Starting phenix.real_space_refine on Thu Jun 19 18:22:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sk8_40558/06_2025/8sk8_40558.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sk8_40558/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sk8_40558/06_2025/8sk8_40558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sk8_40558/06_2025/8sk8_40558.map" model { file = "/net/cci-nas-00/data/ceres_data/8sk8_40558/06_2025/8sk8_40558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sk8_40558/06_2025/8sk8_40558.cif" } resolution = 2.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 14538 2.51 5 N 4020 2.21 5 O 4254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22920 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3820 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3820 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3820 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3820 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3820 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 3820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3820 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 473} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Time building chain proxies: 13.08, per 1000 atoms: 0.57 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: 5.39 Conformation dependent library (CDL) restraints added in 3.0 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5388 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 9 sheets defined 58.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 67 through 88 removed outlier: 3.959A pdb=" N GLU A 71 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 Processing helix chain 'A' and resid 157 through 175 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.581A pdb=" N MET A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 255 removed outlier: 4.372A pdb=" N HIS A 252 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 255 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.519A pdb=" N PHE A 323 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.676A pdb=" N GLN A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 410 through 420 removed outlier: 3.551A pdb=" N LYS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 Processing helix chain 'A' and resid 432 through 448 Processing helix chain 'A' and resid 455 through 479 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 501 through 528 removed outlier: 3.750A pdb=" N ILE A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 552 Processing helix chain 'B' and resid 67 through 88 removed outlier: 3.962A pdb=" N GLU B 71 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 Processing helix chain 'B' and resid 157 through 175 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 194 through 212 removed outlier: 3.525A pdb=" N LYS B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 244 removed outlier: 3.541A pdb=" N MET B 233 " --> pdb=" O GLY B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 255 removed outlier: 4.328A pdb=" N HIS B 252 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 255 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.512A pdb=" N PHE B 323 " --> pdb=" O TYR B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 356 removed outlier: 3.671A pdb=" N GLN B 354 " --> pdb=" O ASP B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 410 through 420 removed outlier: 3.560A pdb=" N LYS B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 432 through 448 Processing helix chain 'B' and resid 455 through 479 Processing helix chain 'B' and resid 490 through 499 Processing helix chain 'B' and resid 501 through 528 removed outlier: 3.757A pdb=" N ILE B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 552 Processing helix chain 'C' and resid 67 through 88 removed outlier: 3.960A pdb=" N GLU C 71 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASP C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LYS C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 110 Processing helix chain 'C' and resid 157 through 175 Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 194 through 212 Processing helix chain 'C' and resid 229 through 244 removed outlier: 3.582A pdb=" N MET C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 255 removed outlier: 4.373A pdb=" N HIS C 252 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL C 255 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 270 through 285 Processing helix chain 'C' and resid 286 through 294 Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.520A pdb=" N PHE C 323 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.671A pdb=" N GLN C 354 " --> pdb=" O ASP C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 410 through 420 removed outlier: 3.553A pdb=" N LYS C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 432 through 448 Processing helix chain 'C' and resid 455 through 479 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 501 through 528 removed outlier: 3.751A pdb=" N ILE C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 552 Processing helix chain 'D' and resid 67 through 88 removed outlier: 3.962A pdb=" N GLU D 71 " --> pdb=" O PHE D 67 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYS D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 110 Processing helix chain 'D' and resid 157 through 175 Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 194 through 212 removed outlier: 3.531A pdb=" N LYS D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 244 removed outlier: 3.541A pdb=" N MET D 233 " --> pdb=" O GLY D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 255 removed outlier: 4.328A pdb=" N HIS D 252 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL D 255 " --> pdb=" O HIS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 270 through 285 removed outlier: 3.500A pdb=" N PHE D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.512A pdb=" N PHE D 323 " --> pdb=" O TYR D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 356 removed outlier: 3.671A pdb=" N GLN D 354 " --> pdb=" O ASP D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 410 through 420 removed outlier: 3.555A pdb=" N LYS D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 431 Processing helix