Starting phenix.real_space_refine on Fri May 30 05:52:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7o_29818/05_2025/8g7o_29818.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7o_29818/05_2025/8g7o_29818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g7o_29818/05_2025/8g7o_29818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7o_29818/05_2025/8g7o_29818.map" model { file = "/net/cci-nas-00/data/ceres_data/8g7o_29818/05_2025/8g7o_29818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7o_29818/05_2025/8g7o_29818.cif" } resolution = 3.4 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= 0.000 sd= 0.092 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 21 5.49 5 S 105 5.16 5 C 20734 2.51 5 N 5621 2.21 5 O 6566 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 33047 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "B" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "C" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "D" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "E" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "F" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "G" Number of atoms: 3933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3933 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 511} Chain: "H" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "I" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "J" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "K" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "L" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "M" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "N" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 757 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.37, per 1000 atoms: 0.56 Number of scatterers: 33047 At special positions: 0 Unit cell: (162.225, 165.006, 156.663, 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 105 16.00 P 21 15.00 O 6566 8.00 N 5621 7.00 C 20734 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: 8.23 Conformation dependent library (CDL) restraints added in 4.4 seconds 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7938 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 48 sheets defined 51.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'A' and resid 7 through 27 removed outlier: 3.884A pdb=" N VAL A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 56 Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.850A pdb=" N GLY A 68 " --> pdb=" O TYR A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 104 Processing helix chain 'A' and resid 110 through 133 Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.562A pdb=" N ILE A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 167 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.525A pdb=" N PHE A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 242 removed outlier: 3.739A pdb=" N ILE A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 253 through 267 Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.518A pdb=" N LEU A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 355 removed outlier: 3.548A pdb=" N ASP A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 384 through 408 removed outlier: 3.533A pdb=" N ARG A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 421 through 427 removed outlier: 3.812A pdb=" N LEU A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER A 427 " --> pdb=" O PRO A 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 421 through 427' Processing helix chain 'A' and resid 432 through 446 Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 460 through 471 Processing helix chain 'A' and resid 487 through 491 Processing helix chain 'A' and resid 496 through 514 removed outlier: 3.797A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 26 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 50 through 57 removed outlier: 3.518A pdb=" N SER B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.932A pdb=" N GLY B 68 " --> pdb=" O TYR B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 104 Processing helix chain 'B' and resid 110 through 133 Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.655A pdb=" N ILE B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 167 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 227 through 242 removed outlier: 3.714A pdb=" N ILE B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 280 through 295 removed outlier: 3.693A pdb=" N LYS B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 311 removed outlier: 3.566A pdb=" N ASP B 310 " --> pdb=" O ASN B 307 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 311 " --> pdb=" O LEU B 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 307 through 311' Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 337 through 353 removed outlier: 3.584A pdb=" N ASP B 353 " --> pdb=" O ILE B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 373 Processing helix chain 'B' and resid 384 through 408 removed outlier: 3.603A pdb=" N ARG B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.564A pdb=" N LEU B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 428 removed outlier: 3.598A pdb=" N SER B 427 