Starting phenix.real_space_refine on Fri Sep 19 05:02:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jd2_6635/09_2025/3jd2_6635.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd2_6635/09_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_6635/09_2025/3jd2_6635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd2_6635/09_2025/3jd2_6635.map" model { file = "/net/cci-nas-00/data/ceres_data/3jd2_6635/09_2025/3jd2_6635.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd2_6635/09_2025/3jd2_6635.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 5.61, per 1000 atoms: 0.24 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: 2.54 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 715.3 nanoseconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 1.08 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: 4.76 Time building geometry restraints manager: 3.19 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.110 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.007 0.001 ARG D 396 TYR 0.025 0.003 TYR A 382 PHE 0.025 0.003 PHE B 399 TRP 0.023 0.003 TRP F 72 HIS 0.007 0.002 HIS B 391 Details of bonding type rmsd covalent geometry : bond 0.01104 (24360) covalent geometry : angle 1.04498 (32994) hydrogen bonds : bond 0.28989 ( 1068) hydrogen bonds : angle 9.47585 ( 3006) *********************** 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 : 0.970 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: 0.2279 time to fit residues: 164.6235 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 : 0.968 ------------------------------------------------------------------------------- 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 197 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0670 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 overall best weight: 3.3724 ------------------------------------------------------------------------------- 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 437 GLN B 40 GLN B 56 ASN B 57 HIS B 84 GLN B 205 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 205 GLN E 209 HIS E 437 GLN F 56 ASN F 57 HIS F 84 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 = 0.3677 r_free = 0.3677 target = 0.114272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083205 restraints weight = 46248.816| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.59 r_work: 0.2976 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24360 Z= 0.152 Angle : 0.584 5.393 32994 Z= 0.309 Chirality : 0.045 0.172 3588 Planarity : 0.006 0.072 4224 Dihedral : 12.232 80.730 4014 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.00 % Allowed : 5.65 % Favored : 93.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.14), residues: 2964 helix: -1.56 (0.12), residues: 1350 sheet: -2.27 (0.23), residues: 432 loop : -2.40 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 478 TYR 0.017 0.001 TYR F 382 PHE 0.025 0.002 PHE A 16 TRP 0.038 0.003 TRP D 281 HIS 0.005 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00357 (24360) covalent geometry : angle 0.58379 (32994) hydrogen bonds : bond 0.04940 ( 1068) hydrogen bonds : angle 4.84263 ( 3006) *********************** 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 334 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 309 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 VAL cc_start: 0.8959 (t) cc_final: 0.8554 (m) REVERT: A 269 LYS cc_start: 0.8227 (ttpt) cc_final: 0.7993 (ptmt) REVERT: A 330 GLN cc_start: 0.8089 (tp40) cc_final: 0.7867 (tp40) REVERT: B 249 VAL cc_start: 0.8947 (t) cc_final: 0.8512 (m) REVERT: C 11 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8243 (mttp) REVERT: C 249 VAL cc_start: 0.8937 (t) cc_final: 0.8555 (m) REVERT: C 281 TRP cc_start: 0.7590 (t60) cc_final: 0.7113 (t60) REVERT: D 181 ASP cc_start: 0.8696 (t70) cc_final: 0.8010 (t70) REVERT: D 249 VAL cc_start: 0.8967 (t) cc_final: 0.8563 (m) REVERT: D 269 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7996 (ptmt) REVERT: D 308 LYS cc_start: 0.7638 (pptt) cc_final: 0.7394 (pttp) REVERT: D 466 ARG cc_start: 0.8356 (ttm110) cc_final: 0.7979 (tpp-160) REVERT: E 249 VAL cc_start: 0.8957 (t) cc_final: 0.8526 (m) REVERT: F 11 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8240 (mttp) REVERT: F 249 VAL cc_start: 0.8941 (t) cc_final: 0.8560 (m) REVERT: F 281 TRP cc_start: 0.7573 (t60) cc_final: 0.7105 (t60) outliers start: 25 outliers final: 19 residues processed: 318 average time/residue: 0.1657 time to fit residues: 82.8788 Evaluate side-chains 254 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 THR 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 373 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 272 THR 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 373 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU 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 5 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 273 optimal weight: 10.0000 chunk 33 optimal weight: 0.0060 chunk 214 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 174 optimal weight: 40.0000 chunk 248 optimal weight: 20.0000 chunk 212 optimal weight: 8.