chain 'D' and resid 432 through 448 Processing helix chain 'D' and resid 455 through 479 Processing helix chain 'D' and resid 490 through 499 Processing helix chain 'D' and resid 501 through 528 removed outlier: 3.758A pdb=" N ILE D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 552 Processing helix chain 'E' and resid 67 through 88 removed outlier: 4.024A pdb=" N GLU E 71 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 110 Processing helix chain 'E' and resid 157 through 175 Processing helix chain 'E' and resid 189 through 193 Processing helix chain 'E' and resid 194 through 212 removed outlier: 3.538A pdb=" N LYS E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 244 removed outlier: 3.561A pdb=" N MET E 233 " --> pdb=" O GLY E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 255 removed outlier: 4.337A pdb=" N HIS E 252 " --> pdb=" O ILE E 249 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL E 255 " --> pdb=" O HIS E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 270 through 285 Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 310 through 323 Processing helix chain 'E' and resid 344 through 356 removed outlier: 3.666A pdb=" N GLN E 354 " --> pdb=" O ASP E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 374 Processing helix chain 'E' and resid 392 through 396 Processing helix chain 'E' and resid 410 through 420 removed outlier: 3.537A pdb=" N LYS E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 416 " --> pdb=" O GLU E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 431 Processing helix chain 'E' and resid 432 through 448 Processing helix chain 'E' and resid 455 through 479 Processing helix chain 'E' and resid 490 through 499 Processing helix chain 'E' and resid 501 through 528 removed outlier: 3.728A pdb=" N ILE E 505 " --> pdb=" O SER E 501 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 552 Processing helix chain 'F' and resid 67 through 88 removed outlier: 4.026A pdb=" N GLU F 71 " --> pdb=" O PHE F 67 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 110 Processing helix chain 'F' and resid 157 through 175 Processing helix chain 'F' and resid 189 through 193 Processing helix chain 'F' and resid 194 through 212 removed outlier: 3.536A pdb=" N LYS F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 244 removed outlier: 3.562A pdb=" N MET F 233 " --> pdb=" O GLY F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 255 removed outlier: 4.338A pdb=" N HIS F 252 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL F 255 " --> pdb=" O HIS F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 270 through 285 Processing helix chain 'F' and resid 286 through 294 Processing helix chain 'F' and resid 310 through 323 Processing helix chain 'F' and resid 344 through 356 removed outlier: 3.670A pdb=" N GLN F 354 " --> pdb=" O ASP F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 374 Processing helix chain 'F' and resid 392 through 396 Processing helix chain 'F' and resid 410 through 420 removed outlier: 3.537A pdb=" N LYS F 415 " --> pdb=" O PRO F 411 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE F 416 " --> pdb=" O GLU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 431 Processing helix chain 'F' and resid 432 through 448 Processing helix chain 'F' and resid 455 through 479 Processing helix chain 'F' and resid 490 through 499 Processing helix chain 'F' and resid 501 through 528 removed outlier: 3.727A pdb=" N ILE F 505 " --> pdb=" O SER F 501 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 552 Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 6.566A pdb=" N CYS A 146 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ALA A 223 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY A 148 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS A 147 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ALA A 184 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY A 149 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL A 186 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 151 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS E 147 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA E 184 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLY E 149 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL E 186 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG E 151 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS E 146 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ALA E 223 " --> pdb=" O CYS E 146 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLY E 148 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 365 through 366 removed outlier: 6.754A pdb=" N PHE A 304 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLY A 331 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 306 " --> pdb=" O GLY A 331 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR A 303 " --> pdb=" O ILE A 378 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE A 380 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A 305 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 379 " --> pdb=" O ALA A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 220 through 223 removed outlier: 6.575A pdb=" N CYS B 146 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA B 223 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 148 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LYS B 147 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA B 184 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY B 149 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL B 186 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG B 151 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS D 147 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA D 184 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY D 149 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL D 186 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG D 151 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS D 146 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ALA D 223 " --> pdb=" O CYS D 146 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY D 148 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 365 through 366 removed outlier: 6.761A pdb=" N PHE B 304 