Starting phenix.real_space_refine on Sun Sep 29 19:49:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/09_2024/3jd2_6635.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/09_2024/3jd2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/09_2024/3jd2_6635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/09_2024/3jd2_6635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/09_2024/3jd2_6635.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jd2_6635/09_2024/3jd2_6635.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 114 5.16 5 C 14976 2.51 5 N 4158 2.21 5 O 4542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23814 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "B" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "C" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "D" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "E" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "F" Number of atoms: 3881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3881 Classifications: {'peptide': 496} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 474} Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'NAI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" C1B NAI A 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI A 602 " occ=0.35 residue: pdb=" C1B NAI B 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI B 602 " occ=0.35 residue: pdb=" C1B NAI C 601 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI C 601 " occ=0.35 residue: pdb=" C1B NAI D 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI D 602 " occ=0.35 residue: pdb=" C1B NAI E 602 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI E 602 " occ=0.35 residue: pdb=" C1B NAI F 601 " occ=0.35 ... (42 atoms not shown) pdb=" PN NAI F 601 " occ=0.35 Time building chain proxies: 13.18, per 1000 atoms: 0.55 Number of scatterers: 23814 At special positions: 0 Unit cell: (114.92, 118.3, 165.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 114 16.00 P 24 15.00 O 4542 8.00 N 4158 7.00 C 14976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.99 Conformation dependent library (CDL) restraints added in 2.9 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5400 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 15 sheets defined 54.8% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.48 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: 7.63 Time building geometry restraints manager: 6.94 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: 0.00 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.130 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 52.200 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.350 ------------------------------------------------------------------------------- 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= 0.721 Angle : 1.045 15.681 32994 Z= 0.484 Chirality : 0.061 0.401 3588 Planarity : 0.005 0.065 4224 Dihedral : 10.879 84.282 9582 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.81 % Allowed : 5.60 % Favored : 93.59 % Rotamer: Outliers : 0.72 % Allowed : 0.48 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.54 (0.11), residues: 2964 helix: -3.94 (0.08), residues: 1374 sheet: -3.14 (0.21), residues: 450 loop : -3.25 (0.15), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP F 72 HIS 0.007 0.002 HIS B 391 PHE 0.025 0.003 PHE B 399 TYR 0.025 0.003 TYR A 382 ARG 0.007 0.001 ARG D 396 *********************** 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 fitting. rotamer outliers: 18 poor density : 487 time to evaluate : 2.575 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: 0.4577 time to fit residues: 330.3217 Evaluate side-chains 249 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 237 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 370 ASP Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 30.0000 chunk 222 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 150 optimal weight: 30.0000 chunk 119 optimal weight: 5.9990 chunk 230 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 266 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 56 ASN A 57 HIS A 84 GLN A 330 GLN A 437 GLN B 40 GLN B 56 ASN B 57 HIS B 84 GLN B 209 HIS B 437 GLN C 56 ASN C 57 HIS C 84 GLN C 205 GLN C 209 HIS D 40 GLN D 56 ASN D 57 HIS D 84 GLN D 330 GLN D 437 GLN E 40 GLN E 56 ASN E 57 HIS E 84 GLN E 209 HIS E 437 GLN F 56 ASN F 57 HIS F 84 GLN F 205 GLN F 209 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24360 Z= 0.298 Angle : 0.617 5.197 32994 Z= 0.326 Chirality : 0.047 0.176 3588 Planarity : 0.006 0.072 4224 Dihedral : 12.054 80.223 4014 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.36 % Allowed : 5.41 % Favored : 93.