Starting phenix.real_space_refine on Fri Jun 20 04:46:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jd2_6635/06_2025/3jd2_6635.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd2_6635/06_2025/3jd2_6635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jd2_6635/06_2025/3jd2_6635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd2_6635/06_2025/3jd2_6635.map" model { file = "/net/cci-nas-00/data/ceres_data/3jd2_6635/06_2025/3jd2_6635.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd2_6635/06_2025/3jd2_6635.cif" } resolution = 3.3 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= 0.005 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 114 5.16 5 C 14976 2.51 5 N 4158 2.21 5 O 4542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23814 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "B" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "C" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "D" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "E" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "F" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" C1B NAI A 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI A 602 " occ=0.35 residue: pdb=" C1B NAI B 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI B 602 " occ=0.35 residue: pdb=" C1B NAI C 601 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI C 601 " occ=0.35 residue: pdb=" C1B NAI D 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI D 602 " occ=0.35 residue: pdb=" C1B NAI E 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI E 602 " occ=0.35 residue: pdb=" C1B NAI F 601 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI F 601 " occ=0.35 Time building chain proxies: 13.12, per 1000 atoms: 0.55 Number of scatterers: 23814 At special positions: 0 Unit cell: (114.92, 118.3, 165.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 24 15.00 O 4542 8.00 N 4158 7.00 C 14976 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: 6.00 Conformation dependent library (CDL) restraints added in 2.9 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: 5400 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 15 sheets defined 54.8% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.628A pdb=" N MET A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU A 14 " --> pdb=" O PHE A 10 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP A 26 " --> pdb=" O SER A 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 52 removed outlier: 3.808A pdb=" N LYS A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 118 removed outlier: 3.634A pdb=" N TYR A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 137 through 154 removed outlier: 3.842A pdb=" N GLU A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 187 removed outlier: 3.700A pdb=" N TRP A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 213 through 228 removed outlier: 3.567A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 237 removed outlier: 3.513A pdb=" N SER A 234 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 265 removed outlier: 3.511A pdb=" N HIS A 258 " --> pdb=" O ASN A 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 removed outlier: 3.557A pdb=" N LYS A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.744A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.603A pdb=" N LEU A 373 " --> pdb=" O PRO A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 removed outlier: 3.539A pdb=" N VAL A 380 " --> pdb=" O GLY A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 418 Processing helix chain 'A' and resid 419 through 420 No H-bonds generated for 'chain 'A' and resid 419 through 420' Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 433 through 441 removed outlier: 3.513A pdb=" N ASP A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 460 removed outlier: 4.050A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA A 454 " --> pdb=" O HIS A 450 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 476 through 495 removed outlier: 3.973A pdb=" N ALA A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 495 " --> pdb=" O ARG A 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.628A pdb=" N MET B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 14 " --> pdb=" O PHE B 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 24 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 52 removed outlier: 3.808A pdb=" N LYS B 41 " --> pdb=" O THR B 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 118 removed outlier: 3.635A pdb=" N TYR B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA B 116 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 137 through 154 removed outlier: 3.842A pdb=" N GLU B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET B 150 " --> pdb=" O ARG B 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 187 removed outlier: 3.699A pdb=" N TRP B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.568A pdb=" N ILE B 223 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B 225 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.513A pdb=" N SER B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 236 " --> pdb=" O TYR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.511A pdb=" N HIS B 258 " --> pdb=" O ASN B 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 297 removed outlier: 3.556A pdb=" N LYS B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.744A pdb=" N LYS B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.602A pdb=" N LEU B 373 " --> pdb=" O PRO B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 391 removed outlier: 3.539A pdb=" N VAL B 380 " --> pdb=" O GLY B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 418 Processing helix chain 'B' and resid 419 through 420 No H-bonds generated for 'chain 'B' and resid 419 through 420' Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 433 through 441 removed outlier: 3.513A pdb=" N ASP B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 removed outlier: 4.050A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 471 Processing helix chain 'B' and resid 476 through 495 removed outlier: 3.972A pdb=" N ALA B 480 " --> pdb=" O ASP B 476 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU B 495 " --> pdb=" O ARG B 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.628A pdb=" N MET C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU C 14 " --> pdb=" O PHE C 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP C 26 " --> pdb=" O SER C 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS C 27 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 removed outlier: 3.808A pdb=" N LYS C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 118 removed outlier: 3.634A pdb=" N TYR C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 116 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 137 through 154 removed outlier: 3.842A pdb=" N GLU C 142 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C 150 " --> pdb=" O ARG C 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 187 removed outlier: 3.700A pdb=" N TRP C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 179 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.566A pdb=" N ILE C 223 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN C 225 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.513A pdb=" N SER C 234 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 236 " --> pdb=" O TYR C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 265 removed outlier: 3.511A pdb=" N HIS C 258 " --> pdb=" O ASN C 254 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 259 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 removed outlier: 3.557A pdb=" N LYS C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.744A pdb=" N LYS C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.603A pdb=" N LEU C 373 " --> pdb=" O PRO C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 391 removed outlier: 3.538A pdb=" N VAL C 380 " --> pdb=" O GLY C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 418 Processing helix chain 'C' and resid 419 through 420 No H-bonds generated for 'chain 'C' and resid 419 through 420' Processing helix chain 'C' and resid 421 through 425 Processing helix chain 'C' and