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N GLY B 331 " --> pdb=" O PHE B 304 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 306 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR B 303 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ILE B 380 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 305 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 379 " --> pdb=" O ALA B 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 220 through 223 removed outlier: 6.566A pdb=" N CYS C 146 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA C 223 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY C 148 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N LYS C 147 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA C 184 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY C 149 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL C 186 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG C 151 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS F 147 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ALA F 184 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY F 149 " --> pdb=" O ALA F 184 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL F 186 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG F 151 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N CYS F 146 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA F 223 " --> pdb=" O CYS F 146 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLY F 148 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.759A pdb=" N PHE C 304 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY C 331 " --> pdb=" O PHE C 304 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 306 " --> pdb=" O GLY C 331 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR C 303 " --> pdb=" O ILE C 378 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE C 380 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C 305 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 379 " --> pdb=" O ALA C 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 365 through 366 removed outlier: 6.763A pdb=" N PHE D 304 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLY D 331 " --> pdb=" O PHE D 304 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL D 306 " --> pdb=" O GLY D 331 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR D 303 " --> pdb=" O ILE D 378 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE D 380 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL D 305 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU D 379 " --> pdb=" O ALA D 402 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 365 through 366 removed outlier: 6.781A pdb=" N PHE E 304 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N GLY E 331 " --> pdb=" O PHE E 304 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL E 306 " --> pdb=" O GLY E 331 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR E 303 " --> pdb=" O ILE E 378 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE E 380 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL E 305 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 379 " --> pdb=" O ALA E 402 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 365 through 366 removed outlier: 6.762A pdb=" N PHE F 304 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY F 331 " --> pdb=" O PHE F 304 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL F 306 " --> pdb=" O GLY F 331 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR F 303 " --> pdb=" O ILE F 378 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE F 380 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL F 305 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU F 379 " --> pdb=" O ALA F 402 " (cutoff:3.500A) 1337 hydrogen bonds defined for protein. 3789 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 6.35 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: 0.17 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 49.710 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.15), residues: 2964 helix: 1.94 (0.12), residues: 1548 sheet: -0.16 (0.31), residues: 306 loop : -0.04 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 442 HIS 0.003 0.001 HIS F 315 PHE 0.011 0.001 PHE A 304 TYR 0.014 0.001 TYR C 170 ARG 0.003 0.000 ARG D 453 Details of bonding type rmsd hydrogen bonds : bond 0.20595 ( 1337) hydrogen bonds : angle 5.91518 ( 3789) covalent geometry : bond 0.00435 (23424) covalent geometry : angle 0.46920 (31656) *********************** 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 : 2.439 Fit side-chains REVERT: A 67 PHE cc_start: 0.8117 (t80) cc_final: 0.7771 (m-80) REVERT: B 67 PHE cc_start: 0.8060 (t80) cc_final: 0.7727 (m-80) REVERT: B 338 TRP cc_start: 0.8803 (t60) cc_final: 0.8368 (t60) REVERT: B 387 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8767 (mp10) REVERT: B 548 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8689 (ttmm) REVERT: C 67 PHE cc_start: 0.8110 (t80) cc_final: 0.7767 (m-80) REVERT: D 67 PHE cc_start: 0.8062 (t80) cc_final: 0.7729 (m-80) REVERT: D 338 TRP cc_start: 0.8804 (t60) cc_final: 0.8361 (t60) REVERT: D 387 GLN cc_start: 0.9229 (mm-40) cc_final: 0.8765 (mp10) REVERT: D 548 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8692 (ttmm) REVERT: E 67 PHE cc_start: 0.8235 (t80) cc_final: 0.7908 (m-80) REVERT: E 307 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8068 (tm-30) REVERT: E 338 TRP cc_start: 0.8882 (t60) cc_final: 0.8491 (t60) REVERT: E 387 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8967 (mp10) REVERT: E 548 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8635 (ttmm) REVERT: F 67 PHE cc_start: 0.8246 (t80) cc_final: 0.7897 (m-80) REVERT: F 307 GLN cc_start: 0.8318 (tm-30) cc_final: 0.8065 (tm-30) REVERT: F 338 TRP cc_start: 0.8874 (t60) cc_final: 0.8496 (t60) REVERT: F 387 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8896 (mp10) REVERT: F 548 LYS cc_start: 0.8905 (ttmm) cc_final: 0.8635 (ttmm) outliers start: 13 outliers final: 8 residues processed: 235 average time/residue: 1.5097 time to fit residues: 401.8409 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 : 2.