pp30) cc_final: 0.8942 (pp30) REVERT: F 387 GLN cc_start: 0.9210 (mm110) cc_final: 0.8763 (mp10) outliers start: 30 outliers final: 25 residues processed: 223 average time/residue: 0.4830 time to fit residues: 125.7833 Evaluate side-chains 214 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 378 ILE 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 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 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 378 ILE 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 378 ILE Chi-restraints excluded: chain F residue 296 THR 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 231 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 chunk 174 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.098350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.067882 restraints weight = 38202.663| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.40 r_work: 0.2754 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1962 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= 0.144 Angle : 0.562 12.280 31656 Z= 0.279 Chirality : 0.043 0.190 3444 Planarity : 0.004 0.039 4128 Dihedral : 4.270 55.742 3248 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.42 % Allowed : 12.31 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.16), residues: 2964 helix: 2.85 (0.13), residues: 1566 sheet: -0.41 (0.28), residues: 342 loop : -0.22 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 136 TYR 0.011 0.001 TYR B 247 PHE 0.033 0.001 PHE A 66 TRP 0.026 0.002 TRP F 338 HIS 0.005 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00342 (23424) covalent geometry : angle 0.56157 (31656) hydrogen bonds : bond 0.03629 ( 1337) hydrogen bonds : angle 3.49887 ( 3789) *********************** 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 232 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.715 Fit side-chains REVERT: A 67 PHE cc_start: 0.8132 (m-80) cc_final: 0.7673 (m-80) REVERT: A 68 LYS cc_start: 0.8902 (mtmm) cc_final: 0.8545 (mmmt) REVERT: A 151 ARG cc_start: 0.8536 (ttt180) cc_final: 0.8273 (ttt90) REVERT: A 307 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8392 (tm-30) REVERT: B 67 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: B 68 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8567 (mmmt) REVERT: B 307 GLN cc_start: 0.8786 (tm-30) cc_final: 0.7691 (tm-30) REVERT: B 387 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8863 (mp10) REVERT: C 66 PHE cc_start: 0.8274 (p90) cc_final: 0.7940 (p90) REVERT: C 67 PHE cc_start: 0.8177 (m-80) cc_final: 0.7615 (m-80) REVERT: C 68 LYS cc_start: 0.8894 (mtmm) cc_final: 0.8543 (mmmt) REVERT: C 151 ARG cc_start: 0.8546 (ttt180) cc_final: 0.8287 (ttt90) REVERT: C 307 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8386 (tm-30) REVERT: D 67 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: D 68 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8561 (mmmt) REVERT: D 233 MET cc_start: 0.9118 (mmp) cc_final: 0.8885 (mmt) REVERT: D 307 GLN cc_start: 0.8829 (tm-30) cc_final: 0.7752 (tm-30) REVERT: D 387 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8852 (mp10) REVERT: E 67 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: E 68 LYS cc_start: 0.8942 (mtmm) cc_final: 0.8609 (mmmt) REVERT: E 151 ARG cc_start: 0.8614 (ttt180) cc_final: 0.8397 (ttt90) REVERT: E 307 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8167 (tm-30) REVERT: E 354 GLN cc_start: 0.9294 (pp30) cc_final: 0.8931 (pp30) REVERT: E 387 GLN cc_start: 0.9240 (mm110) cc_final: 0.8814 (mp10) REVERT: E 476 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.7758 (ttp80) REVERT: F 67 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.8153 (m-80) REVERT: F 68 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8603 (mmmt) REVERT: F 151 ARG cc_start: 0.8602 (ttt180) cc_final: 0.8387 (ttt90) REVERT: F 307 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8193 (tm-30) REVERT: F 354 GLN cc_start: 0.9302 (pp30) cc_final: 0.8952 (pp30) REVERT: F 387 GLN cc_start: 0.9227 (mm110) cc_final: 0.8802 (mp10) REVERT: F 476 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.7806 (ptp90) outliers start: 34 outliers final: 27 residues processed: 224 average time/residue: 0.5083 time to fit residues: 131.5458 Evaluate side-chains 226 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL 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 378 ILE 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 255 VAL 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 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 378 ILE 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 67 PHE Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 476 ARG Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 476 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 176 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 292 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** 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 = 0.3405 r_free = 0.3405 target = 0.097244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.066462 restraints weight = 