resid 433 through 441 removed outlier: 3.513A pdb=" N ASP C 438 " --> pdb=" O ALA C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 460 removed outlier: 4.050A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA C 454 " --> pdb=" O HIS C 450 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 471 Processing helix chain 'C' and resid 476 through 495 removed outlier: 3.973A pdb=" N ALA C 480 " --> pdb=" O ASP C 476 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 30 removed outlier: 3.628A pdb=" N MET D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 14 " --> pdb=" O PHE D 10 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 24 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP D 26 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU D 30 " --> pdb=" O ASP D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 52 removed outlier: 3.808A pdb=" N LYS D 41 " --> pdb=" O THR D 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 118 removed outlier: 3.634A pdb=" N TYR D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 154 removed outlier: 3.842A pdb=" N GLU D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 187 removed outlier: 3.700A pdb=" N TRP D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.567A pdb=" N ILE D 223 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN D 225 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 237 removed outlier: 3.513A pdb=" N SER D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 235 " --> pdb=" O SER D 231 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU D 236 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 265 removed outlier: 3.511A pdb=" N HIS D 258 " --> pdb=" O ASN D 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 297 removed outlier: 3.557A pdb=" N LYS D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.744A pdb=" N LYS D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.603A pdb=" N LEU D 373 " --> pdb=" O PRO D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 391 removed outlier: 3.539A pdb=" N VAL D 380 " --> pdb=" O GLY D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 418 Processing helix chain 'D' and resid 419 through 420 No H-bonds generated for 'chain 'D' and resid 419 through 420' Processing helix chain 'D' and resid 421 through 425 Processing helix chain 'D' and resid 433 through 441 removed outlier: 3.513A pdb=" N ASP D 438 " --> pdb=" O ALA D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 460 removed outlier: 4.050A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU D 458 " --> pdb=" O ALA D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 471 Processing helix chain 'D' and resid 476 through 495 removed outlier: 3.973A pdb=" N ALA D 480 " --> pdb=" O ASP D 476 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 491 " --> pdb=" O GLU D 487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL D 492 " --> pdb=" O LYS D 488 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU D 495 " --> pdb=" O ARG D 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 30 removed outlier: 3.628A pdb=" N MET E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU E 14 " --> pdb=" O PHE E 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 24 " --> pdb=" O GLY E 20 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ASP E 26 " --> pdb=" O SER E 22 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS E 27 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 52 removed outlier: 3.808A pdb=" N LYS E 41 " --> pdb=" O THR E 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 118 removed outlier: 3.635A pdb=" N TYR E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA E 116 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 154 removed outlier: 3.842A pdb=" N GLU E 142 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 187 removed outlier: 3.699A pdb=" N TRP E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 228 removed outlier: 3.568A pdb=" N ILE E 223 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN E 225 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE E 226 " --> pdb=" O GLY E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 237 removed outlier: 3.513A pdb=" N SER E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE E 235 " --> pdb=" O SER E 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 236 " --> pdb=" O TYR E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 265 removed outlier: 3.511A pdb=" N HIS E 258 " --> pdb=" O ASN E 254 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR E 262 " --> pdb=" O HIS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 297 removed outlier: 3.556A pdb=" N LYS E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN E 297 " --> pdb=" O ASP E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 362 removed outlier: 3.744A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.602A pdb=" N LEU E 373 " --> pdb=" O PRO E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 391 removed outlier: 3.539A pdb=" N VAL E 380 " --> pdb=" O GLY E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 418 Processing helix chain 'E' and resid 419 through 420 No H-bonds generated for 'chain 'E' and resid 419 through 420' Processing helix chain 'E' and resid 421 through 425 Processing helix chain 'E' and resid 433 through 441 removed outlier: 3.513A pdb=" N ASP E 438 " --> pdb=" O ALA E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 460 removed outlier: 4.050A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA E 454 " --> pdb=" O HIS E 450 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 471 Processing helix chain 'E' and resid 476 through 495 removed outlier: 3.972A pdb=" N ALA E 480 " --> pdb=" O ASP E 476 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG E 491 " --> pdb=" O GLU E 487 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL E 492 " --> pdb=" O LYS E 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR E 493 " --> pdb=" O VAL E 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU E 495 " --> pdb=" O ARG E 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 30 removed outlier: 3.628A pdb=" N MET F 12 " --> pdb=" O ASN F 8 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU F 14 " --> pdb=" O PHE F 10 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ASP F 26 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LYS F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU F 30 " --> pdb=" O ASP F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 52 removed outlier: 3.808A pdb=" N LYS F 41 " --> pdb=" O THR F 37 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 118 removed outlier: 3.634A pdb=" N TYR F 113 " --> pdb=" O SER F 109 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 137 through 154 removed outlier: 3.842A pdb=" N GLU F 142 " --> pdb=" O ASP F 138 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU F 152 " --> pdb=" O PHE F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 187 removed outlier: 3.700A pdb=" N TRP F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 197 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 213 through 228 removed outlier: 3.566A pdb=" N ILE F 223 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN F 225 " --> pdb=" O HIS F 221 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE F 226 " --> pdb=" O GLY F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 removed outlier: 3.513A pdb=" N SER F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE F 235 " --> pdb=" O SER F 231 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 236 " --> pdb=" O TYR F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 265 removed outlier: 3.511A pdb=" N HIS F 258 " --> pdb=" O ASN F 254 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR F 262 " --> pdb=" O HIS F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 297 removed outlier: 3.557A pdb=" N LYS F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN F 297 " --> pdb=" O ASP F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 362 removed outlier: 3.744A pdb=" N LYS F 358 " --> pdb=" O PRO F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 374 removed outlier: 3.603A pdb=" N LEU F 373 " --> pdb=" O PRO