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 428 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 446 Processing helix chain 'B' and resid 447 through 457 removed outlier: 3.593A pdb=" N ALA B 457 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 470 Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 496 through 514 removed outlier: 3.582A pdb=" N LEU B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 27 removed outlier: 4.002A pdb=" N VAL C 27 " --> pdb=" O ASP C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 57 Processing helix chain 'C' and resid 62 through 84 removed outlier: 3.626A pdb=" N ASN C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY C 68 " --> pdb=" O TYR C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 104 removed outlier: 3.651A pdb=" N ALA C 90 " --> pdb=" O GLY C 86 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 133 Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.665A pdb=" N ILE C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 167 removed outlier: 3.618A pdb=" N GLY C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 227 through 242 removed outlier: 3.597A pdb=" N ILE C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 253 through 268 Processing helix chain 'C' and resid 279 through 295 Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 312 through 316 removed outlier: 3.659A pdb=" N LEU C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 353 Processing helix chain 'C' and resid 357 through 373 Processing helix chain 'C' and resid 384 through 408 removed outlier: 3.620A pdb=" N ARG C 394 " --> pdb=" O GLU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 421 through 426 removed outlier: 3.764A pdb=" N LEU C 425 " --> pdb=" O CYS C 421 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP C 426 " --> pdb=" O ILE C 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 421 through 426' Processing helix chain 'C' and resid 432 through 446 Processing helix chain 'C' and resid 447 through 457 removed outlier: 3.553A pdb=" N ALA C 457 " --> pdb=" O ILE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 471 Processing helix chain 'C' and resid 496 through 514 removed outlier: 3.502A pdb=" N LEU C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 27 removed outlier: 3.563A pdb=" N ARG D 11 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 56 Processing helix chain 'D' and resid 64 through 84 removed outlier: 3.849A pdb=" N GLY D 68 " --> pdb=" O TYR D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 105 removed outlier: 3.713A pdb=" N ALA D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 133 Processing helix chain 'D' and resid 138 through 150 removed outlier: 3.501A pdb=" N ILE D 142 " --> pdb=" O THR D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 168 removed outlier: 3.739A pdb=" N GLY D 157 " --> pdb=" O ASP D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 227 through 230 Processing helix chain 'D' and resid 231 through 242 Processing helix chain 'D' and resid 253 through 268 Processing helix chain 'D' and resid 280 through 295 removed outlier: 3.728A pdb=" N LYS D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 311 Processing helix chain 'D' and resid 312 through 316 removed outlier: 3.587A pdb=" N LEU D 316 " --> pdb=" O PRO D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 355 removed outlier: 3.696A pdb=" N ASP D 353 " --> pdb=" O ILE D 349 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR D 355 " --> pdb=" O GLN D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 373 Processing helix chain 'D' and resid 384 through 408 removed outlier: 3.544A pdb=" N ARG D 394 " --> pdb=" O GLU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 Processing helix chain 'D' and resid 421 through 428 removed outlier: 3.659A pdb=" N LEU D 428 " --> pdb=" O LEU D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 446 Processing helix chain 'D' and resid 447 through 457 Processing helix chain 'D' and resid 460 through 471 Processing helix chain 'D' and resid 487 through 491 Processing helix chain 'D' and resid 496 through 514 removed outlier: 3.527A pdb=" N LEU D 512 " --> pdb=" O GLY D 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 27 removed outlier: 3.997A pdb=" N VAL E 27 " --> pdb=" O ASP E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 57 Processing helix chain 'E' and resid 62 through 83 removed outlier: 3.677A pdb=" N ILE E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 104 removed outlier: 3.615A pdb=" N ALA E 90 " --> pdb=" O GLY E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 133 Processing helix chain 'E' and resid 138 through 150 removed outlier: 3.520A pdb=" N ILE E 142 " --> pdb=" O THR E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 167 removed outlier: 3.581A pdb=" N GLY E 157 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 227 through 230 Processing helix chain 'E' and resid 231 through 242 Processing helix chain 'E' and resid 253 through 268 Processing helix chain 'E' and resid 280 through 295 removed outlier: 3.510A pdb=" N LYS E 284 " --> pdb=" O GLY E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 311 removed outlier: 3.741A pdb=" N ASP E 310 " --> pdb=" O