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.14), residues: 2964 helix: -1.65 (0.12), residues: 1362 sheet: -2.36 (0.23), residues: 444 loop : -2.40 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP D 281 HIS 0.005 0.001 HIS B 85 PHE 0.025 0.003 PHE A 16 TYR 0.020 0.001 TYR D 382 ARG 0.013 0.001 ARG D 478 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 297 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 VAL cc_start: 0.8982 (t) cc_final: 0.8776 (m) REVERT: A 269 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8335 (ptmt) REVERT: A 308 LYS cc_start: 0.7573 (pptt) cc_final: 0.7299 (pttp) REVERT: A 500 PHE cc_start: 0.6830 (m-10) cc_final: 0.6336 (t80) REVERT: B 249 VAL cc_start: 0.8979 (t) cc_final: 0.8748 (m) REVERT: B 500 PHE cc_start: 0.6677 (m-10) cc_final: 0.6201 (t80) REVERT: C 249 VAL cc_start: 0.8975 (t) cc_final: 0.8770 (m) REVERT: C 500 PHE cc_start: 0.6799 (m-10) cc_final: 0.6294 (t80) REVERT: D 249 VAL cc_start: 0.8982 (t) cc_final: 0.8775 (m) REVERT: D 269 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8338 (ptmt) REVERT: D 308 LYS cc_start: 0.7569 (pptt) cc_final: 0.7181 (pttp) REVERT: D 466 ARG cc_start: 0.8432 (ttm110) cc_final: 0.8059 (tpp-160) REVERT: E 249 VAL cc_start: 0.8978 (t) cc_final: 0.8745 (m) REVERT: F 249 VAL cc_start: 0.8977 (t) cc_final: 0.8769 (m) outliers start: 34 outliers final: 28 residues processed: 316 average time/residue: 0.3348 time to fit residues: 168.6945 Evaluate side-chains 262 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 234 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain C residue 469 MET Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain F residue 469 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 chunk 222 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 267 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 chunk 238 optimal weight: 8.9990 chunk 265 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN B 56 ASN B 437 GLN C 56 ASN D 56 ASN E 56 ASN E 437 GLN F 56 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 24360 Z= 0.360 Angle : 0.612 5.297 32994 Z= 0.322 Chirality : 0.047 0.169 3588 Planarity : 0.005 0.044 4224 Dihedral : 11.012 77.312 4002 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.92 % Allowed : 8.25 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.15), residues: 2964 helix: -0.80 (0.13), residues: 1398 sheet: -2.05 (0.24), residues: 450 loop : -1.97 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP F 281 HIS 0.004 0.001 HIS E 57 PHE 0.022 0.003 PHE D 122 TYR 0.020 0.002 TYR C 382 ARG 0.005 0.001 ARG A 478 *********************** 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 306 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 258 time to evaluate : 2.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8627 (m-80) cc_final: 0.8365 (m-80) REVERT: A 269 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8336 (ptmt) REVERT: A 500 PHE cc_start: 0.6730 (m-10) cc_final: 0.6325 (t80) REVERT: B 500 PHE cc_start: 0.6759 (m-10) cc_final: 0.6344 (t80) REVERT: C 437 GLN cc_start: 0.8577 (tp40) cc_final: 0.8306 (tp40) REVERT: D 78 TYR cc_start: 0.8627 (m-80) cc_final: 0.8365 (m-80) REVERT: D 249 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8856 (m) REVERT: D 269 LYS cc_start: 0.8592 (ttpt) cc_final: 0.8339 (ptmt) REVERT: D 466 ARG cc_start: 0.8480 (ttm110) cc_final: 0.8075 (tpp-160) REVERT: E 181 ASP cc_start: 0.8571 (t70) cc_final: 0.8354 (t70) REVERT: F 437 GLN cc_start: 0.8576 (tp40) cc_final: 0.8308 (tp40) outliers start: 48 outliers final: 27 residues processed: 284 average time/residue: 0.3333 time to fit residues: 150.4069 Evaluate side-chains 247 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 219 time to evaluate : 2.991 ------------------------------------------------------------------------------- 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 469 MET Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 355 GLU 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 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 469 MET Chi-restraints excluded: chain D residue 500 PHE 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 E residue 500 PHE 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 264 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 284 optimal weight: 0.9990 chunk 140 optimal weight: 0.0050 chunk 254 optimal weight: 0.9980 chunk 76 optimal weight: 40.0000 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 40 GLN B 437 GLN ** C 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 GLN D 209 HIS ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN E 437 GLN F 225 ASN ** F 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3662 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= 0.143 Angle : 0.485 6.002 32994 Z= 0.257 Chirality : 0.042 0.150 3588 Planarity : 0.004 0.040 4224 Dihedral : 10.404 71.965 4002 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.24 % Allowed : 9.90 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.15), residues: 2964 helix: 0.08 (0.14), residues: 1398 sheet: -1.39 (0.26), residues: 438 loop : -1.73 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 281 HIS 0.003 0.001 HIS F 85 PHE 0.015 0.001 PHE F 500 TYR 0.009 0.001 TYR D 382 ARG 0.004 0.000 ARG D 478 *********************** 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 313 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 282 time to evaluate : 2.894 Fit side-chains revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8480 (m-80) cc_final: 0.8271 (m-80) REVERT: A 233 MET cc_start: 0.8230 (mmm) cc_final: 0.7715 (mmp) REVERT: A 269 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8297 (ptmt) REVERT: A 308 LYS cc_start: 0.7570 (pptt) cc_final: 0.7055 (pttp) REVERT: B 11 LYS cc_start: 0.7069 (pttt) cc_final: 0.6854 (mtmm) REVERT: B 181 ASP cc_start: 0.8384 (t70) cc_final: 0.7988 (t0) REVERT: B 500 PHE cc_start: 0.6698 (m-10) cc_final: 0.6304 (t80) REVERT: C 78 TYR cc_start: 0.8505 (m-80) cc_final: 0.8042 (m-80) REVERT: C 138 ASP cc_start: 0.8488 (m-30) cc_final: 0.8284 (m-30) REVERT: D 78 TYR cc_start: 0.8473 (m-80) cc_final: 0.8264 (m-80) REVERT: D 269 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8308 (ptmt) REVERT: D 308 LYS cc_start: 0.7548 (pptt) cc_final: 0.7031 (pttp) REVERT: D 466 ARG cc_start: 0.8455 (ttm110) cc_final: 0.8118 (tpp-160) REVERT: E 11 LYS cc_start: 0.7072 (pttt) cc_final: 0.6857 (mtmm) REVERT: E 181 ASP cc_start: 0.8463 (t70) cc_final: 0.8125 (t0) REVERT: F 78 TYR cc_start: 0.8505 (m-80) cc_final: 0.8042 (m-80) REVERT: F 138 ASP cc_start: 0.8475 (m-30) cc_final: 0.8270 (m-30) outliers start: 31 outliers final: 14 residues processed: 291 average time/residue: 0.3585 time to fit residues: 165.4223 Evaluate side-chains 248 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 234 time to evaluate : 2.613 ------------------------------------------------------------------------------- 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 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain D residue 272 THR 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 E residue 469 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 242 optimal weight: 6.9990 chunk 196 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 145 optimal weight: 8.9990 chunk 255 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN A 364 ASN A 437 GLN B 437 GLN C 40 GLN C 364 ASN C 437 GLN D 330 GLN D 364 ASN D 437 GLN E 437 GLN F 40 GLN F 364 ASN F 437 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24360 Z= 0.273 Angle : 0.536 5.231 32994 Z= 0.281 Chirality : 0.045 0.152 3588 Planarity : 0.004 0.042 4224 Dihedral : 9.983 73.895 4002 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.00 % Allowed : 9.78 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.16), residues: 2964 helix: 0.30 (0.14), residues: 1398 sheet: -1.37 (0.25), residues: 450 loop : -1.66 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 281 HIS 0.003 0.001 HIS B 85 PHE 0.020 0.002 PHE D 122 TYR 0.014 0.001 TYR D 382 ARG 0.003 0.000 ARG E 147 *********************** 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 fitting. rotamer outliers: 50 poor density : 256 time to evaluate : 2.750 Fit side-chains REVERT: A 78 TYR cc_start: 0.8563 (m-80) cc_final: 0.8261 (m-80) REVERT: A 269 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8297 (ptmt) REVERT: A 330 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: B 291 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8649 (tt) REVERT: D 78 TYR cc_start: 0.8559 (m-80) cc_final: 0.8260 (m-80) REVERT: D 269 LYS cc_start: 0.8532 (ttpt) cc_final: 0.8299 (ptmt) REVERT: D 330 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: D 466 ARG cc_start: 0.8488 (ttm110) cc_final: 0.8130 (tpp-160) REVERT: E 181 ASP cc_start: 0.8604 (t70) cc_final: 0.8258 (t0) REVERT: E 291 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8645 (tt) outliers start: 50 outliers final: 29 residues processed: 279 average time/residue: 0.3739 time to fit residues: 162.0012 Evaluate side-chains 263 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 230 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE 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 330 GLN Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 