F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 391 removed outlier: 3.538A pdb=" N VAL F 380 " --> pdb=" O GLY F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 418 Processing helix chain 'F' and resid 419 through 420 No H-bonds generated for 'chain 'F' and resid 419 through 420' Processing helix chain 'F' and resid 421 through 425 Processing helix chain 'F' and resid 433 through 441 removed outlier: 3.513A pdb=" N ASP F 438 " --> pdb=" O ALA F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 460 removed outlier: 4.050A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA F 454 " --> pdb=" O HIS F 450 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 458 " --> pdb=" O ALA F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 460 through 471 Processing helix chain 'F' and resid 476 through 495 removed outlier: 3.973A pdb=" N ALA F 480 " --> pdb=" O ASP F 476 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG F 491 " --> pdb=" O GLU F 487 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL F 492 " --> pdb=" O LYS F 488 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR F 493 " --> pdb=" O VAL F 489 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU F 495 " --> pdb=" O ARG F 491 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.592A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG A 79 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG E 79 " --> pdb=" O LEU E 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY E 92 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain 'A' and resid 63 through 66 Processing sheet with id=C, first strand: chain 'A' and resid 308 through 309 removed outlier: 3.625A pdb=" N GLY A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE A 247 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR A 272 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 321 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 344 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain 'B' and resid 163 through 166 removed outlier: 6.591A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY B 92 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG B 79 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG D 79 " --> pdb=" O LEU D 59 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLY D 92 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=E, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=F, first strand: chain 'B' and resid 308 through 309 removed outlier: 3.625A pdb=" N GLY B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE B 247 " --> pdb=" O CYS B 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR B 272 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 321 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE B 344 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=G, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.592A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY C 92 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 79 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG F 79 " --> pdb=" O LEU F 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain 'C' and resid 63 through 66 Processing sheet with id=I, first strand: chain 'C' and resid 308 through 309 removed outlier: 3.626A pdb=" N GLY C 278 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N PHE C 247 " --> pdb=" O CYS C 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR C 272 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 321 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE C 344 " --> pdb=" O ILE C 368 " (cutoff:3.500A) Processing sheet with id=J, first strand: chain 'D' and resid 63 through 66 Processing sheet with id=K, first strand: chain 'D' and resid 308 through 309 removed outlier: 3.625A pdb=" N GLY D 278 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE D 247 " --> pdb=" O CYS D 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR D 272 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 321 " --> pdb=" O THR D 246 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE D 344 " --> pdb=" O ILE D 368 " (cutoff:3.500A) Processing sheet with id=L, first strand: chain 'E' and resid 63 through 66 Processing sheet with id=M, first strand: chain 'E' and resid 308 through 309 removed outlier: 3.625A pdb=" N GLY E 278 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N PHE E 247 " --> pdb=" O CYS E 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR E 272 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 321 " --> pdb=" O THR E 246 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 344 " --> pdb=" O ILE E 368 " (cutoff:3.500A) Processing sheet with id=N, first strand: chain 'F' and resid 63 through 66 Processing sheet with id=O, first strand: chain 'F' and resid 308 through 309 removed outlier: 3.626A pdb=" N GLY F 278 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N PHE F 247 " --> pdb=" O CYS F 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR F 272 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 321 " --> pdb=" O THR F 246 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE F 344 " --> pdb=" O ILE F 368 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3006 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: 8.54 Time building geometry restraints manager: 7.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7714 1.33 - 1.45: 3666 1.45 - 1.57: 12740 1.57 - 1.69: 48 1.69 - 1.81: 192 Bond restraints: 24360 Sorted by residual: bond pdb=" C3N NAI C 601 " pdb=" C7N NAI C 601 " ideal model delta sigma weight residual 1.473 1.592 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C3N NAI F 601 " pdb=" C7N NAI F 601 " ideal model delta sigma weight residual 1.473 1.592 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" C3N NAI A 602 " pdb=" C7N NAI A 602 " ideal model delta sigma weight residual 1.473 1.591 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C3N NAI D 602 " pdb=" C7N NAI D 602 " ideal model delta sigma weight residual 1.473 1.591 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" C3N NAI B 602 " pdb=" C7N NAI B 602 " ideal model delta sigma weight residual 1.473 1.591 -0.118 2.00e-02 2.50e+03 3.46e+01 ... (remaining 24355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 32428 3.14 - 6.27: 430 6.27 - 9.41: 94 9.41 - 12.55: 18 12.55 - 15.68: 24 Bond angle restraints: 32994 Sorted by residual: angle pdb=" O2A NAI E 601 " pdb=" PA NAI E 601 " pdb=" O5B NAI E 601 " ideal model delta sigma weight residual 105.34 121.02 -15.68 3.00e+00 1.11e-01 2.73e+01 angle pdb=" O2A NAI B 601 " pdb=" PA NAI B 601 " pdb=" O5B NAI B 601 " ideal model delta sigma weight residual 105.34 121.02 -15.68 3.00e+00 1.11e-01 2.73e+01 angle pdb=" O2A NAI D 601 " pdb=" PA NAI D 601 " pdb=" O5B NAI D 601 " ideal model delta sigma weight residual 105.34 121.00 -15.66 3.00e+00 1.11e-01 2.72e+01 angle pdb=" O2A NAI A 601 " pdb=" PA NAI A 601 " pdb=" O5B NAI A 601 " ideal model delta sigma weight residual 105.34 121.00 -15.66 3.00e+00 1.11e-01 2.72e+01 angle pdb=" O2A NAI F 602 " pdb=" PA NAI F 602 " pdb=" O5B NAI F 602 " ideal model delta sigma weight residual 105.34 120.98 -15.64 3.00e+00 1.11e-01 2.72e+01 ... (remaining 32989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.86: 14410 16.86 - 33.71: 320 33.71 - 50.57: 162 50.57 - 67.43: 66 67.43 - 84.28: 24 Dihedral angle restraints: 14982 sinusoidal: 6504 harmonic: 8478 Sorted by residual: dihedral pdb=" CA ALA F 375 " pdb=" C ALA F 375 " pdb=" N GLY F 376 " pdb=" CA GLY F 376 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ALA C 375 " pdb=" C ALA C 375 " pdb=" N GLY C 376 " pdb=" CA GLY C 376 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA ALA A 375 " pdb=" C ALA A 375 " pdb=" N GLY A 376 " pdb=" CA GLY A 376 " ideal model delta harmonic sigma weight residual 180.00 154.61 25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 14979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3142 0.080 - 0.161: 386 0.161 - 0.241: 20 0.241 - 0.321: 28 0.321 - 0.401: 12 Chirality restraints: 3588 Sorted by residual: chirality pdb=" C3B NAI B 601 " pdb=" C2B NAI B 601 " pdb=" C4B NAI B 601 " pdb=" O3B NAI B 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.32 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C3B