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain F residue 454 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 266 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.096742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.065678 restraints weight = 38306.490| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.42 r_work: 0.2664 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 23424 Z= 0.228 Angle : 0.566 7.394 31656 Z= 0.294 Chirality : 0.044 0.147 3444 Planarity : 0.004 0.035 4128 Dihedral : 4.616 55.181 3256 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.01 % Allowed : 7.54 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.16), residues: 2964 helix: 2.50 (0.13), residues: 1578 sheet: -0.20 (0.30), residues: 306 loop : 0.02 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 442 HIS 0.004 0.001 HIS F 315 PHE 0.020 0.002 PHE E 66 TYR 0.012 0.002 TYR D 170 ARG 0.003 0.000 ARG C 151 Details of bonding type rmsd hydrogen bonds : bond 0.04870 ( 1337) hydrogen bonds : angle 4.02722 ( 3789) covalent geometry : bond 0.00541 (23424) covalent geometry : angle 0.56596 (31656) *********************** 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 213 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 2.468 Fit side-chains REVERT: A 67 PHE cc_start: 0.8702 (t80) cc_final: 0.8220 (m-80) REVERT: B 67 PHE cc_start: 0.8562 (t80) cc_final: 0.8074 (m-80) REVERT: B 307 GLN cc_start: 0.8668 (tm-30) cc_final: 0.7728 (tm-30) REVERT: B 338 TRP cc_start: 0.8743 (t60) cc_final: 0.8173 (t60) REVERT: B 387 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8791 (mp10) REVERT: C 67 PHE cc_start: 0.8701 (t80) cc_final: 0.8226 (m-80) REVERT: D 67 PHE cc_start: 0.8562 (t80) cc_final: 0.8065 (m-80) REVERT: D 307 GLN cc_start: 0.8696 (tm-30) cc_final: 0.7756 (tm-30) REVERT: D 338 TRP cc_start: 0.8751 (t60) cc_final: 0.8184 (t60) REVERT: D 387 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8777 (mp10) REVERT: E 67 PHE cc_start: 0.8733 (t80) cc_final: 0.8341 (m-80) REVERT: E 307 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8152 (tm-30) REVERT: E 338 TRP cc_start: 0.8814 (t60) cc_final: 0.8324 (t60) REVERT: E 387 GLN cc_start: 0.9208 (mm110) cc_final: 0.8800 (mp10) REVERT: E 548 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8793 (ttmm) REVERT: F 67 PHE cc_start: 0.8743 (t80) cc_final: 0.8356 (m-80) REVERT: F 307 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8117 (tm-30) REVERT: F 338 TRP cc_start: 0.8783 (t60) cc_final: 0.8314 (t60) REVERT: F 387 GLN cc_start: 0.9209 (mm110) cc_final: 0.8794 (mp10) REVERT: F 548 LYS cc_start: 0.9006 (ttmm) cc_final: 0.8783 (ttmm) outliers start: 24 outliers final: 20 residues processed: 207 average time/residue: 1.2452 time to fit residues: 299.7567 Evaluate side-chains 196 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 556 THR Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 556 THR Chi-restraints excluded: chain F residue 66 PHE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 556 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 285 optimal weight: 0.9980 chunk 264 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 chunk 223 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 205 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.100325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.070483 restraints weight = 37784.651| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.34 r_work: 0.2794 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23424 Z= 0.105 Angle : 0.488 8.078 31656 Z= 0.248 Chirality : 0.041 0.142 3444 Planarity : 0.004 0.036 4128 Dihedral : 4.327 54.416 3252 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.68 % Allowed : 7.71 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.16), residues: 2964 helix: 2.81 (0.13), residues: 1566 sheet: 0.02 (0.32), residues: 288 loop : 0.01 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 338 HIS 0.004 0.001 HIS C 355 PHE 0.025 0.001 PHE A 66 TYR 0.008 0.001 TYR D 247 ARG 0.002 0.000 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 1337) hydrogen bonds : angle 3.68562 ( 3789) covalent geometry : bond 0.00238 (23424) covalent geometry : angle 0.48760 (31656) *********************** 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 262 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 222 time to evaluate : 2.426 Fit side-chains REVERT: A 67 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.8347 (m-80) REVERT: B 67 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.8155 (m-80) REVERT: B 307 GLN cc_start: 0.8857 (tm-30) cc_final: 0.7895 (tm-30) REVERT: B 387 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8824 (mp10) REVERT: C 67 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.8355 (m-80) REVERT: D 67 PHE cc_start: 0.8380 (t80) cc_final: 0.8144 (m-80) REVERT: D 307 GLN cc_start: 0.8857 (tm-30) cc_final: 0.7888 (tm-30) REVERT: D 387 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8813 (mp10) REVERT: E 307 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8204 (tm-30) REVERT: E 338 TRP cc_start: 0.8752 (t60) cc_final: 0.8344 (t60) REVERT: E 387 GLN cc_start: 0.9244 (mm110) cc_final: 0.8842 (mp10) REVERT: E 548 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8884 (ttmm) REVERT: F 307 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8148 (tm-30) REVERT: F 338 TRP cc_start: 0.8734 (t60) cc_final: 0.8342 (t60) REVERT: F 387 GLN cc_start: 0.9234 (mm110) cc_final: 0.8833 (mp10) REVERT: F 548 LYS cc_start: 0.9084 (ttmm) cc_final: 0.8878 (ttmm) outliers start: 40 outliers final: 11 residues processed: 258 average time/residue: 1.1834 time to fit residues: 355.3921 Evaluate side-chains 208 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 2.464 ------------------------------------------------------------------------------- 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 B residue 67 PHE 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 D residue 296 THR Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain E residue 66 PHE Chi-restraints excluded: chain F residue 66 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 58 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 251 optimal weight: 20.0000 chunk 226 optimal weight: 6.9990 chunk 283 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 HIS A 355 HIS B 262 GLN B 278 HIS C 278 HIS C 355 HIS D 278 HIS E 278 HIS E 355 HIS F 278 HIS F 355 