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 437 GLN B 84 GLN B 437 GLN C 56 ASN D 84 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN E 84 GLN E 437 GLN F 56 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.111419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.079406 restraints weight = 46391.778| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.61 r_work: 0.2919 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24360 Z= 0.150 Angle : 0.531 4.945 32994 Z= 0.280 Chirality : 0.044 0.164 3588 Planarity : 0.005 0.041 4224 Dihedral : 10.799 80.205 4002 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.52 % Allowed : 7.45 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.15), residues: 2964 helix: -0.55 (0.13), residues: 1398 sheet: -1.81 (0.25), residues: 438 loop : -1.96 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 478 TYR 0.016 0.001 TYR A 382 PHE 0.019 0.002 PHE E 16 TRP 0.033 0.002 TRP A 281 HIS 0.004 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00355 (24360) covalent geometry : angle 0.53131 (32994) hydrogen bonds : bond 0.04569 ( 1068) hydrogen bonds : angle 4.42448 ( 3006) *********************** 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 297 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 259 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7640 (mtp) cc_final: 0.7396 (mtm) REVERT: A 249 VAL cc_start: 0.8989 (t) cc_final: 0.8629 (m) REVERT: A 269 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7948 (ptmt) REVERT: B 249 VAL cc_start: 0.8957 (t) cc_final: 0.8573 (m) REVERT: C 11 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8288 (mttp) REVERT: C 249 VAL cc_start: 0.8938 (t) cc_final: 0.8584 (m) REVERT: C 281 TRP cc_start: 0.7596 (t60) cc_final: 0.7064 (t60) REVERT: D 12 MET cc_start: 0.7628 (mtp) cc_final: 0.7385 (mtm) REVERT: D 249 VAL cc_start: 0.8990 (t) cc_final: 0.8625 (m) REVERT: D 269 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7941 (ptmt) REVERT: D 330 GLN cc_start: 0.7951 (tp40) cc_final: 0.7668 (tt0) REVERT: D 466 ARG cc_start: 0.8387 (ttm110) cc_final: 0.8000 (tpp-160) REVERT: E 249 VAL cc_start: 0.8958 (t) cc_final: 0.8577 (m) REVERT: F 11 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8285 (mttp) REVERT: F 249 VAL cc_start: 0.8932 (t) cc_final: 0.8576 (m) REVERT: F 281 TRP cc_start: 0.7576 (t60) cc_final: 0.7060 (t60) outliers start: 38 outliers final: 31 residues processed: 277 average time/residue: 0.1713 time to fit residues: 75.3613 Evaluate side-chains 261 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 230 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 THR 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 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 276 optimal weight: 0.9980 chunk 269 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 7 optimal weight: 0.0670 chunk 212 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 overall best weight: 3.0122 ------------------------------------------------------------------------------- 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 209 HIS B 40 GLN B 56 ASN B 437 GLN C 225 ASN D 40 GLN D 56 ASN D 209 HIS E 40 GLN E 56 ASN E 437 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.111996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079712 restraints weight = 46248.415| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.68 r_work: 0.2927 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- 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 = 0.80 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 = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3536 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= 0.125 Angle : 0.493 5.550 32994 Z= 0.258 Chirality : 0.043 0.148 3588 Planarity : 0.004 0.039 4224 Dihedral : 10.233 70.807 4002 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.48 % Allowed : 8.53 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.15), residues: 