373 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 B residue 469 MET 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 D residue 158 ILE Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 330 GLN Chi-restraints excluded: chain D residue 333 LYS Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain 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 E residue 469 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 9.9990 chunk 255 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 284 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 B 437 GLN C 364 ASN C 437 GLN D 40 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN F 364 ASN F 437 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24360 Z= 0.224 Angle : 0.517 6.570 32994 Z= 0.271 Chirality : 0.044 0.153 3588 Planarity : 0.004 0.041 4224 Dihedral : 9.595 74.422 4002 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.72 % Allowed : 10.50 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.16), residues: 2964 helix: 0.60 (0.14), residues: 1398 sheet: -1.20 (0.26), residues: 450 loop : -1.63 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 281 HIS 0.003 0.001 HIS D 57 PHE 0.021 0.002 PHE A 500 TYR 0.012 0.001 TYR D 382 ARG 0.004 0.000 ARG C 46 *********************** 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 fitting. rotamer outliers: 43 poor density : 247 time to evaluate : 2.757 Fit side-chains REVERT: A 78 TYR cc_start: 0.8549 (m-80) cc_final: 0.8239 (m-80) REVERT: A 269 LYS cc_start: 0.8540 (ttpt) cc_final: 0.8323 (ptmt) REVERT: A 389 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9143 (mp) REVERT: B 291 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8643 (tt) REVERT: B 389 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9148 (mp) REVERT: D 78 TYR cc_start: 0.8542 (m-80) cc_final: 0.8292 (m-80) REVERT: D 269 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8312 (ptmt) REVERT: D 389 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9143 (mp) REVERT: D 466 ARG cc_start: 0.8476 (ttm110) cc_final: 0.8121 (tpp-160) REVERT: E 181 ASP cc_start: 0.8592 (t70) cc_final: 0.8137 (t0) REVERT: E 291 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8640 (tt) REVERT: E 389 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9150 (mp) outliers start: 43 outliers final: 27 residues processed: 272 average time/residue: 0.3427 time to fit residues: 149.2001 Evaluate side-chains 267 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 234 time to evaluate : 2.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 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 B residue 389 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 198 VAL 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 D residue 198 VAL 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 373 LEU Chi-restraints excluded: chain D residue 389 LEU 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 E residue 389 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 9.9990 chunk 32 optimal weight: 30.0000 chunk 162 optimal weight: 8.9990 chunk 207 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 239 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 177 optimal weight: 8.9990 chunk 172 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 437 GLN C 225 ASN D 40 GLN D 364 ASN D 437 GLN E 437 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4039 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= 0.188 Angle : 0.491 6.629 32994 Z= 0.258 Chirality : 0.043 0.157 3588 Planarity : 0.004 0.043 4224 Dihedral : 9.289 73.618 4002 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.84 % Allowed : 10.78 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2964 helix: 0.93 (0.14), residues: 1398 sheet: -0.99 (0.26), residues: 450 loop : -1.56 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 281 HIS 0.003 0.001 HIS A 57 PHE 0.022 0.002 PHE B 500 TYR 0.010 0.001 TYR D 382 ARG 0.004 0.000 ARG D 46 *********************** 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 285 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 239 time to evaluate : 2.775 Fit side-chains REVERT: A 78 TYR cc_start: 0.8517 (m-80) cc_final: 0.8260 (m-80) REVERT: A 269 LYS cc_start: 0.8481 (ttpt) cc_final: 0.8280 (ptmt) REVERT: A 389 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9177 (mp) REVERT: B 11 LYS cc_start: 0.7080 (pttt) cc_final: 0.6577 (mtmm) REVERT: B 389 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9147 (mp) REVERT: C 78 TYR cc_start: 0.8516 (m-80) cc_final: 0.8102 (m-80) REVERT: D 78 TYR cc_start: 0.8508 (m-80) cc_final: 0.8256 (m-80) REVERT: D 269 LYS cc_start: 