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.098883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.067065 restraints weight = 38490.097| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.48 r_work: 0.2626 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 23424 Z= 0.291 Angle : 0.590 7.316 31656 Z= 0.306 Chirality : 0.047 0.135 3444 Planarity : 0.004 0.038 4128 Dihedral : 4.538 56.651 3248 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.76 % Allowed : 9.55 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.16), residues: 2964 helix: 2.68 (0.13), residues: 1566 sheet: -0.33 (0.30), residues: 312 loop : -0.11 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 442 HIS 0.007 0.001 HIS E 355 PHE 0.015 0.002 PHE A 67 TYR 0.016 0.002 TYR F 170 ARG 0.004 0.000 ARG F 453 Details of bonding type rmsd hydrogen bonds : bond 0.04906 ( 1337) hydrogen bonds : angle 3.79677 ( 3789) covalent geometry : bond 0.00694 (23424) covalent geometry : angle 0.59004 (31656) *********************** 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 231 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 2.644 Fit side-chains REVERT: A 67 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: A 354 GLN cc_start: 0.9201 (pp30) cc_final: 0.8872 (pp30) REVERT: B 67 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8181 (m-80) REVERT: B 68 LYS cc_start: 0.8922 (mtmm) cc_final: 0.8716 (mmmt) REVERT: B 233 MET cc_start: 0.9090 (mmp) cc_final: 0.8867 (mmt) REVERT: B 307 GLN cc_start: 0.8680 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 387 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8810 (mp10) REVERT: C 67 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: C 307 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8171 (tm-30) REVERT: D 67 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.8173 (m-80) REVERT: D 68 LYS cc_start: 0.8926 (mtmm) cc_final: 0.8706 (mmmt) REVERT: D 233 MET cc_start: 0.9088 (mmp) cc_final: 0.8864 (mmt) REVERT: D 307 GLN cc_start: 0.8694 (tm-30) cc_final: 0.7686 (tm-30) REVERT: D 387 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8810 (mp10) REVERT: E 68 LYS cc_start: 0.8905 (mtmm) cc_final: 0.8656 (mmmt) REVERT: E 307 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8066 (tm-30) REVERT: E 387 GLN cc_start: 0.9237 (mm110) cc_final: 0.8851 (mp10) REVERT: E 548 LYS cc_start: 0.9020 (ttmm) cc_final: 0.8792 (ttmm) REVERT: F 68 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8663 (mmmt) REVERT: F 307 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8150 (tm-30) REVERT: F 387 GLN cc_start: 0.9233 (mm110) cc_final: 0.8841 (mp10) REVERT: F 548 LYS cc_start: 0.9000 (ttmm) cc_final: 0.8776 (ttmm) outliers start: 42 outliers final: 28 residues processed: 217 average time/residue: 1.1747 time to fit residues: 299.1334 Evaluate side-chains 212 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 2.649 ------------------------------------------------------------------------------- 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 508 SER 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 B residue 556 THR Chi-restraints excluded: chain C residue 66 PHE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 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 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 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 271 optimal weight: 5.9990 chunk 249 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.103134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.072274 restraints weight = 38070.307| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.45 r_work: 0.2717 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23424 Z= 0.113 Angle : 0.514 11.316 31656 Z= 0.259 Chirality : 0.042 0.131 3444 Planarity : 0.004 0.041 4128 Dihedral : 4.258 55.161 3248 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.34 % Allowed : 10.51 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.16), residues: 2964 helix: 2.80 (0.13), residues: 1566 sheet: -0.18 (0.31), residues: 294 loop : -0.17 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 338 HIS 0.004 0.001 HIS D 315 PHE 0.018 0.001 PHE B 66 TYR 0.010 0.001 TYR F 247 ARG 0.002 0.000 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 1337) hydrogen bonds : angle 3.58444 ( 3789) covalent geometry : bond 0.00259 (23424) covalent geometry : angle 0.51382 (31656) *********************** 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 236 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 204 time to evaluate : 2.699 Fit side-chains REVERT: B 67 PHE cc_start: 0.8511 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: B 307 GLN cc_start: 0.8813 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 387 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8818 (mp10) REVERT: D 67 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: D 307 GLN cc_start: 0.8806 (tm-30) cc_final: 0.7794 (tm-30) REVERT: D 387 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8812 (mp10) REVERT: E 67 PHE cc_start: 0.8384 (m-80) cc_final: 0.8180 (m-80) REVERT: E 68 LYS cc_start: 0.8905 (mtmm) cc_final: 0.8584 (mmmt) REVERT: E 307 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8207 (tm-30) REVERT: E 387 GLN cc_start: 0.9213 (mm110) cc_final: 0.8798 (mp10) REVERT: E 548 LYS cc_start: 0.9051 (ttmm) cc_final: 0.8846 (ttmm) REVERT: F 67 PHE cc_start: 0.8389 (m-80) cc_final: 0.8186 (m-80) REVERT: F 68 LYS cc_start: 0.8913 (mtmm) cc_final: 0.8598 (mmmt) REVERT: F 307 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8184 (tm-30) REVERT: F 387 GLN cc_start: 0.9202 (mm110) cc_final: 0.8846 (mp10) REVERT: F 548 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8838 (ttmm) outliers start: 32 outliers final: 21 residues processed: 232 average time/residue: 1.3172 time to fit residues: 354.6198 Evaluate side-chains 205 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 2.824 ------------------------------------------------------------------------------- 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 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 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 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 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 109 optimal