2964 helix: 0.10 (0.14), residues: 1398 sheet: -1.39 (0.26), residues: 438 loop : -1.77 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 478 TYR 0.013 0.001 TYR A 382 PHE 0.015 0.002 PHE D 122 TRP 0.025 0.001 TRP A 281 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00293 (24360) covalent geometry : angle 0.49290 (32994) hydrogen bonds : bond 0.03926 ( 1068) hydrogen bonds : angle 4.11614 ( 3006) *********************** 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 311 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 274 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7551 (mtp) cc_final: 0.7224 (mtm) REVERT: A 233 MET cc_start: 0.8108 (mmm) cc_final: 0.7356 (mmp) REVERT: A 238 MET cc_start: 0.6635 (ptt) cc_final: 0.6216 (pmm) REVERT: A 249 VAL cc_start: 0.8940 (t) cc_final: 0.8554 (m) REVERT: A 269 LYS cc_start: 0.8142 (ttpt) cc_final: 0.7931 (ptmt) REVERT: B 181 ASP cc_start: 0.8745 (t70) cc_final: 0.8445 (t0) REVERT: B 249 VAL cc_start: 0.8951 (t) cc_final: 0.8582 (m) REVERT: B 281 TRP cc_start: 0.7574 (t60) cc_final: 0.7133 (t60) REVERT: B 500 PHE cc_start: 0.5576 (t80) cc_final: 0.5370 (t80) REVERT: C 11 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8249 (mttp) REVERT: C 249 VAL cc_start: 0.8852 (t) cc_final: 0.8521 (m) REVERT: C 281 TRP cc_start: 0.7589 (t60) cc_final: 0.7046 (t60) REVERT: D 12 MET cc_start: 0.7559 (mtp) cc_final: 0.7222 (mtm) REVERT: D 233 MET cc_start: 0.8100 (mmm) cc_final: 0.7387 (mmp) REVERT: D 238 MET cc_start: 0.6622 (ptt) cc_final: 0.6209 (pmm) REVERT: D 249 VAL cc_start: 0.8941 (t) cc_final: 0.8562 (m) REVERT: D 269 LYS cc_start: 0.8147 (ttpt) cc_final: 0.7937 (ptmt) REVERT: D 308 LYS cc_start: 0.7623 (pptt) cc_final: 0.7190 (pttp) REVERT: D 466 ARG cc_start: 0.8391 (ttm110) cc_final: 0.8031 (tpp-160) REVERT: E 181 ASP cc_start: 0.8756 (t70) cc_final: 0.8471 (t0) REVERT: E 249 VAL cc_start: 0.8949 (t) cc_final: 0.8584 (m) REVERT: E 281 TRP cc_start: 0.7586 (t60) cc_final: 0.7130 (t60) REVERT: F 11 LYS cc_start: 0.8562 (mmtt) cc_final: 0.8236 (mttp) REVERT: F 249 VAL cc_start: 0.8851 (t) cc_final: 0.8517 (m) REVERT: F 281 TRP cc_start: 0.7593 (t60) cc_final: 0.7040 (t60) outliers start: 37 outliers final: 25 residues processed: 292 average time/residue: 0.1658 time to fit residues: 77.5074 Evaluate side-chains 265 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR 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 431 VAL 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 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 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 333 LYS Chi-restraints excluded: chain D residue 373 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 469 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 130 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 193 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 277 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 237 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 364 ASN B 437 GLN C 364 ASN C 437 GLN D 40 GLN D 364 ASN E 437 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 = 0.3647 r_free = 0.3647 target = 0.112402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.080179 restraints weight = 46017.265| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.67 r_work: 0.2936 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3762 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= 0.109 Angle : 0.473 6.095 32994 Z= 0.247 Chirality : 0.042 0.156 3588 Planarity : 0.004 0.039 4224 Dihedral : 9.747 70.839 4002 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.64 % Allowed : 9.17 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.16), residues: 2964 helix: 0.61 (0.14), residues: 1398 sheet: -1.02 (0.27), residues: 438 loop : -1.58 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 19 TYR 0.011 0.001 TYR F 382 PHE 0.013 0.001 PHE D 122 TRP 0.033 0.002 TRP A 281 HIS 0.003 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00254 (24360) covalent geometry : angle 0.47260 (32994) hydrogen bonds : bond 0.03607 ( 1068) hydrogen bonds : angle 3.95135 ( 3006) *********************** 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 306 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7550 (mtp) cc_final: 0.7206 (mtm) REVERT: A 238 MET cc_start: 0.6669 (ptt) cc_final: 0.6312 (pmm) REVERT: A 249 VAL cc_start: 0.8885 (t) cc_final: 0.8521 (m) REVERT: A 250 GLN cc_start: 0.7570 (tt0) cc_final: 0.7199 (tt0) REVERT: A 330 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7603 (tt0) REVERT: B 11 LYS cc_start: 0.8373 (mtpp) cc_final: 0.8093 (mttp) REVERT: B 181 ASP cc_start: 0.8814 (t70) cc_final: 0.8572 (t70) REVERT: B 249 VAL cc_start: 0.8931 (t) cc_final: 0.8575 (m) REVERT: B 291 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8708 (tt) REVERT: B 500 PHE cc_start: 0.5615 (t80) cc_final: 0.5409 (t80) REVERT: C 11 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8307 (mttp) REVERT: C 12 MET cc_start: 0.7632 (mtp) cc_final: 0.7333 (mtm) REVERT: C 249 VAL cc_start: 0.8839 (t) cc_final: 0.8484 (m) REVERT: C 281 TRP cc_start: 0.7603 (t60) cc_final: 0.7048 (t60) REVERT: D 12 MET cc_start: 0.7552 (mtp) cc_final: 0.7208 (mtm) REVERT: D 238 MET cc_start: 0.6677 (ptt) cc_final: 0.6328 (pmm) REVERT: D 249 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8227 (m) REVERT: D 466 ARG cc_start: 0.8429 (ttm110) cc_final: 0.8070 (tpp-160) REVERT: E 11 LYS cc_start: 0.8370 (mtpp) cc_final: 0.8088 (mttp) REVERT: E 181 ASP cc_start: 0.8845 (t70) cc_final: 0.8452 (t0) REVERT: E 249 VAL cc_start: 0.8936 (t) cc_final: 0.8578 (m) REVERT: E 291 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8705 (tt) REVERT: F 11 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8292 (mttp) REVERT: F 12 MET cc_start: 0.7621 (mtp) cc_final: 0.7326 (mtm) REVERT: F 249 VAL cc_start: 0.8841 (t) cc_final: 0.8472 (m) REVERT: F 281 TRP cc_start: 0.7611 (t60) cc_final: 0.7044 (t60) outliers start: 41 outliers final: 21 residues processed: 284 average time/residue: 0.1671 time to fit residues: 74.5984 Evaluate side-chains 269 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 244 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR 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 272 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 373 LEU 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 208 ILE 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 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 272 THR Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 373 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 28 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 280 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 224 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 364 ASN A 437 GLN B 40 GLN B 437 GLN C 40 GLN C 364 ASN C 437 GLN D 40 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN E 40 GLN E 437 GLN F 40 GLN F 437 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.108365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.076509 restraints weight = 46459.716| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.58 r_work: 0.2857 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 24360 Z= 0.263 Angle : 0.608 6.949 32994 Z= 0.318 Chirality : 0.047 0.153 3588 Planarity : 0.005 0.043 4224 Dihedral : 9.914 74.771 4002 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.88 % Allowed : 10.14 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.15), residues: 2964 helix: 0.33 (0.14), residues: 1404 sheet: -1.27 (0.26), residues: 450 loop : -1.62 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 396 TYR 0.016 0.002 TYR D 382 PHE 0.025 0.003 PHE E 157 TRP 0.023 0.002 TRP A 281 HIS 0.005 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00624 (24360) covalent geometry : angle 0.60760 (32994) hydrogen bonds : bond 0.05121 ( 1068) hydrogen bonds : angle 4.36820 ( 3006) *********************** 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 290 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 243 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.7557 (mtp) cc_final: 0.7282 (mtm) REVERT: A 249 VAL cc_start: 0.8924 (t) cc_final: 0.8478 (m) REVERT: A 389 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9034 (mp) REVERT: B 181 ASP cc_start: 0.8889 (t70) cc_final: 0.8626 (t0) REVERT: B 291 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8743 (tt) REVERT: B 357 ASP cc_start: 0.7966 (m-30) cc_final: 0.7691 (m-30) REVERT: B 500 PHE cc_start: 0.5817 (t80) cc_final: 0.5527 (t80) REVERT: C 11 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8317 (ttmm) REVERT: C 12 MET cc_start: 0.7624 (mtp) cc_final: 0.7307 (mtm) REVERT: C 249 VAL cc_start: 0.8812 (t) cc_final: 0.8385 (m) REVERT: C 389 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9172 (mp) REVERT: C 437 GLN cc_start: 0.8570 (tp-100) cc_final: 0.8311 (tp40) REVERT: D 12 MET cc_start: 0.7554 (mtp) cc_final: 0.7283 (mtm) REVERT: D 249 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8246 (m) REVERT: D 389 