0.8492 (ttpt) cc_final: 0.8277 (ptmt) REVERT: D 389 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9167 (mp) REVERT: D 466 ARG cc_start: 0.8489 (ttm110) cc_final: 0.8136 (tpp-160) REVERT: E 181 ASP cc_start: 0.8545 (t70) cc_final: 0.8107 (t0) REVERT: E 389 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9147 (mp) REVERT: F 78 TYR cc_start: 0.8514 (m-80) cc_final: 0.8100 (m-80) outliers start: 46 outliers final: 27 residues processed: 267 average time/residue: 0.3360 time to fit residues: 143.9916 Evaluate side-chains 264 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 233 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain C residue 198 VAL 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 D residue 198 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 E residue 198 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 198 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 140 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 222 optimal weight: 50.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN B 437 GLN C 330 GLN D 437 GLN E 40 GLN E 437 GLN F 330 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24360 Z= 0.159 Angle : 0.483 6.404 32994 Z= 0.253 Chirality : 0.043 0.150 3588 Planarity : 0.004 0.042 4224 Dihedral : 9.057 74.083 4002 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.28 % Allowed : 11.82 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.16), residues: 2964 helix: 1.19 (0.14), residues: 1398 sheet: -0.59 (0.27), residues: 432 loop : -1.52 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 281 HIS 0.003 0.001 HIS D 57 PHE 0.015 0.001 PHE F 500 TYR 0.009 0.001 TYR D 382 ARG 0.004 0.000 ARG A 46 *********************** 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 284 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 252 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8488 (m-80) cc_final: 0.8176 (m-80) REVERT: A 269 LYS cc_start: 0.8454 (ttpt) cc_final: 0.8250 (ptmt) REVERT: B 11 LYS cc_start: 0.7016 (pttt) cc_final: 0.6503 (mtmm) REVERT: B 78 TYR cc_start: 0.8537 (m-80) cc_final: 0.8213 (m-80) REVERT: C 11 LYS cc_start: 0.6890 (pttt) cc_final: 0.6611 (mttp) REVERT: C 78 TYR cc_start: 0.8476 (m-80) cc_final: 0.8144 (m-80) REVERT: D 78 TYR cc_start: 0.8486 (m-80) cc_final: 0.8178 (m-80) REVERT: D 269 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8281 (ptmt) REVERT: D 466 ARG cc_start: 0.8486 (ttm110) cc_final: 0.8140 (tpp-160) REVERT: E 78 TYR cc_start: 0.8533 (m-80) cc_final: 0.8211 (m-80) REVERT: E 181 ASP cc_start: 0.8530 (t70) cc_final: 0.8088 (t0) REVERT: F 11 LYS cc_start: 0.6885 (pttt) cc_final: 0.6606 (mttp) REVERT: F 78 TYR cc_start: 0.8472 (m-80) cc_final: 0.8141 (m-80) outliers start: 32 outliers final: 22 residues processed: 275 average time/residue: 0.3527 time to fit residues: 153.4965 Evaluate side-chains 263 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 241 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL 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 B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain C residue 198 VAL 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 D residue 198 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 373 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 6.9990 chunk 271 optimal weight: 30.0000 chunk 247 optimal weight: 3.9990 chunk 264 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 238 optimal weight: 6.9990 chunk 249 optimal weight: 3.9990 chunk 263 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN B 40 GLN B 437 GLN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN D 437 GLN E 40 GLN E 437 GLN ** F 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4331 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= 0.140 Angle : 0.468 6.336 32994 Z= 0.244 Chirality : 0.042 0.150 3588 Planarity : 0.004 0.042 4224 Dihedral : 8.703 74.565 4002 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.16 % Allowed : 12.02 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.16), residues: 2964 helix: 1.48 (0.14), residues: 1398 sheet: -0.45 (0.27), residues: 432 loop : -1.42 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 281 HIS 0.003 0.001 HIS A 57 PHE 0.014 0.001 PHE F 500 TYR 0.007 0.001 TYR C 382 ARG 0.005 0.000 ARG D 46 *********************** 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 283 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 254 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8421 (m-80) cc_final: 0.8136 (m-80) REVERT: B 11 LYS cc_start: 0.6984 (pttt) cc_final: 0.6417 (mtmm) REVERT: B 78 TYR cc_start: 0.8507 (m-80) cc_final: 0.8212 (m-80) REVERT: C 11 LYS