NAI E 601 " pdb=" C2B NAI E 601 " pdb=" C4B NAI E 601 " pdb=" O3B NAI E 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.32 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C3B NAI A 601 " pdb=" C2B NAI A 601 " pdb=" C4B NAI A 601 " pdb=" O3B NAI A 601 " both_signs ideal model delta sigma weight residual False -2.72 -2.32 -0.40 2.00e-01 2.50e+01 3.99e+00 ... (remaining 3585 not shown) Planarity restraints: 4224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 336 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO D 337 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 337 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 337 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 336 " 0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO A 337 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 336 " -0.043 5.00e-02 4.00e+02 6.49e-02 6.74e+00 pdb=" N PRO E 337 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 337 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 337 " -0.036 5.00e-02 4.00e+02 ... (remaining 4221 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4320 2.75 - 3.29: 22798 3.29 - 3.83: 36841 3.83 - 4.36: 47046 4.36 - 4.90: 78853 Nonbonded interactions: 189858 Sorted by model distance: nonbonded pdb=" O THR B 239 " pdb=" NZ LYS B 245 " model vdw 2.219 3.120 nonbonded pdb=" O THR E 239 " pdb=" NZ LYS E 245 " model vdw 2.219 3.120 nonbonded pdb=" O THR F 239 " pdb=" NZ LYS F 245 " model vdw 2.219 3.120 nonbonded pdb=" O THR C 239 " pdb=" NZ LYS C 245 " model vdw 2.219 3.120 nonbonded pdb=" O THR A 239 " pdb=" NZ LYS A 245 " model vdw 2.220 3.120 ... (remaining 189853 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: 0.19 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=0.35 max=1.00 mean=0.99 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: 1.300 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: 1.040 Check model and map are aligned: 0.170 Set scattering table: 0.190 Process input model: 52.930 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.120 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:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.011 0.119 24360 Z= 0.521 Angle : 1.045 15.681 32994 Z= 0.484 Chirality : 0.061 0.401 3588 Planarity : 0.005 0.065 4224 Dihedral : 10.879 84.282 9582 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.81 % Allowed : 5.60 % Favored : 93.59 % Rotamer: Outliers : 0.72 % Allowed : 0.48 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -5.54 (0.11), residues: 2964 helix: -3.94 (0.08), residues: 1374 sheet: -3.14 (0.21), residues: 450 loop : -3.25 (0.15), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 72 HIS 0.007 0.002 HIS B 391 PHE 0.025 0.003 PHE B 399 TYR 0.025 0.003 TYR A 382 ARG 0.007 0.001 ARG D 396 Details of bonding type rmsd hydrogen bonds : bond 0.28989 ( 1068) hydrogen bonds : angle 9.47585 ( 3006) covalent geometry : bond 0.01104 (24360) covalent geometry : angle 1.04498 (32994) *********************** 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 505 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 487 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 PHE cc_start: 0.7108 (m-10) cc_final: 0.6127 (m-10) REVERT: B 500 PHE cc_start: 0.7200 (m-10) cc_final: 0.5813 (m-10) REVERT: C 500 PHE cc_start: 0.7076 (m-10) cc_final: 0.5977 (t80) REVERT: D 500 PHE cc_start: 0.7103 (m-10) cc_final: 0.6126 (m-10) REVERT: E 500 PHE cc_start: 0.7191 (m-10) cc_final: 0.5805 (m-10) REVERT: F 500 PHE cc_start: 0.7073 (m-10) cc_final: 0.5975 (t80) outliers start: 18 outliers final: 12 residues processed: 505 average time/residue: 0.4605 time to fit residues: 333.0925 Evaluate side-chains 249 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 237 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 30.0000 chunk 222 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 150 optimal weight: 30.0000 chunk 119 optimal weight: 5.9990 chunk 230 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 56 ASN A 57 HIS A 84 GLN A 330 GLN A 437 GLN B 40 GLN B 56 ASN B 57 HIS B 84 GLN B 209 HIS B 437 GLN C 56 ASN C 57 HIS C 84 GLN C 205 GLN C 209 HIS D 40 GLN D 56 ASN D 57 HIS D 84 GLN D 330 GLN D 437 GLN E 40 GLN E 56 ASN E 57 HIS E 84 GLN E 209 HIS E 437 GLN F 56 ASN F 57 HIS F 84 GLN F 205 GLN F 209 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.112947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.081487 restraints weight = 46057.183| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.59 r_work: 0.2943 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24360 Z= 0.191 Angle : 0.617 5.197 32994 Z= 0.326 Chirality : 0.047 0.176 3588 Planarity : 0.006 0.072 4224 Dihedral : 12.054 80.223 4014 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.36 % Allowed : 5.41 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -3.19 (0.14), residues: 2964 helix: -1.65 (0.12), residues: 1362 sheet: -2.36 (0.23), residues: 444 loop : -2.40 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 281 HIS 0.005 0.001 HIS B 85 PHE 0.025 0.003 PHE A 16 TYR 0.020 0.001 TYR D 382 ARG 0.013 0.001 ARG D 478 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 1068) hydrogen bonds : angle 4.95398 ( 3006) covalent geometry : bond 0.00456 (24360) covalent geometry : angle 0.61672 (32994) *********************** 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 331 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 297 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 VAL cc_start: 0.8948 (t) cc_final: 0.8547 (m) REVERT: A 269 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7970 (ptmt) REVERT: A 281 TRP cc_start: 0.7466 (t60) cc_final: 0.7259 (t60) REVERT: A 308 LYS cc_start: 0.7624 (pptt) cc_final: 0.7408 (pttp) REVERT: B 249 VAL cc_start: 0.8923 (t) cc_final: 0.8471 (m) REVERT: C 11 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8242 (mttp) REVERT: C 249 VAL cc_start: 0.8912 (t) cc_final: 0.8504 (m) REVERT: C 281 TRP cc_start: 0.7571 (t60) cc_final: 0.7135 (t60) REVERT: D 249 VAL cc_start: 0.8952 (t) cc_final: 0.8549 (m) REVERT: D 269 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7972 (ptmt) REVERT: D 281 TRP cc_start: 0.7470 (t60) cc_final: 0.7259 (t60) REVERT: D 308 LYS cc_start: 0.7621 (pptt) cc_final: 0.7328 (pttp) REVERT: D 466 ARG cc_start: 0.8348 (ttm110) cc_final: 0.7950 (tpp-160) REVERT: E 249 VAL cc_start: 0.8930 (t) cc_final: 0.8481 (m) REVERT: F 11 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8239 (mttp) REVERT: F 249 VAL cc_start: 0.8917 (t) cc_final: 0.8510 (m) REVERT: F 281 TRP cc_start: 0.7566 (t60) cc_final: 0.7130 (t60) outliers start: 34 outliers final: 28 residues processed: 316 average time/residue: 0.3408 time to fit residues: 172.4192 Evaluate side-chains 262 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 469 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 219 optimal weight: 20.0000 chunk 191 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 154 optimal weight: 9.9990 chunk 274 optimal weight: 30.0000 chunk 280 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 199 optimal weight: 0.0670 chunk 67 optimal weight: 0.6980 overall best weight: 2.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN B 437 GLN C 56 ASN C 225 ASN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN E 437 GLN F 56 ASN F 225 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.112495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.081183 restraints weight = 45768.560| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.59 r_work: 0.2953 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24360 Z= 0.114 Angle : 0.500 5.107 32994 Z= 0.263 Chirality : 0.043 0.161 3588 Planarity : 0.004 0.041 4224 Dihedral : 10.720 81.167 4002 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.64 % Allowed : 7.49 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -1.87 (0.15), residues: 2964 helix: -0.31 (0.14), residues: 1356 sheet: -1.77 (0.25), residues: 438 loop : -2.04 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 281 HIS 0.003 0.001 HIS B 85 PHE 0.018 0.002 PHE B 500 TYR 0.013 0.001 TYR E 382 ARG 0.006 0.000 ARG A 478 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 1068) hydrogen bonds : angle 4.30198 ( 3006) covalent geometry : bond 0.00260 (24360) covalent geometry : angle 0.49985 (32994) *********************** 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 324 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 283 time to evaluate : 3.