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9042 (mp) REVERT: D 466 ARG cc_start: 0.8481 (ttm110) cc_final: 0.8032 (tpp-160) REVERT: E 181 ASP cc_start: 0.8874 (t70) cc_final: 0.8624 (t0) REVERT: E 291 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8742 (tt) REVERT: E 357 ASP cc_start: 0.7959 (m-30) cc_final: 0.7676 (m-30) REVERT: F 11 LYS cc_start: 0.8607 (mmtt) cc_final: 0.8305 (ttmm) REVERT: F 12 MET cc_start: 0.7593 (mtp) cc_final: 0.7280 (mtm) REVERT: F 249 VAL cc_start: 0.8812 (t) cc_final: 0.8380 (m) REVERT: F 389 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9169 (mp) REVERT: F 437 GLN cc_start: 0.8567 (tp-100) cc_final: 0.8312 (tp40) outliers start: 47 outliers final: 26 residues processed: 266 average time/residue: 0.1630 time to fit residues: 68.6679 Evaluate side-chains 262 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 333 LYS Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 248 VAL 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 246 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 389 LEU 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 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 500 PHE Chi-restraints excluded: chain E residue 248 VAL 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 246 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 389 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 93 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 364 ASN B 40 GLN B 437 GLN C 364 ASN D 40 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN E 40 GLN E 437 GLN F 225 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.078759 restraints weight = 46111.168| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.61 r_work: 0.2904 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 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 = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24360 Z= 0.147 Angle : 0.508 7.462 32994 Z= 0.266 Chirality : 0.044 0.153 3588 Planarity : 0.004 0.040 4224 Dihedral : 9.686 75.750 4002 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.60 % Allowed : 10.86 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.16), residues: 2964 helix: 0.76 (0.14), residues: 1398 sheet: -1.00 (0.26), residues: 450 loop : -1.57 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 396 TYR 0.012 0.001 TYR D 382 PHE 0.017 0.002 PHE D 122 TRP 0.036 0.002 TRP A 281 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00348 (24360) covalent geometry : angle 0.50816 (32994) hydrogen bonds : bond 0.04054 ( 1068) hydrogen bonds : angle 4.05351 ( 3006) *********************** 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 278 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 238 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 248 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8118 (t) REVERT: A 249 VAL cc_start: 0.8910 (t) cc_final: 0.8495 (m) REVERT: A 389 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9175 (mp) REVERT: B 181 ASP cc_start: 0.8850 (t70) cc_final: 0.8416 (t0) REVERT: B 291 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8687 (tt) REVERT: B 389 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9162 (mp) REVERT: C 11 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8353 (mtpp) REVERT: C 12 MET cc_start: 0.7607 (mtp) cc_final: 0.7286 (mtm) REVERT: C 249 VAL cc_start: 0.8832 (t) cc_final: 0.8458 (m) REVERT: C 389 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9246 (mp) REVERT: D 249 VAL cc_start: 0.8806 (t) cc_final: 0.8374 (m) REVERT: D 389 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9185 (mp) REVERT: D 466 ARG cc_start: 0.8444 (ttm110) cc_final: 0.8031 (tpp-160) REVERT: E 11 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7893 (mttp) REVERT: E 181 ASP cc_start: 0.8858 (t70) cc_final: 0.8444 (t0) REVERT: E 291 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8690 (tt) REVERT: E 389 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9166 (mp) REVERT: F 11 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8338 (mtpp) REVERT: F 12 MET cc_start: 0.7580 (mtp) cc_final: 0.7261 (mtm) REVERT: F 249 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8460 (m) REVERT: F 389 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9247 (mp) outliers start: 40 outliers final: 24 residues processed: 260 average time/residue: 0.1487 time to fit residues: 62.0142 Evaluate side-chains 268 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 198 VAL 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 333 