38321.023| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.39 r_work: 0.2680 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23424 Z= 0.190 Angle : 0.587 11.031 31656 Z= 0.294 Chirality : 0.044 0.171 3444 Planarity : 0.004 0.039 4128 Dihedral : 4.394 55.408 3248 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.42 % Allowed : 12.52 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.16), residues: 2964 helix: 2.81 (0.13), residues: 1566 sheet: -0.57 (0.29), residues: 306 loop : -0.14 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 136 TYR 0.011 0.002 TYR B 240 PHE 0.027 0.002 PHE F 66 TRP 0.033 0.002 TRP F 338 HIS 0.005 0.001 HIS F 315 Details of bonding type rmsd covalent geometry : bond 0.00454 (23424) covalent geometry : angle 0.58668 (31656) hydrogen bonds : bond 0.04031 ( 1337) hydrogen bonds : angle 3.56839 ( 3789) ********************** 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 226 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 1.123 Fit side-chains REVERT: A 67 PHE cc_start: 0.8287 (m-80) cc_final: 0.7952 (m-80) REVERT: A 68 LYS cc_start: 0.8973 (mtmm) cc_final: 0.8530 (mmmt) REVERT: A 307 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8380 (tm-30) REVERT: A 476 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7789 (ttp80) REVERT: B 67 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: B 307 GLN cc_start: 0.8759 (tm-30) cc_final: 0.7642 (tm-30) REVERT: B 387 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8846 (mp10) REVERT: C 66 PHE cc_start: 0.8423 (p90) cc_final: 0.8108 (p90) REVERT: C 67 PHE cc_start: 0.8298 (m-80) cc_final: 0.7774 (m-80) REVERT: C 68 LYS cc_start: 0.8969 (mtmm) cc_final: 0.8576 (mmmt) REVERT: C 307 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8383 (tm-30) REVERT: D 67 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.8298 (m-80) REVERT: D 233 MET cc_start: 0.9158 (mmp) cc_final: 0.8895 (mmt) REVERT: D 307 GLN cc_start: 0.8770 (tm-30) cc_final: 0.7676 (tm-30) REVERT: D 387 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8839 (mp10) REVERT: E 68 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8630 (mmmt) REVERT: E 151 ARG cc_start: 0.8638 (ttt180) cc_final: 0.8435 (ttt90) REVERT: E 307 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8176 (tm-30) REVERT: E 354 GLN cc_start: 0.9302 (pp30) cc_final: 0.8925 (pp30) REVERT: E 387 GLN cc_start: 0.9239 (mm110) cc_final: 0.8778 (mp10) REVERT: E 476 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.7704 (ttp80) REVERT: F 67 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8166 (m-80) REVERT: F 68 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8625 (mmmt) REVERT: F 151 ARG cc_start: 0.8623 (ttt180) cc_final: 0.8421 (ttt90) REVERT: F 307 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8160 (tm-30) REVERT: F 387 GLN cc_start: 0.9233 (mm110) cc_final: 0.8776 (mp10) REVERT: F 476 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.7732 (ttp80) outliers start: 34 outliers final: 27 residues processed: 220 average time/residue: 0.5161 time to fit residues: 132.0648 Evaluate side-chains 214 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL 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 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 378 ILE 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 255 VAL 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 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 378 ILE 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 378 ILE Chi-restraints excluded: chain E residue 476 ARG Chi-restraints excluded: chain F residue 67 PHE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 476 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 56 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 275 optimal weight: 30.0000 chunk 146 optimal weight: 0.7980 chunk 137 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 225 optimal weight: 0.0470 chunk 157 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** 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 = 0.3500 r_free = 0.3500 target = 0.105029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.075502 restraints weight = 38306.533| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.39 r_work: 0.2840 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 23424 Z= 0.102 Angle : 0.550 11.497 31656 Z= 0.271 Chirality : 0.042 0.178 3444 Planarity : 0.004 0.039 4128 Dihedral : 4.119 54.271 3248 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.88 % Allowed : 13.07 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.16), residues: 2964 helix: 2.88 (0.13), residues: 1572 sheet: -0.56 (0.28), residues: 354 loop : -0.23 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 274 TYR 0.011 0.001 TYR B 240 PHE 0.032 0.001 PHE A 66 TRP 0.036 0.002 TRP E 338 HIS 0.004 0.001 HIS D 246 Details of bonding type rmsd covalent geometry : bond 0.00236 (23424) covalent geometry : angle 0.54961 (31656) hydrogen bonds : bond 0.03036 ( 1337) hydrogen bonds : angle 3.41574 ( 3789) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8685.02 seconds wall clock time: 148 minutes 38.46 seconds (8918.46 seconds total)