weight: 0.0970 chunk 219 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 206 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 169 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 36 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.103754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.072867 restraints weight = 37912.520| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.49 r_work: 0.2743 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23424 Z= 0.100 Angle : 0.503 11.642 31656 Z= 0.251 Chirality : 0.041 0.151 3444 Planarity : 0.004 0.041 4128 Dihedral : 4.140 54.784 3248 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.17 % Allowed : 11.18 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.16), residues: 2964 helix: 2.90 (0.13), residues: 1566 sheet: -0.50 (0.28), residues: 354 loop : -0.21 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 338 HIS 0.004 0.001 HIS C 315 PHE 0.030 0.001 PHE E 66 TYR 0.009 0.001 TYR F 247 ARG 0.001 0.000 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 1337) hydrogen bonds : angle 3.44539 ( 3789) covalent geometry : bond 0.00227 (23424) covalent geometry : angle 0.50308 (31656) *********************** 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 247 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 2.754 Fit side-chains REVERT: A 66 PHE cc_start: 0.8027 (p90) cc_final: 0.7690 (p90) REVERT: A 67 PHE cc_start: 0.8126 (m-80) cc_final: 0.7857 (m-80) REVERT: B 307 GLN cc_start: 0.8835 (tm-30) cc_final: 0.7798 (tm-30) REVERT: B 387 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8790 (mp10) REVERT: C 66 PHE cc_start: 0.8014 (p90) cc_final: 0.7667 (p90) REVERT: C 67 PHE cc_start: 0.8124 (m-80) cc_final: 0.7853 (m-80) REVERT: C 307 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8112 (tm-30) REVERT: D 67 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: D 307 GLN cc_start: 0.8837 (tm-30) cc_final: 0.7794 (tm-30) REVERT: D 387 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8777 (mp10) REVERT: E 68 LYS cc_start: 0.8905 (mtmm) cc_final: 0.8565 (mmmt) REVERT: E 307 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8206 (tm-30) REVERT: E 387 GLN cc_start: 0.9181 (mm110) cc_final: 0.8762 (mp10) REVERT: F 67 PHE cc_start: 0.8294 (m-80) cc_final: 0.8082 (m-80) REVERT: F 68 LYS cc_start: 0.8911 (mtmm) cc_final: 0.8576 (mmmt) REVERT: F 307 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8181 (tm-30) REVERT: F 387 GLN cc_start: 0.9171 (mm110) cc_final: 0.8756 (mp10) outliers start: 28 outliers final: 14 residues processed: 239 average time/residue: 1.1616 time to fit residues: 326.0301 Evaluate side-chains 206 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 378 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 508 SER Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 378 ILE 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 508 SER Chi-restraints excluded: chain E residue 296 THR Chi-restraints excluded: chain F residue 296 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 102 optimal weight: 2.9990 chunk 268 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 chunk 205 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 239 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.102367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.071214 restraints weight = 38003.319| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.48 r_work: 0.2710 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23424 Z= 0.129 Angle : 0.524 11.103 31656 Z= 0.262 Chirality : 0.043 0.179 3444 Planarity : 0.004 0.043 4128 Dihedral : 3.683 15.140 3240 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.05 % Allowed : 11.89 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.16), residues: 2964 helix: 2.88 (0.13), residues: 1566 sheet: -0.50 (0.28), residues: 348 loop : -0.13 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 338 HIS 0.004 0.001 HIS A 315 PHE 0.023 0.001 PHE A 66 TYR 0.010 0.001 TYR A 247 ARG 0.002 0.000 ARG F 136 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 1337) hydrogen bonds : angle 3.45779 ( 3789) covalent geometry : bond 0.00302 (23424) covalent geometry : angle 0.52353 (31656) *********************** 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 225 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 2.638 Fit side-chains REVERT: A 67 PHE cc_start: 0.8193 (m-80) cc_final: 0.7825 (m-80) REVERT: A 68 LYS cc_start: 0.8721 (mtmm) cc_final: 0.8490 (mmmt) REVERT: B 67 PHE cc_start: 0.8311 (m-80) cc_final: 0.8080 (m-80) REVERT: B 68 LYS cc_start: 0.8870 (mtmm) cc_final: 0.8518 (mmmt) REVERT: B 233 MET cc_start: 0.9079 (mmp) cc_final: 0.8847 (mmt) REVERT: B 295 MET cc_start: 0.8544 (ptp) cc_final: 0.8304 (ptp) REVERT: B 307 GLN cc_start: 0.8805 (tm-30) cc_final: 0.7766 (tm-30) REVERT: B 387 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8756 (mp10) REVERT: C 67 PHE cc_start: 0.8195 (m-80) cc_final: 0.7825 (m-80) REVERT: C 68 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8480 (mmmt) REVERT: D 67 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: D 68 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8526 (mmmt) REVERT: D 233 MET cc_start: 0.9088 (mmp) cc_final: 0.8855 (mmt) REVERT: D 307 GLN cc_start: 0.8811 (tm-30) cc_final: 0.7764 (tm-30) REVERT: D 387 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8749 (mp10) REVERT: E 68 LYS cc_start: 0.8906 (mtmm) cc_final: 0.8510 (mmmt) REVERT: E 307 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8182 (tm-30) REVERT: E 387 GLN cc_start: 0.9190 (mm110) cc_final: 0.8836 (mp10) REVERT: F 67 PHE cc_start: 0.8387 (m-80) cc_final: 0.8178 (m-80) REVERT: F 68 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8530 (mmmt) REVERT: F 307 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8163 (tm-30) REVERT: F 387 GLN cc_start: 0.9188 (mm110) cc_final: 0.8826 (mp10) outliers start: 25 outliers final: 16 residues processed: 221 average time/residue: 1.1803 time to fit residues: 306.7515 Evaluate side-chains 209 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 454 LEU 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 289 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 206 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 262 