LYS Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU 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 B residue 389 LEU 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 389 LEU 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 333 LYS Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 389 LEU 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 E residue 389 LEU Chi-restraints excluded: chain F residue 246 THR 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 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 163 optimal weight: 0.0470 chunk 94 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 171 optimal weight: 20.0000 chunk 289 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 195 optimal weight: 0.3980 chunk 46 optimal weight: 8.9990 chunk 169 optimal weight: 7.9990 overall best weight: 1.6882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 364 ASN B 40 GLN B 225 ASN B 437 GLN C 437 GLN D 40 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN E 40 GLN E 225 ASN E 437 GLN F 437 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.112939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.081315 restraints weight = 45803.329| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.63 r_work: 0.2954 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 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 = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 24360 Z= 0.094 Angle : 0.469 8.957 32994 Z= 0.243 Chirality : 0.042 0.154 3588 Planarity : 0.004 0.038 4224 Dihedral : 9.177 73.276 4002 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.24 % Allowed : 11.54 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.16), residues: 2964 helix: 1.20 (0.14), residues: 1398 sheet: -0.62 (0.27), residues: 438 loop : -1.52 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 46 TYR 0.008 0.001 TYR D 382 PHE 0.012 0.001 PHE F 63 TRP 0.031 0.002 TRP A 281 HIS 0.003 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00216 (24360) covalent geometry : angle 0.46941 (32994) hydrogen bonds : bond 0.03271 ( 1068) hydrogen bonds : angle 3.80283 ( 3006) *********************** 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 285 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 254 time to evaluate : 0.708 Fit side-chains REVERT: A 12 MET cc_start: 0.7618 (mtp) cc_final: 0.7333 (mtm) REVERT: A 249 VAL cc_start: 0.8907 (t) cc_final: 0.8528 (m) REVERT: A 466 ARG cc_start: 0.8181 (ttm170) cc_final: 0.7893 (tpp-160) REVERT: B 78 TYR cc_start: 0.8923 (m-80) cc_final: 0.8618 (m-80) REVERT: B 181 ASP cc_start: 0.8819 (t70) cc_final: 0.8390 (t0) REVERT: B 249 VAL cc_start: 0.8905 (t) cc_final: 0.8542 (m) REVERT: B 308 LYS cc_start: 0.8345 (ptpp) cc_final: 0.7901 (pttm) REVERT: B 466 ARG cc_start: 0.8219 (ttm170) cc_final: 0.7902 (tpp-160) REVERT: C 11 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8351 (mtpp) REVERT: C 12 MET cc_start: 0.7596 (mtp) cc_final: 0.7271 (mtm) REVERT: C 78 TYR cc_start: 0.8902 (m-80) cc_final: 0.8353 (m-80) REVERT: C 249 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8230 (m) REVERT: C 407 TYR cc_start: 0.8467 (m-80) cc_final: 0.8128 (m-10) REVERT: C 437 GLN cc_start: 0.8540 (tp-100) cc_final: 0.8297 (tp40) REVERT: D 12 MET cc_start: 0.7599 (mtp) cc_final: 0.7315 (mtm) REVERT: D 248 VAL cc_start: 0.8281 (m) cc_final: 0.8036 (t) REVERT: D 249 VAL cc_start: 0.8807 (t) cc_final: 0.8415 (m) REVERT: D 466 ARG cc_start: 0.8445 (ttm110) cc_final: 0.8062 (tpp-160) REVERT: E 11 LYS cc_start: 0.8341 (mtpp) cc_final: 0.7901 (mttp) REVERT: E 78 TYR cc_start: 0.8928 (m-80) cc_final: 0.8624 (m-80) REVERT: E 181 ASP cc_start: 0.8837 (t70) cc_final: 0.8423 (t0) REVERT: E 249 VAL cc_start: 0.8900 (t) cc_final: 0.8537 (m) REVERT: E 308 LYS cc_start: 0.8328 (ptpp) cc_final: 0.7916 (pttm) REVERT: F 11 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8338 (mtpp) REVERT: F 12 MET cc_start: 0.7575 (mtp) cc_final: 0.7250 (mtm) REVERT: F 78 TYR cc_start: 0.8925 (m-80) cc_final: 0.8334 (m-80) REVERT: F 249 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8224 (m) REVERT: F 407 TYR cc_start: 0.8484 (m-80) cc_final: 0.8140 (m-10) REVERT: F 437 GLN cc_start: 0.8528 (tp-100) cc_final: 0.8288 (tp40) outliers start: 31 outliers final: 18 residues processed: 274 average time/residue: 0.1536 time to fit residues: 67.9885 Evaluate side-chains 262 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU 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 D residue 78 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 10 optimal