cc_start: 0.6925 (pttt) cc_final: 0.6479 (mtmm) REVERT: C 78 TYR cc_start: 0.8456 (m-80) cc_final: 0.8154 (m-80) REVERT: C 407 TYR cc_start: 0.8406 (m-80) cc_final: 0.8205 (m-10) REVERT: D 78 TYR cc_start: 0.8414 (m-80) cc_final: 0.8133 (m-80) REVERT: D 466 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8145 (tpp-160) REVERT: E 78 TYR cc_start: 0.8511 (m-80) cc_final: 0.8215 (m-80) REVERT: E 181 ASP cc_start: 0.8514 (t70) cc_final: 0.8086 (t0) REVERT: F 11 LYS cc_start: 0.6921 (pttt) cc_final: 0.6472 (mtmm) REVERT: F 78 TYR cc_start: 0.8453 (m-80) cc_final: 0.8152 (m-80) outliers start: 29 outliers final: 24 residues processed: 272 average time/residue: 0.3586 time to fit residues: 156.3731 Evaluate side-chains 267 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 243 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 30.0000 chunk 279 optimal weight: 20.0000 chunk 170 optimal weight: 0.9990 chunk 132 optimal weight: 30.0000 chunk 194 optimal weight: 0.7980 chunk 292 optimal weight: 0.8980 chunk 269 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN B 40 GLN B 437 GLN C 250 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN E 40 GLN E 437 GLN F 250 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24360 Z= 0.140 Angle : 0.477 8.450 32994 Z= 0.248 Chirality : 0.042 0.149 3588 Planarity : 0.004 0.041 4224 Dihedral : 8.391 74.666 3994 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.88 % Allowed : 12.34 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2964 helix: 1.69 (0.14), residues: 1404 sheet: -0.47 (0.27), residues: 438 loop : -1.35 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 281 HIS 0.002 0.001 HIS D 57 PHE 0.014 0.001 PHE F 500 TYR 0.007 0.001 TYR D 382 ARG 0.004 0.000 ARG D 46 ********************** 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 275 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 253 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 TYR cc_start: 0.8414 (m-80) cc_final: 0.8142 (m-80) REVERT: A 238 MET cc_start: 0.6189 (pmm) cc_final: 0.5254 (pmm) REVERT: B 11 LYS cc_start: 0.6944 (pttt) cc_final: 0.6325 (mtmm) REVERT: B 78 TYR cc_start: 0.8506 (m-80) cc_final: 0.8217 (m-80) REVERT: B 466 ARG cc_start: 0.8238 (ttm170) cc_final: 0.7946 (tpp-160) REVERT: C 11 LYS cc_start: 0.6913 (pttt) cc_final: 0.6560 (mttp) REVERT: C 78 TYR cc_start: 0.8442 (m-80) cc_final: 0.8158 (m-80) REVERT: C 407 TYR cc_start: 0.8412 (m-80) cc_final: 0.8191 (m-10) REVERT: D 78 TYR cc_start: 0.8402 (m-80) cc_final: 0.8130 (m-80) REVERT: D 466 ARG cc_start: 0.8493 (ttm110) cc_final: 0.8157 (tpp-160) REVERT: E 11 LYS cc_start: 0.7014 (pttt) cc_final: 0.6477 (mtmm) REVERT: E 78 TYR cc_start: 0.8510 (m-80) cc_final: 0.8219 (m-80) REVERT: E 181 ASP cc_start: 0.8515 (t70) cc_final: 0.8091 (t0) REVERT: E 466 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7961 (tpp-160) REVERT: F 11 LYS cc_start: 0.6889 (pttt) cc_final: 0.6537 (mttp) REVERT: F 78 TYR cc_start: 0.8446 (m-80) cc_final: 0.8167 (m-80) outliers start: 22 outliers final: 20 residues processed: 266 average time/residue: 0.3437 time to fit residues: 145.6304 Evaluate side-chains 256 residues out of total 2496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 236 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 215 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 233 optimal weight: 0.4980 chunk 97 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 chunk 29 optimal weight: 30.0000 chunk 43 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 GLN B 40 GLN B 437 GLN ** D 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN E 40 GLN E 225 ASN E 437 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.115185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.083427 restraints weight = 46111.329| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.60 r_work: 0.2982 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 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 = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24360 Z= 0.175 Angle : 0.501 9.728 32994 Z= 0.259 Chirality : 0.043 0.147 3588 Planarity : 0.004 0.043 4224 Dihedral : 8.319 75.594 3994 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.04 % Allowed : 12.42 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 2964 helix: 1.75 (0.14), residues: 1404 sheet: -0.54 (0.29), residues: 378 loop : -1.32 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP F 281 HIS 0.003 0.001 HIS A 57 PHE 0.015 0.001 PHE D 122 TYR 0.009 0.001 TYR D 382 ARG 0.004 0.000 ARG D 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4662.80 seconds wall clock time: 84 minutes 39.91 seconds (5079.91 seconds total)