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 285 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.101254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.069940 restraints weight = 37846.478| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.48 r_work: 0.2692 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1952 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 : 0.557 11.424 31656 Z= 0.277 Chirality : 0.043 0.194 3444 Planarity : 0.004 0.043 4128 Dihedral : 3.774 15.575 3240 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.26 % Allowed : 11.73 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.16), residues: 2964 helix: 2.85 (0.13), residues: 1566 sheet: -0.43 (0.28), residues: 342 loop : -0.19 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 338 HIS 0.004 0.001 HIS A 315 PHE 0.031 0.001 PHE F 66 TYR 0.010 0.001 TYR A 170 ARG 0.002 0.000 ARG E 136 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 1337) hydrogen bonds : angle 3.49189 ( 3789) covalent geometry : bond 0.00378 (23424) covalent geometry : angle 0.55686 (31656) *********************** 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 225 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 2.697 Fit side-chains REVERT: A 67 PHE cc_start: 0.8259 (m-80) cc_final: 0.7919 (m-80) REVERT: A 68 LYS cc_start: 0.8802 (mtmm) cc_final: 0.8556 (mmmt) REVERT: B 67 PHE cc_start: 0.8395 (m-80) cc_final: 0.8172 (m-80) REVERT: B 68 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8544 (mmmt) REVERT: B 307 GLN cc_start: 0.8768 (tm-30) cc_final: 0.7713 (tm-30) REVERT: B 387 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8723 (mp10) REVERT: B 476 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8671 (ptp90) REVERT: C 67 PHE cc_start: 0.8264 (m-80) cc_final: 0.7922 (m-80) REVERT: C 68 LYS cc_start: 0.8792 (mtmm) cc_final: 0.8551 (mmmt) REVERT: D 67 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: D 68 LYS cc_start: 0.8878 (mtmm) cc_final: 0.8621 (mmmt) REVERT: D 233 MET cc_start: 0.9090 (mmp) cc_final: 0.8834 (mmt) REVERT: D 307 GLN cc_start: 0.8767 (tm-30) cc_final: 0.7718 (tm-30) REVERT: D 387 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8805 (mp10) REVERT: D 476 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8664 (ptp90) REVERT: E 68 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8533 (mmmt) REVERT: E 307 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8203 (tm-30) REVERT: E 387 GLN cc_start: 0.9197 (mm110) cc_final: 0.8819 (mp10) REVERT: E 476 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.7857 (ptp90) REVERT: F 67 PHE cc_start: 0.8433 (m-80) cc_final: 0.8170 (m-80) REVERT: F 68 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8558 (mmmt) REVERT: F 307 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8168 (tm-30) REVERT: F 387 GLN cc_start: 0.9191 (mm110) cc_final: 0.8791 (mp10) REVERT: F 476 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.7882 (ptp90) outliers start: 30 outliers final: 22 residues processed: 223 average time/residue: 1.2108 time to fit residues: 315.1960 Evaluate side-chains 210 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 183 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 508 SER Chi-restraints excluded: chain 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 476 ARG Chi-restraints excluded: chain B residue 508 SER 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 476 ARG Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 378 ILE Chi-restraints excluded: chain E residue 476 ARG Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain F residue 476 ARG Chi-restraints excluded: chain F residue 543 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 150 optimal weight: 5.9990 chunk 173 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 113 optimal weight: 0.0470 chunk 28 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 overall best weight: 2.0084 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.098216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.067199 restraints weight = 38387.145| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.45 r_work: 0.2690 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23424 Z= 0.165 Angle : 0.564 10.671 31656 Z= 0.283 Chirality : 0.044 0.192 3444 Planarity : 0.004 0.043 4128 Dihedral : 3.830 15.708 3240 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.34 % Allowed : 11.98 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.16), residues: 2964 helix: 2.83 (0.13), residues: 1566 sheet: -0.45 (0.28), residues: 342 loop : -0.22 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 338 HIS 0.004 0.001 HIS E 315 PHE 0.027 0.002 PHE C 66 TYR 0.010 0.001 TYR B 247 ARG 0.002 0.000 ARG F 136 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 1337) hydrogen bonds : angle 3.51083 ( 3789) covalent geometry : bond 0.00393 (23424) covalent geometry : angle 0.56380 (31656) *********************** 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 226 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 2.193 Fit side-chains REVERT: A 66 PHE cc_start: 0.8434 (p90) cc_final: 0.8206 (p90) REVERT: A 67 PHE cc_start: 0.8345 (m-80) cc_final: 0.7889 (m-80) REVERT: A 68 LYS cc_start: 0.8850 (mtmm) cc_final: 0.8570 (mmmt) REVERT: A 476 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.7807 (ttp80) REVERT: B 67 PHE cc_start: 0.8412 (m-80) cc_final: 0.8172 (m-80) REVERT: B 68 LYS cc_start: 0.8914 (mtmm) cc_final: 0.8575 (mmmt) REVERT: B 307 GLN cc_start: 0.8785 (tm-30) cc_final: 0.7719 (tm-30) REVERT: B 387 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8790 (mp10) REVERT: B 476 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8615 (ptp90) REVERT: C 66 PHE cc_start: 0.8433 (p90) cc_final: 0.8207 (p90) REVERT: C 67 PHE cc_start: 0.8341 (m-80) cc_final: 0.7886 (m-80) REVERT: C 68 LYS cc_start: 0.8843 (mtmm) cc_final: 0.8567 (mmmt) REVERT: C 476 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.7805 (ttp80) REVERT: D 67 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8198 (m-80) REVERT: D 68 LYS cc_start: 0.8871 (mtmm) cc_final: 0.8636 (mmmt) REVERT: D 233 MET cc_start: 0.9089 (mmp) cc_final: 0.8833 (mmt) REVERT: D 307 GLN cc_start: 0.8772 (tm-30) cc_final: 0.7690 (tm-30) REVERT: D 387 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8785 (mp10) REVERT: D 476 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8622 (ptp90) REVERT: E 68 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8567 (mmmt) REVERT: E 307 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8192 (tm-30) REVERT: E 387 GLN cc_start: 0.9192 (mm110) cc_final: 0.8795 (mp10) REVERT: F 68 LYS cc_start: 0.8966 (mtmm) cc_final: 0.8578 (mmmt) REVERT: F 307 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8162 (tm-30) REVERT: F 387 GLN cc_start: 0.9194 (mm110) cc_final: 0.8735 (mp10) outliers start: 32 outliers final: 26 residues processed: 222 average time/residue: 1.3226 time to fit residues: 341.5034 Evaluate side-chains 213 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 508 SER 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 476 ARG Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 476 ARG Chi-restraints excluded: chain C residue 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 476 ARG Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 66 PHE 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 E residue 543 ILE Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 378 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 215 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 181 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 241 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.098840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.068443 restraints weight = 38443.448| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.41 r_work: 0.2754 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23424 Z= 0.124 Angle : 0.565 11.496 31656 Z= 0.280 Chirality : 0.043 0.177 3444 Planarity : 0.004 0.044 4128 Dihedral : 3.759 15.318 3240 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.26 % Allowed : 12.44 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.16), residues: 2964 helix: 2.87 (0.13), residues: 1566 sheet: -0.46 (0.28), residues: 342 loop : -0.20 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 338 HIS 0.004 0.001 HIS C 315 PHE 0.034 0.001 PHE F 66 TYR 0.010 0.001 TYR D 247 ARG 0.001 0.000 ARG E 136 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1337) hydrogen bonds : angle 3.47808 ( 3789) covalent geometry : bond 0.00292 (23424) covalent geometry : angle 0.56452 (31656) ********************** 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 230 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 2.431 Fit side-chains REVERT: A 66 PHE cc_start: 0.8433 (p90) cc_final: 0.8213 (p90) REVERT: A 67 PHE cc_start: 0.8309 (m-80) cc_final: 0.7822 (m-80) REVERT: A 68 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8553 (mmmt) REVERT: A 476 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7815 (ttp80) REVERT: B 67 PHE cc_start: 0.8350 (m-80) cc_final: 0.8116 (m-80) REVERT: B 68 LYS cc_start: 0.8914 (mtmm) cc_final: 0.8572 (mmmt) REVERT: B 307 GLN cc_start: 0.8826 (tm-30) cc_final: 0.7745 (tm-30) REVERT: B 387 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8731 (mp-120) REVERT: B 476 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8684 (ptp90) REVERT: C 66 PHE cc_start: 0.8423 (p90) cc_final: 0.8199 (p90) REVERT: C 67 PHE cc_start: 0.8306 (m-80) cc_final: 0.7819 (m-80) REVERT: C 68 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8552 (mmmt) REVERT: C 476 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7785 (ttp80) REVERT: D 67 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8171 (m-80) REVERT: D 68 LYS cc_start: 0.8822 (mtmm) cc_final: 0.8566 (mmmt) REVERT: D 307 GLN cc_start: 0.8824 (tm-30) cc_final: 0.7746 (tm-30) REVERT: D 387 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8822 (mp10) REVERT: D 476 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8652 (ptp90) REVERT: E 68 LYS cc_start: 0.8972 (mtmm) cc_final: 0.8605 (mmmt) REVERT: E 307 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8224 (tm-30) REVERT: E 387 GLN cc_start: 0.9218 (mm110) cc_final: 0.8854 (mp10) REVERT: E 476 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.7769 (ptp90) REVERT: F 68 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8537 (mmmt) REVERT: F 307 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8179 (tm-30) REVERT: F 387 GLN cc_start: 0.9206 (mm110) cc_final: 0.8837 (mp10) REVERT: F 476 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.7803 (ptp90) outliers start: 30 outliers final: 22 residues processed: 228 average time/residue: 1.2379 time to fit residues: 327.6914 Evaluate side-chains 222 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 476 ARG Chi-restraints excluded: chain A residue 508 SER 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 476 ARG Chi-restraints excluded: chain B residue 508 SER Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 476 ARG 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 476 ARG Chi-restraints excluded: chain D residue 508 SER Chi-restraints excluded: chain E residue 66 PHE 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 E residue 476 ARG 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 31 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 189 optimal weight: 0.0020 chunk 260 optimal weight: 0.9980 chunk 214 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.3457 r_free = 0.3457 target = 0.103762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.073254 restraints weight = 38424.990| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.45 r_work: 0.2768 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23424 Z= 0.134 Angle : 0.564 11.732 31656 Z= 0.280 Chirality : 0.043 0.153 3444 Planarity : 0.004 0.048 4128 Dihedral : 3.743 15.296 3240 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.16), residues: 2964 helix: 2.87 (0.13), residues: 1566 sheet: -0.45 (0.28), residues: 342 loop : -0.21 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 338 HIS 0.004 0.001 HIS A 315 PHE 0.027 0.001 PHE C 66 TYR 0.010 0.001 TYR B 247 ARG 0.002 0.000 ARG E 136 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 1337) hydrogen bonds : angle 3.46213 ( 3789) covalent geometry : bond 0.00318 (23424) covalent geometry : angle 0.56433 (31656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20887.77 seconds wall clock time: 359 minutes 23.75 seconds (21563.75 seconds total)