weight: 5.9990 chunk 236 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 0.0060 chunk 107 optimal weight: 3.9990 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 364 ASN B 40 GLN B 437 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 364 ASN E 40 GLN E 437 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.078093 restraints weight = 46336.571| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.63 r_work: 0.2900 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 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 = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24360 Z= 0.159 Angle : 0.516 8.767 32994 Z= 0.269 Chirality : 0.044 0.147 3588 Planarity : 0.004 0.044 4224 Dihedral : 9.293 76.394 4002 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.16 % Allowed : 11.90 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.16), residues: 2964 helix: 1.16 (0.14), residues: 1398 sheet: -0.71 (0.27), residues: 450 loop : -1.51 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 396 TYR 0.013 0.001 TYR D 382 PHE 0.019 0.002 PHE D 122 TRP 0.030 0.002 TRP D 281 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00379 (24360) covalent geometry : angle 0.51641 (32994) hydrogen bonds : bond 0.04069 ( 1068) hydrogen bonds : angle 3.96942 ( 3006) *********************** 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 262 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 233 time to evaluate : 0.809 Fit side-chains REVERT: A 11 LYS cc_start: 0.8364 (mtmm) cc_final: 0.8087 (mttp) REVERT: A 12 MET cc_start: 0.7591 (mtp) cc_final: 0.7318 (mtm) REVERT: A 248 VAL cc_start: 0.8281 (m) cc_final: 0.8060 (t) REVERT: A 249 VAL cc_start: 0.8907 (t) cc_final: 0.8500 (m) REVERT: B 181 ASP cc_start: 0.8867 (t70) cc_final: 0.8442 (t0) REVERT: B 330 GLN cc_start: 0.7859 (mm110) cc_final: 0.7594 (mm-40) REVERT: C 11 LYS cc_start: 0.8626 (mmtt) cc_final: 0.8387 (mtpp) REVERT: C 12 MET cc_start: 0.7592 (mtp) cc_final: 0.7275 (mtm) REVERT: C 78 TYR cc_start: 0.8932 (m-80) cc_final: 0.8332 (m-80) REVERT: C 249 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8299 (m) REVERT: C 437 GLN cc_start: 0.8532 (tp-100) cc_final: 0.8281 (tp40) REVERT: D 12 MET cc_start: 0.7591 (mtp) cc_final: 0.7322 (mtm) REVERT: D 249 VAL cc_start: 0.8831 (t) cc_final: 0.8415 (m) REVERT: D 466 ARG cc_start: 0.8471 (ttm110) cc_final: 0.8053 (tpp-160) REVERT: E 11 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7867 (mttp) REVERT: E 181 ASP cc_start: 0.8887 (t70) cc_final: 0.8473 (t0) REVERT: E 308 LYS cc_start: 0.8369 (ptpp) cc_final: 0.7966 (pttm) REVERT: E 330 GLN cc_start: 0.7870 (mm110) cc_final: 0.7604 (mm-40) REVERT: F 11 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8376 (mtpp) REVERT: F 12 MET cc_start: 0.7577 (mtp) cc_final: 0.7259 (mtm) REVERT: F 78 TYR cc_start: 0.8939 (m-80) cc_final: 0.8342 (m-80) REVERT: F 249 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8288 (m) REVERT: F 437 GLN cc_start: 0.8511 (tp-100) cc_final: 0.8261 (tp40) outliers start: 29 outliers final: 21 residues processed: 250 average time/residue: 0.1677 time to fit residues: 67.6694 Evaluate side-chains 253 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 373 LEU 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 249 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 78 TYR 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 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 249 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 249 optimal weight: 0.0270 chunk 33 optimal weight: 0.0980 chunk 120 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 chunk 5 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 190 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN B 40 GLN B 437 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 364 ASN E 40 GLN E 437 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.112464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.080340 restraints weight = 46337.903| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.65 r_work: 0.2943 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 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 = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24360 Z= 0.102 Angle : 0.479 13.052 32994 Z= 0.247 Chirality : 0.042 0.149 3588 Planarity : 0.004 0.043 4224 Dihedral : 8.829 74.655 4002 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.72 % Allowed : 12.18 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.16), residues: 2964 helix: 1.48 (0.14), residues: 1398 sheet: -0.58 (0.27), residues: 450 loop : -1.44 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 46 TYR 0.008 0.001 TYR D 382 PHE 0.019 0.001 PHE F 63 TRP 0.032 0.002 TRP D 281 HIS 0.003 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00239 (24360) covalent geometry : angle 0.47856 (32994) hydrogen bonds : bond 0.03310 ( 1068) hydrogen bonds : angle 3.78638 ( 3006) ********************** 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 261 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 0.861 Fit side-chains REVERT: A 12 MET cc_start: 0.7604 (mtp) cc_final: 0.7391 (mtm) REVERT: A 238 MET cc_start: 0.6470 (ptt) cc_final: 0.6173 (pmm) REVERT: A 248 VAL cc_start: 0.8217 (m) cc_final: 0.7981 (t) REVERT: A 249 VAL cc_start: 0.8771 (t) cc_final: 0.8361 (m) REVERT: A 466 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7922 (tpp-160) REVERT: B 78 TYR cc_start: 0.8933 (m-80) cc_final: 0.8625 (m-80) REVERT: B 181 ASP cc_start: 0.8842 (t70) cc_final: 0.8422 (t0) REVERT: B 308 LYS cc_start: 0.8364 (ptpp) cc_final: 0.7936 (pttm) REVERT: B 330 GLN cc_start: 0.7857 (mm110) cc_final: 0.7621 (mm-40) REVERT: B 466 ARG cc_start: 0.8215 (ttm170) cc_final: 0.7898 (tpp-160) REVERT: C 11 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8381 (mtpp) REVERT: C 12 MET cc_start: 0.7590 (mtp) cc_final: 0.7263 (mtm) REVERT: C 78 TYR cc_start: 0.8849 (m-80) cc_final: 0.8323 (m-80) REVERT: C 249 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8327 (m) REVERT: C 407 TYR cc_start: 0.8485 (m-80) cc_final: 0.8185 (m-10) REVERT: D 12 MET cc_start: 0.7594 (mtp) cc_final: 0.7379 (mtm) REVERT: D 238 MET cc_start: 0.6498 (ptt) cc_final: 0.6121 (pmm) REVERT: D 248 VAL cc_start: 0.8246 (m) cc_final: 0.8027 (t) REVERT: D 249 VAL cc_start: 0.8838 (t) cc_final: 0.8459 (m) REVERT: D 466 ARG cc_start: 0.8447 (ttm110) cc_final: 0.8038 (tpp-160) REVERT: E 11 LYS cc_start: 0.8304 (mtpp) cc_final: 0.7876 (mttp) REVERT: E 78 TYR cc_start: 0.8940 (m-80) cc_final: 0.8634 (m-80) REVERT: E 181 ASP cc_start: 0.8865 (t70) cc_final: 0.8453 (t0) REVERT: E 308 LYS cc_start: 0.8368 (ptpp) cc_final: 0.7931 (pttm) REVERT: E 330 GLN cc_start: 0.7877 (mm110) cc_final: 0.7640 (mm-40) REVERT: E 466 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7892 (tpp-160) REVERT: F 11 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8373 (mtpp) REVERT: F 12 MET cc_start: 0.7574 (mtp) cc_final: 0.7248 (mtm) REVERT: F 78 TYR cc_start: 0.8866 (m-80) cc_final: 0.8338 (m-80) REVERT: F 249 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8319 (m) REVERT: F 407 TYR cc_start: 0.8494 (m-80) cc_final: 0.8190 (m-10) outliers start: 18 outliers final: 13 residues processed: 254 average time/residue: 0.1753 time to fit residues: 70.3159 Evaluate side-chains 251 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 TYR 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 C residue 249 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain D residue 78 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 364 ASN Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 249 VAL 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 181 optimal weight: 1.9990 chunk 261 optimal weight: 0.0770 chunk 275 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 222 optimal weight: 30.0000 chunk 242 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 364 ASN B 40 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN D 40 GLN D 364 ASN E 40 GLN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.110913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079216 restraints weight = 45967.366| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.61 r_work: 0.2917 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24360 Z= 0.138 Angle : 0.503 12.350 32994 Z= 0.260 Chirality : 0.044 0.164 3588 Planarity : 0.004 0.045 4224 Dihedral : 8.787 75.513 3994 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.84 % Allowed : 12.10 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.16), residues: 2964 helix: 1.47 (0.14), residues: 1404 sheet: -0.60 (0.27), residues: 450 loop : -1.41 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 46 TYR 0.011 0.001 TYR D 382 PHE 0.021 0.002 PHE C 63 TRP 0.030 0.002 TRP D 281 HIS 0.003 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00330 (24360) covalent geometry : angle 0.50305 (32994) hydrogen bonds : bond 0.03745 ( 1068) hydrogen bonds : angle 3.86520 ( 3006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5225.70 seconds wall clock time: 90 minutes 43.60 seconds (5443.60 seconds total)