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7649 (mtp) cc_final: 0.7385 (mtm) REVERT: A 111 MET cc_start: 0.9007 (tpp) cc_final: 0.8754 (tpt) REVERT: A 249 VAL cc_start: 0.8997 (t) cc_final: 0.8661 (m) REVERT: A 269 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7991 (ptmt) REVERT: A 281 TRP cc_start: 0.7514 (t60) cc_final: 0.7025 (t60) REVERT: A 330 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: B 181 ASP cc_start: 0.8732 (t70) cc_final: 0.8241 (t0) REVERT: B 249 VAL cc_start: 0.8982 (t) cc_final: 0.8616 (m) REVERT: B 281 TRP cc_start: 0.7585 (t60) cc_final: 0.7232 (t60) REVERT: C 11 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8347 (mttp) REVERT: C 12 MET cc_start: 0.7784 (mtp) cc_final: 0.7375 (mtm) REVERT: C 78 TYR cc_start: 0.8903 (m-80) cc_final: 0.8429 (m-80) REVERT: C 249 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8632 (m) REVERT: C 281 TRP cc_start: 0.7576 (t60) cc_final: 0.7091 (t60) REVERT: C 330 GLN cc_start: 0.8090 (tp40) cc_final: 0.7887 (tp40) REVERT: D 12 MET cc_start: 0.7650 (mtp) cc_final: 0.7382 (mtm) REVERT: D 249 VAL cc_start: 0.9011 (t) cc_final: 0.8669 (m) REVERT: D 269 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7995 (ptmt) REVERT: D 281 TRP cc_start: 0.7518 (t60) cc_final: 0.7026 (t60) REVERT: D 330 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: D 466 ARG cc_start: 0.8386 (ttm110) cc_final: 0.8021 (tpp-160) REVERT: E 181 ASP cc_start: 0.8732 (t70) cc_final: 0.8254 (t0) REVERT: E 249 VAL cc_start: 0.8985 (t) cc_final: 0.8620 (m) REVERT: E 281 TRP cc_start: 0.7591 (t60) cc_final: 0.7255 (t60) REVERT: E 355 GLU cc_start: 0.8061 (mp0) cc_final: 0.7832 (pm20) REVERT: F 11 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8343 (mttp) REVERT: F 12 MET cc_start: 0.7787 (mtp) cc_final: 0.7374 (mtm) REVERT: F 78 TYR cc_start: 0.8906 (m-80) cc_final: 0.8435 (m-80) REVERT: F 249 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8633 (m) REVERT: F 281 TRP cc_start: 0.7580 (t60) cc_final: 0.7093 (t60) REVERT: F 330 GLN cc_start: 0.8096 (tp40) cc_final: 0.7890 (tp40) outliers start: 41 outliers final: 27 residues processed: 300 average time/residue: 0.3741 time to fit residues: 175.5927 Evaluate side-chains 268 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 469 MET Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 431 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 57 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 chunk 147 optimal weight: 30.0000 chunk 153 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 18 optimal weight: 0.0010 chunk 3 optimal weight: 0.8980 chunk 268 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS A 437 GLN B 437 GLN C 330 GLN D 209 HIS D 437 GLN E 437 GLN F 330 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.115389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.083695 restraints weight = 46372.744| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.70 r_work: 0.3003 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 24360 Z= 0.085 Angle : 0.455 5.411 32994 Z= 0.237 Chirality : 0.042 0.152 3588 Planarity : 0.004 0.037 4224 Dihedral : 9.964 77.328 4002 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.28 % Allowed : 9.01 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.16), residues: 2964 helix: 0.47 (0.14), residues: 1374 sheet: -1.20 (0.26), residues: 432 loop : -1.63 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.003 0.000 HIS F 85 PHE 0.014 0.001 PHE F 500 TYR 0.008 0.001 TYR A 382 ARG 0.005 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 1068) hydrogen bonds : angle 3.83816 ( 3006) covalent geometry : bond 0.00182 (24360) covalent geometry : angle 0.45460 (32994) *********************** 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 357 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 325 time to evaluate : 2.605 Fit side-chains REVERT: A 12 MET cc_start: 0.7489 (mtp) cc_final: 0.7108 (mtm) REVERT: A 233 MET cc_start: 0.8135 (mmm) cc_final: 0.7344 (mmp) REVERT: A 238 MET cc_start: 0.6595 (ptt) cc_final: 0.6235 (pmm) REVERT: A 249 VAL cc_start: 0.8900 (t) cc_final: 0.8580 (m) REVERT: A 281 TRP cc_start: 0.7533 (t60) cc_final: 0.7201 (t60) REVERT: A 330 GLN cc_start: 0.7886 (tp40) cc_final: 0.7667 (mm110) REVERT: A 500 PHE cc_start: 0.5574 (t80) cc_final: 0.5358 (t80) REVERT: B 78 TYR cc_start: 0.8798 (m-80) cc_final: 0.8470 (m-80) REVERT: B 181 ASP cc_start: 0.8722 (t70) cc_final: 0.8372 (t0) REVERT: B 249 VAL cc_start: 0.8889 (t) cc_final: 0.8569 (m) REVERT: B 291 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8748 (tt) REVERT: B 308 LYS cc_start: 0.8347 (ptpp) cc_final: 0.7981 (pttm) REVERT: C 11 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8298 (mttp) REVERT: C 12 MET cc_start: 0.7658 (mtp) cc_final: 0.7328 (mtm) REVERT: C 78 TYR cc_start: 0.8795 (m-80) cc_final: 0.8488 (m-80) REVERT: C 249 VAL cc_start: 0.8811 (t) cc_final: 0.8500 (m) REVERT: C 281 TRP cc_start: 0.7601 (t60) cc_final: 0.6964 (t60) REVERT: C 330 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7644 (mm110) REVERT: D 12 MET cc_start: 0.7488 (mtp) cc_final: 0.7101 (mtm) REVERT: D 233 MET cc_start: 0.8149 (mmm) cc_final: 0.7316 (mmp) REVERT: D 238 MET cc_start: 0.6611 (ptt) cc_final: 0.6259 (pmm) REVERT: D 249 VAL cc_start: 0.8896 (t) cc_final: 0.8570 (m) REVERT: D 281 TRP cc_start: 0.7526 (t60) cc_final: 0.7180 (t60) REVERT: D 330 GLN cc_start: 0.7882 (tp40) cc_final: 0.7662 (mm110) REVERT: D 466 ARG cc_start: 0.8374 (ttm110) cc_final: 0.8095 (tpp-160) REVERT: E 78 TYR cc_start: 0.8815 (m-80) cc_final: 0.8487 (m-80) REVERT: E 181 ASP cc_start: 0.8715 (t70) cc_final: 0.8375 (t0) REVERT: E 249 VAL cc_start: 0.8885 (t) cc_final: 0.8565 (m) REVERT: E 291 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8727 (tt) REVERT: E 308 LYS cc_start: 0.8303 (ptpp) cc_final: 0.7956 (pttm) REVERT: F 11 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8283 (mttp) REVERT: F 12 MET cc_start: 0.7672 (mtp) cc_final: 0.7344 (mtm) REVERT: F 78 TYR cc_start: 0.8808 (m-80) cc_final: 0.8511 (m-80) REVERT: F 249 VAL cc_start: 0.8806 (t) cc_final: 0.8494 (m) REVERT: F 281 TRP cc_start: 0.7608 (t60) cc_final: 0.7015 (t60) REVERT: F 330 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7656 (mm110) REVERT: F 437 GLN cc_start: 0.8599 (tp40) cc_final: 0.8320 (tp40) outliers start: 32 outliers final: 20 residues processed: 334 average time/residue: 0.3498 time to fit residues: 182.5509 Evaluate side-chains 266 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 2.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 330 GLN Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 76 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 220 optimal weight: 20.0000 chunk 266 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 202 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN A 437 GLN B 40 GLN B 437 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN C 364 ASN C 437 GLN D 56 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN E 40 GLN E 437 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 GLN F 437 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.110926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078809 restraints weight = 46451.565| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.66 r_work: 0.2902 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24360 Z= 0.161 Angle : 0.526 5.049 32994 Z= 0.275 Chirality : 0.044 0.149 3588 Planarity : 0.004 0.040 4224 Dihedral : 9.547 68.480 4002 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.84 % Allowed : 9.78 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.16), residues: 2964 helix: 0.56 (0.14), residues: 1398 sheet: -1.11 (0.26), residues: 450 loop : -1.48 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 281 HIS 0.003 0.001 HIS B 85 PHE 0.020 0.002 PHE A 122 TYR 0.016 0.001 TYR C 382 ARG 0.003 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 1068) hydrogen bonds : angle 4.08689 ( 3006) covalent geometry : bond 0.00381 (24360) covalent geometry : angle 0.52640 (32994) *********************** 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 304 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 258 time to evaluate : 2.574 Fit side-chains REVERT: A 12 MET cc_start: 0.7607 (mtp) cc_final: 0.7294 (mtm) REVERT: A 238 MET cc_start: 0.6649 (ptt) cc_final: 0.6347 (pmm) REVERT: A 248 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8091 (t) REVERT: A 249 VAL cc_start: 0.8888 (t) cc_final: 0.8467 (m) REVERT: A 281 TRP cc_start: 0.7590 (t60) cc_final: 0.7331 (t60) REVERT: A 330 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: B 46 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7739 (mtt90) REVERT: B 181 ASP cc_start: 0.8902 (t70) cc_final: 0.8486 (t0) REVERT: B 249 VAL cc_start: 0.8857 (t) cc_final: 0.8454 (m) REVERT: B 357 ASP cc_start: 0.7892 (m-30) cc_final: 0.7607 (m-30) REVERT: C 11 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8324 (mttp) REVERT: C 12 MET cc_start: 0.7682 (mtp) cc_final: 0.7407 (mtm) REVERT: C 249 VAL cc_start: 0.8780 (t) cc_final: 0.8350 (m) REVERT: C 281 TRP cc_start: 0.7615 (t60) cc_final: 0.7005 (t60) REVERT: C 330 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7620 (mm-40) REVERT: D 12 MET cc_start: 0.7587 (mtp) cc_final: 0.7272 (mtm) REVERT: D 233 MET cc_start: 0.8132 (mmm) cc_final: 0.7561 (mmp) REVERT: D 238 MET cc_start: 0.6625 (ptt) cc_final: 0.6338 (pmm) REVERT: D 248 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8082 (t) REVERT: D 249 VAL cc_start: 0.8905 (t) cc_final: 0.8474 (m) REVERT: D 281 TRP cc_start: 0.7592 (t60) cc_final: 0.7326 (t60) REVERT: D 330 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: D 466 ARG cc_start: 0.8411 (ttm110) cc_final: 0.8034 (tpp-160) REVERT: E 46 ARG cc_start: 0.8031 (mtt90) cc_final: 0.7735 (mtt90) REVERT: E 181 ASP cc_start: 0.8911 (t70) cc_final: 0.8402 (t0) REVERT: E 249 VAL cc_start: 0.8858 (t) cc_final: 0.8458 (m) REVERT: F 11 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8316 (mttp) REVERT: F 12 MET cc_start: 0.7662 (mtp) cc_final: 0.7384 (mtm) REVERT: F 249 VAL cc_start: 0.8779 (t) cc_final: 0.8348 (m) REVERT: F 330 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7619 (mm-40) outliers start: 46 outliers final: 28 residues processed: 279 average time/residue: 0.3447 time to fit residues: 152.7054 Evaluate side-chains 269 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 330 GLN Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 431 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 268 optimal weight: 10.0000 chunk 283 optimal weight: 0.0060 chunk 173 optimal weight: 3.9990 chunk 179 optimal weight: 40.0000 chunk 140 optimal weight: 8.9990 chunk 241 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 102 optimal weight: 0.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN A 437 GLN B 40 GLN B 437 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN C 437 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN E 40 GLN E 437 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 GLN F 437 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.080120 restraints weight = 45892.904| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.62 r_work: 0.2926 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24360 Z= 0.126 Angle : 0.482 4.565 32994 Z= 0.252 Chirality : 0.043 0.147 3588 Planarity : 0.004 0.039 4224 Dihedral : 9.177 69.935 4002 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.80 % Allowed : 10.78 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2964 helix: 0.92 (0.14), residues: 1398 sheet: -0.79 (0.27), residues: 438 loop : -1.44 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 72 HIS 0.003 0.001 HIS A 57 PHE 0.016 0.002 PHE F 500 TYR 0.011 0.001 TYR D 382 ARG 0.003 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 1068) hydrogen bonds : angle 3.90221 ( 3006) covalent geometry : bond 0.00298 (24360) covalent geometry : angle 0.48211 (32994) *********************** 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 294 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 249 time to evaluate : 2.576 Fit side-chains REVERT: A 248 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.8033 (t) REVERT: A 249 VAL cc_start: 0.8930 (t) cc_final: 0.8512 (m) REVERT: A 281 TRP cc_start: 0.7644 (t60) cc_final: 0.7274 (t60) REVERT: A 330 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7613 (mm110) REVERT: A 389 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9196 (mp) REVERT: B 181 ASP cc_start: 0.8845 (t70) cc_final: 0.8300 (t0) REVERT: B 249 VAL cc_start: 0.8864 (t) cc_final: 0.8474 (m) REVERT: B 366 MET cc_start: 0.8553 (ttm) cc_final: 0.8222 (ttm) REVERT: C 11 LYS cc_start: 0.8555 (mmtt) cc_final: 0.8328 (mttp) REVERT: C 12 MET cc_start: 0.7667 (mtp) cc_final: 0.7381 (mtm) REVERT: C 249 VAL cc_start: 0.8796 (t) cc_final: 0.8406 (m) REVERT: D 248 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8033 (t) REVERT: D 249 VAL cc_start: 0.8919 (t) cc_final: 0.8500 (m) REVERT: D 281 TRP cc_start: 0.7643 (t60) cc_final: 0.7276 (t60) REVERT: D 330 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7619 (mm110) REVERT: D 389 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9202 (mp) REVERT: D 466 ARG cc_start: 0.8420 (ttm110) cc_final: 0.8040 (tpp-160) REVERT: E 181 ASP cc_start: 0.8868 (t70) cc_final: 0.8360 (t0) REVERT: E 249 VAL cc_start: 0.8872 (t) cc_final: 0.8492 (m) REVERT: E 308 LYS cc_start: 0.8347 (ptpp) cc_final: 0.7937 (pttm) REVERT: E 355 GLU cc_start: 0.8087 (mp0) cc_final: 0.7858 (pm20) REVERT: F 11 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8327 (mttp) REVERT: F 12 MET cc_start: 0.7659 (mtp) cc_final: 0.7329 (mtm) REVERT: F 249 VAL cc_start: 0.8805 (t) cc_final: 0.8415 (m) outliers start: 45 outliers final: 24 residues processed: 269 average time/residue: 0.3285 time to fit residues: 141.4497 Evaluate side-chains 265 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 330 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 330 GLN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 330 GLN Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 431 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 15 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 255 optimal weight: 6.9990 chunk 203 optimal weight: 10.0000 chunk 277 optimal weight: 30.0000 chunk 6 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN B 40 GLN B 437 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN E 437 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.111190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.079203 restraints weight = 46442.374| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.64 r_work: 0.2909 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24360 Z= 0.148 Angle : 0.501 6.068 32994 Z= 0.261 Chirality : 0.044 0.148 3588 Planarity : 0.004 0.040 4224 Dihedral : 9.163 70.322 4002 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.40 % Allowed : 11.86 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2964 helix: 1.00 (0.14), residues: 1398 sheet: -0.83 (0.27), residues: 450 loop : -1.45 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 72 HIS 0.003 0.001 HIS A 57 PHE 0.018 0.002 PHE D 122 TYR 0.012 0.001 TYR D 382 ARG 0.003 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 1068) hydrogen bonds : angle 3.94232 ( 3006) covalent geometry : bond 0.00352 (24360) covalent geometry : angle 0.50085 (32994) *********************** 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 284 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 249 time to evaluate : 2.803 Fit side-chains REVERT: A 12 MET cc_start: 0.7612 (mtp) cc_final: 0.7381 (mtm) REVERT: A 248 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.8041 (t) REVERT: A 249 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8494 (m) REVERT: A 281 TRP cc_start: 0.7642 (t60) cc_final: 0.7235 (t60) REVERT: A 389 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9159 (mp) REVERT: B 181 ASP cc_start: 0.8852 (t70) cc_final: 0.8317 (t0) REVERT: B 249 VAL cc_start: 0.8893 (t) cc_final: 0.8504 (m) REVERT: B 389 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9153 (mp) REVERT: C 11 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8343 (mttp) REVERT: C 12 MET cc_start: 0.7640 (mtp) cc_final: 0.7296 (mtm) REVERT: C 46 ARG cc_start: 0.8113 (mtt90) cc_final: 0.7814 (mtt90) REVERT: C 249 VAL cc_start: 0.8815 (t) cc_final: 0.8442 (m) REVERT: C 330 GLN cc_start: 0.8100 (tp40) cc_final: 0.7765 (mm110) REVERT: D 12 MET cc_start: 0.7596 (mtp) cc_final: 0.7369 (mtm) REVERT: D 248 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8040 (t) REVERT: D 249 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8475 (m) REVERT: D 281 TRP cc_start: 0.7643 (t60) cc_final: 0.7173 (t60) REVERT: D 366 MET cc_start: 0.8439 (ttm) cc_final: 0.8116 (ttm) REVERT: D 389 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9158 (mp) REVERT: D 466 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8022 (tpp-160) REVERT: E 181 ASP cc_start: 0.8886 (t70) cc_final: 0.8382 (t0) REVERT: E 249 VAL cc_start: 0.8893 (t) cc_final: 0.8499 (m) REVERT: E 281 TRP cc_start: 0.7719 (t60) cc_final: 0.7437 (t60) REVERT: E 308 LYS cc_start: 0.8340 (ptpp) cc_final: 0.7922 (pttm) REVERT: E 355 GLU cc_start: 0.8055 (mp0) cc_final: 0.7847 (pm20) REVERT: E 389 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9151 (mp) REVERT: F 11 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8333 (mttp) REVERT: F 12 MET cc_start: 0.7630 (mtp) cc_final: 0.7300 (mtm) REVERT: F 249 VAL cc_start: 0.8811 (t) cc_final: 0.8432 (m) REVERT: F 330 GLN cc_start: 0.8118 (tp40) cc_final: 0.7781 (mm110) outliers start: 35 outliers final: 23 residues processed: 267 average time/residue: 0.3935 time to fit residues: 173.6317 Evaluate side-chains 270 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 212 optimal weight: 20.0000 chunk 65 optimal weight: 0.0980 chunk 51 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 chunk 263 optimal weight: 0.0770 overall best weight: 2.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN A 437 GLN B 40 GLN B 437 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN D 250 GLN E 40 GLN E 437 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.112159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.080283 restraints weight = 46065.123| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.64 r_work: 0.2930 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24360 Z= 0.117 Angle : 0.479 8.289 32994 Z= 0.249 Chirality : 0.043 0.145 3588 Planarity : 0.004 0.039 4224 Dihedral : 8.894 70.901 3998 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.32 % Allowed : 12.06 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.16), residues: 2964 helix: 1.18 (0.14), residues: 1404 sheet: -0.57 (0.27), residues: 438 loop : -1.48 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 72 HIS 0.003 0.001 HIS A 57 PHE 0.015 0.001 PHE D 122 TYR 0.010 0.001 TYR D 382 ARG 0.002 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03620 ( 1068) hydrogen bonds : angle 3.82721 ( 3006) covalent geometry : bond 0.00276 (24360) covalent geometry : angle 0.47874 (32994) *********************** 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 282 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 2.801 Fit side-chains REVERT: A 12 MET cc_start: 0.7592 (mtp) cc_final: 0.7368 (mtm) REVERT: A 248 VAL cc_start: 0.8253 (OUTLIER) cc_final: 0.8006 (t) REVERT: A 249 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8512 (m) REVERT: A 281 TRP cc_start: 0.7622 (t60) cc_final: 0.7186 (t60) REVERT: A 330 GLN cc_start: 0.7880 (mm110) cc_final: 0.7635 (mm-40) REVERT: A 466 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7931 (tpp-160) REVERT: B 78 TYR cc_start: 0.8937 (m-80) cc_final: 0.8591 (m-80) REVERT: B 181 ASP cc_start: 0.8833 (t70) cc_final: 0.8285 (t0) REVERT: B 249 VAL cc_start: 0.8882 (t) cc_final: 0.8497 (m) REVERT: B 308 LYS cc_start: 0.8454 (ptpp) cc_final: 0.7984 (pttm) REVERT: B 389 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9185 (mp) REVERT: C 11 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8334 (mttp) REVERT: C 12 MET cc_start: 0.7671 (mtp) cc_final: 0.7340 (mtm) REVERT: C 248 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7909 (t) REVERT: C 249 VAL cc_start: 0.8794 (t) cc_final: 0.8426 (m) REVERT: C 330 GLN cc_start: 0.8092 (tp40) cc_final: 0.7787 (mm110) REVERT: D 12 MET cc_start: 0.7582 (mtp) cc_final: 0.7361 (mtm) REVERT: D 248 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.7997 (t) REVERT: D 249 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8471 (m) REVERT: D 281 TRP cc_start: 0.7623 (t60) cc_final: 0.7194 (t60) REVERT: D 330 GLN cc_start: 0.7890 (mm110) cc_final: 0.7639 (mm-40) REVERT: D 366 MET cc_start: 0.8378 (ttm) cc_final: 0.8019 (ttm) REVERT: D 466 ARG cc_start: 0.8457 (ttm110) cc_final: 0.8046 (tpp-160) REVERT: E 78 TYR cc_start: 0.8947 (m-80) cc_final: 0.8604 (m-80) REVERT: E 181 ASP cc_start: 0.8849 (t70) cc_final: 0.8342 (t0) REVERT: E 248 VAL cc_start: 0.8149 (m) cc_final: 0.7934 (t) REVERT: E 281 TRP cc_start: 0.7749 (t60) cc_final: 0.7475 (t60) REVERT: E 308 LYS cc_start: 0.8366 (ptpp) cc_final: 0.7913 (pttm) REVERT: E 355 GLU cc_start: 0.8097 (mp0) cc_final: 0.7829 (pm20) REVERT: E 389 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9183 (mp) REVERT: F 11 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8338 (mttp) REVERT: F 12 MET cc_start: 0.7656 (mtp) cc_final: 0.7326 (mtm) REVERT: F 248 VAL cc_start: 0.8169 (m) cc_final: 0.7906 (t) REVERT: F 249 VAL cc_start: 0.8791 (t) cc_final: 0.8419 (m) REVERT: F 330 GLN cc_start: 0.8104 (tp40) cc_final: 0.7795 (mm110) outliers start: 33 outliers final: 17 residues processed: 266 average time/residue: 0.3576 time to fit residues: 152.6028 Evaluate side-chains 265 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 48 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 9 optimal weight: 0.0020 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 overall best weight: 2.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 40 GLN B 437 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN E 40 GLN E 437 GLN ** F 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.080074 restraints weight = 45862.549| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.64 r_work: 0.2926 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24360 Z= 0.121 Angle : 0.481 9.478 32994 Z= 0.249 Chirality : 0.043 0.146 3588 Planarity : 0.004 0.043 4224 Dihedral : 8.719 70.236 3994 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.24 % Allowed : 12.10 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.16), residues: 2964 helix: 1.30 (0.14), residues: 1404 sheet: -0.50 (0.28), residues: 438 loop : -1.47 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 72 HIS 0.003 0.001 HIS A 57 PHE 0.015 0.001 PHE D 122 TYR 0.010 0.001 TYR D 382 ARG 0.003 0.000 ARG D 19 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 1068) hydrogen bonds : angle 3.82258 ( 3006) covalent geometry : bond 0.00286 (24360) covalent geometry : angle 0.48099 (32994) *********************** 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 271 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 2.698 Fit side-chains REVERT: A 12 MET cc_start: 0.7577 (mtp) cc_final: 0.7312 (mtm) REVERT: A 248 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.8005 (t) REVERT: A 249 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8490 (m) REVERT: A 281 TRP cc_start: 0.7653 (t60) cc_final: 0.7224 (t60) REVERT: A 330 GLN cc_start: 0.7884 (mm110) cc_final: 0.7644 (mm-40) REVERT: A 389 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.8596 (mp) REVERT: A 466 ARG cc_start: 0.8237 (ttm170) cc_final: 0.7923 (tpp-160) REVERT: B 11 LYS cc_start: 0.8029 (mttp) cc_final: 0.7825 (mttp) REVERT: B 46 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7740 (mtt90) REVERT: B 78 TYR cc_start: 0.8937 (m-80) cc_final: 0.8587 (m-80) REVERT: B 181 ASP cc_start: 0.8837 (t70) cc_final: 0.8287 (t0) REVERT: B 248 VAL cc_start: 0.8127 (m) cc_final: 0.7915 (t) REVERT: B 308 LYS cc_start: 0.8451 (ptpp) cc_final: 0.7983 (pttm) REVERT: B 389 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9177 (mp) REVERT: C 11 LYS cc_start: 0.8593 (mmtt) cc_final: 0.8290 (mttp) REVERT: C 12 MET cc_start: 0.7678 (mtp) cc_final: 0.7352 (mtm) REVERT: C 78 TYR cc_start: 0.8933 (m-80) cc_final: 0.8568 (m-80) REVERT: C 248 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7920 (t) REVERT: C 249 VAL cc_start: 0.8816 (t) cc_final: 0.8466 (m) REVERT: C 330 GLN cc_start: 0.8069 (tp40) cc_final: 0.7714 (mm110) REVERT: D 12 MET cc_start: 0.7578 (mtp) cc_final: 0.7315 (mtm) REVERT: D 248 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7994 (t) REVERT: D 249 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8480 (m) REVERT: D 281 TRP cc_start: 0.7650 (t60) cc_final: 0.7154 (t60) REVERT: D 330 GLN cc_start: 0.7891 (mm110) cc_final: 0.7645 (mm-40) REVERT: D 389 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.8590 (mp) REVERT: D 466 ARG cc_start: 0.8442 (ttm110) cc_final: 0.8031 (tpp-160) REVERT: E 11 LYS cc_start: 0.8026 (mttp) cc_final: 0.7820 (mttp) REVERT: E 46 ARG cc_start: 0.8029 (mtt90) cc_final: 0.7748 (mtt90) REVERT: E 78 TYR cc_start: 0.8952 (m-80) cc_final: 0.8603 (m-80) REVERT: E 181 ASP cc_start: 0.8861 (t70) cc_final: 0.8351 (t0) REVERT: E 248 VAL cc_start: 0.8110 (m) cc_final: 0.7892 (t) REVERT: E 281 TRP cc_start: 0.7713 (t60) cc_final: 0.7450 (t60) REVERT: E 308 LYS cc_start: 0.8384 (ptpp) cc_final: 0.7932 (pttm) REVERT: E 355 GLU cc_start: 0.8068 (mp0) cc_final: 0.7808 (pm20) REVERT: E 389 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9176 (mp) REVERT: F 11 LYS cc_start: 0.8601 (mmtt) cc_final: 0.8293 (mttp) REVERT: F 12 MET cc_start: 0.7661 (mtp) cc_final: 0.7339 (mtm) REVERT: F 78 TYR cc_start: 0.8939 (m-80) cc_final: 0.8570 (m-80) REVERT: F 248 VAL cc_start: 0.8190 (m) cc_final: 0.7921 (t) REVERT: F 249 VAL cc_start: 0.8818 (t) cc_final: 0.8466 (m) REVERT: F 330 GLN cc_start: 0.8061 (tp40) cc_final: 0.7700 (mm110) outliers start: 31 outliers final: 17 residues processed: 253 average time/residue: 0.3484 time to fit residues: 140.8474 Evaluate side-chains 264 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 238 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 17 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 102 optimal weight: 0.3980 chunk 247 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 40 GLN B 437 GLN C 205 GLN C 437 GLN E 40 GLN E 437 GLN F 205 GLN F 437 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.112983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.081268 restraints weight = 46809.897| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.69 r_work: 0.2942 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24360 Z= 0.102 Angle : 0.469 9.654 32994 Z= 0.242 Chirality : 0.042 0.146 3588 Planarity : 0.004 0.041 4224 Dihedral : 8.335 71.027 3990 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.92 % Allowed : 12.46 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.16), residues: 2964 helix: 1.54 (0.14), residues: 1404 sheet: -0.44 (0.27), residues: 438 loop : -1.40 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 72 HIS 0.003 0.001 HIS A 57 PHE 0.013 0.001 PHE D 122 TYR 0.008 0.001 TYR D 382 ARG 0.003 0.000 ARG A 19 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 1068) hydrogen bonds : angle 3.73163 ( 3006) covalent geometry : bond 0.00241 (24360) covalent geometry : angle 0.46922 (32994) ********************** 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 270 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 247 time to evaluate : 2.660 Fit side-chains REVERT: A 12 MET cc_start: 0.7482 (mtp) cc_final: 0.7213 (mtm) REVERT: A 175 GLU cc_start: 0.8557 (mp0) cc_final: 0.8286 (mp0) REVERT: A 248 VAL cc_start: 0.8200 (m) cc_final: 0.7969 (t) REVERT: A 249 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8480 (m) REVERT: A 281 TRP cc_start: 0.7650 (t60) cc_final: 0.7267 (t60) REVERT: A 330 GLN cc_start: 0.7877 (mm110) cc_final: 0.7646 (mm-40) REVERT: A 389 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.8552 (mp) REVERT: A 466 ARG cc_start: 0.8228 (ttm170) cc_final: 0.7908 (tpp-160) REVERT: B 46 ARG cc_start: 0.8021 (mtt90) cc_final: 0.7712 (mtt90) REVERT: B 78 TYR cc_start: 0.8914 (m-80) cc_final: 0.8570 (m-80) REVERT: B 181 ASP cc_start: 0.8775 (t70) cc_final: 0.8233 (t0) REVERT: B 248 VAL cc_start: 0.8103 (m) cc_final: 0.7871 (t) REVERT: B 308 LYS cc_start: 0.8441 (ptpp) cc_final: 0.7980 (pttm) REVERT: B 330 GLN cc_start: 0.8001 (mm110) cc_final: 0.7766 (mm-40) REVERT: B 466 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7814 (tpp-160) REVERT: C 11 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8317 (mttp) REVERT: C 12 MET cc_start: 0.7676 (mtp) cc_final: 0.7356 (mtm) REVERT: C 78 TYR cc_start: 0.8877 (m-80) cc_final: 0.8546 (m-80) REVERT: C 248 VAL cc_start: 0.8177 (m) cc_final: 0.7923 (t) REVERT: C 249 VAL cc_start: 0.8804 (t) cc_final: 0.8456 (m) REVERT: C 308 LYS cc_start: 0.8371 (ptpp) cc_final: 0.8131 (pttm) REVERT: C 330 GLN cc_start: 0.8057 (tp40) cc_final: 0.7715 (mm110) REVERT: C 407 TYR cc_start: 0.8477 (m-80) cc_final: 0.8154 (m-10) REVERT: D 12 MET cc_start: 0.7490 (mtp) cc_final: 0.7220 (mtm) REVERT: D 36 GLU cc_start: 0.6176 (pt0) cc_final: 0.5949 (pt0) REVERT: D 175 GLU cc_start: 0.8544 (mp0) cc_final: 0.8263 (mp0) REVERT: D 248 VAL cc_start: 0.8212 (m) cc_final: 0.7969 (t) REVERT: D 249 VAL cc_start: 0.8902 (OUTLIER) cc_final: 0.8465 (m) REVERT: D 281 TRP cc_start: 0.7643 (t60) cc_final: 0.7195 (t60) REVERT: D 330 GLN cc_start: 0.7899 (mm110) cc_final: 0.7662 (mm-40) REVERT: D 466 ARG cc_start: 0.8435 (ttm110) cc_final: 0.8031 (tpp-160) REVERT: E 46 ARG cc_start: 0.8034 (mtt90) cc_final: 0.7736 (mtt90) REVERT: E 78 TYR cc_start: 0.8932 (m-80) cc_final: 0.8591 (m-80) REVERT: E 181 ASP cc_start: 0.8812 (t70) cc_final: 0.8304 (t0) REVERT: E 248 VAL cc_start: 0.8095 (m) cc_final: 0.7852 (t) REVERT: E 249 VAL cc_start: 0.8897 (t) cc_final: 0.8513 (m) REVERT: E 308 LYS cc_start: 0.8383 (ptpp) cc_final: 0.7929 (pttm) REVERT: E 355 GLU cc_start: 0.8108 (mp0) cc_final: 0.7836 (pm20) REVERT: E 466 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7818 (tpp-160) REVERT: F 11 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8322 (mttp) REVERT: F 12 MET cc_start: 0.7666 (mtp) cc_final: 0.7348 (mtm) REVERT: F 78 TYR cc_start: 0.8888 (m-80) cc_final: 0.8551 (m-80) REVERT: F 248 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7918 (t) REVERT: F 249 VAL cc_start: 0.8805 (t) cc_final: 0.8451 (m) REVERT: F 308 LYS cc_start: 0.8352 (ptpp) cc_final: 0.8121 (pttm) REVERT: F 330 GLN cc_start: 0.8069 (tp40) cc_final: 0.7720 (mm110) REVERT: F 407 TYR cc_start: 0.8487 (m-80) cc_final: 0.8160 (m-10) outliers start: 23 outliers final: 14 residues processed: 256 average time/residue: 0.3664 time to fit residues: 147.3861 Evaluate side-chains 257 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 162 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 242 optimal weight: 0.4980 chunk 277 optimal weight: 30.0000 chunk 125 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 98 optimal weight: 30.0000 chunk 89 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 chunk 269 optimal weight: 4.9990 chunk 245 optimal weight: 30.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 40 GLN B 437 GLN C 437 GLN E 40 GLN E 437 GLN F 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.110868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.078723 restraints weight = 46037.414| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.61 r_work: 0.2898 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24360 Z= 0.166 Angle : 0.524 8.903 32994 Z= 0.272 Chirality : 0.044 0.150 3588 Planarity : 0.004 0.049 4224 Dihedral : 8.609 70.165 3990 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.00 % Allowed : 12.46 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2964 helix: 1.40 (0.14), residues: 1410 sheet: -0.54 (0.27), residues: 444 loop : -1.46 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 72 HIS 0.003 0.001 HIS B 85 PHE 0.020 0.002 PHE D 122 TYR 0.013 0.001 TYR D 382 ARG 0.002 0.000 ARG C 396 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 1068) hydrogen bonds : angle 3.94884 ( 3006) covalent geometry : bond 0.00397 (24360) covalent geometry : angle 0.52413 (32994) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11304.96 seconds wall clock time: 197 minutes 41.24 seconds (11861.24 seconds total)