ASN E 307 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 311 " --> pdb=" O LEU E 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 307 through 311' Processing helix chain 'E' and resid 312 through 316 removed outlier: 3.844A pdb=" N LEU E 316 " --> pdb=" O PRO E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 355 removed outlier: 3.583A pdb=" N ASP E 353 " --> pdb=" O ILE E 349 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 354 " --> pdb=" O GLU E 350 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR E 355 " --> pdb=" O GLN E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 373 Processing helix chain 'E' and resid 384 through 408 removed outlier: 3.535A pdb=" N ARG E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 420 Processing helix chain 'E' and resid 421 through 426 removed outlier: 3.942A pdb=" N LEU E 425 " --> pdb=" O CYS E 421 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP E 426 " --> pdb=" O ILE E 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 421 through 426' Processing helix chain 'E' and resid 432 through 446 Processing helix chain 'E' and resid 447 through 457 Processing helix chain 'E' and resid 460 through 470 Processing helix chain 'E' and resid 487 through 491 Processing helix chain 'E' and resid 496 through 514 removed outlier: 3.608A pdb=" N LEU E 512 " --> pdb=" O GLY E 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 27 removed outlier: 4.068A pdb=" N VAL F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 57 removed outlier: 3.533A pdb=" N VAL F 54 " --> pdb=" O ASP F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 84 removed outlier: 3.761A pdb=" N ILE F 67 " --> pdb=" O LYS F 63 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY F 68 " --> pdb=" O TYR F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 104 Processing helix chain 'F' and resid 110 through 133 Processing helix chain 'F' and resid 138 through 150 removed outlier: 3.602A pdb=" N ILE F 142 " --> pdb=" O THR F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 167 removed outlier: 3.522A pdb=" N GLY F 157 " --> pdb=" O ASP F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 227 through 230 Processing helix chain 'F' and resid 231 through 242 Processing helix chain 'F' and resid 253 through 268 Processing helix chain 'F' and resid 280 through 295 removed outlier: 3.812A pdb=" N LYS F 284 " --> pdb=" O GLY F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 311 removed outlier: 3.558A pdb=" N ASP F 310 " --> pdb=" O ASN F 307 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 311 " --> pdb=" O LEU F 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 307 through 311' Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 337 through 355 removed outlier: 3.539A pdb=" N ASP F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR F 355 " --> pdb=" O GLN F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 373 Processing helix chain 'F' and resid 384 through 408 removed outlier: 3.574A pdb=" N ARG F 394 " --> pdb=" O GLU F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 Processing helix chain 'F' and resid 421 through 426 removed outlier: 3.793A pdb=" N LEU F 425 " --> pdb=" O CYS F 421 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP F 426 " --> pdb=" O ILE F 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 421 through 426' Processing helix chain 'F' and resid 432 through 446 Processing helix chain 'F' and resid 447 through 457 Processing helix chain 'F' and resid 460 through 470 removed outlier: 3.534A pdb=" N ILE F 464 " --> pdb=" O GLU F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 491 Processing helix chain 'F' and resid 496 through 514 Processing helix chain 'G' and resid 7 through 27 removed outlier: 4.019A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 56 Processing helix chain 'G' and resid 64 through 84 removed outlier: 3.849A pdb=" N GLY G 68 " --> pdb=" O TYR G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 104 removed outlier: 3.614A pdb=" N ALA G 90 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 133 Processing helix chain 'G' and resid 138 through 150 removed outlier: 3.604A pdb=" N ILE G 142 " --> pdb=" O THR G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 167 removed outlier: 3.613A pdb=" N GLY G 157 " --> pdb=" O ASP G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 203 Processing helix chain 'G' and resid 227 through 230 Processing helix chain 'G' and resid 231 through 242 Processing helix chain 'G' and resid 253 through 268 Processing helix chain 'G' and resid 279 through 295 removed outlier: 3.656A pdb=" N LYS G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 311 removed outlier: 3.625A pdb=" N ASP G 310 " --> pdb=" O ASN G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 316 removed outlier: 3.766A pdb=" N LEU G 316 " --> pdb=" O PRO G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 353 removed outlier: 3.536A pdb=" N ILE G 341 " --> pdb=" O ASP G 337 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP G 353 " --> pdb=" O ILE G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 357 through 373 Processing helix chain 'G' and resid 384 through 408 removed outlier: 3.508A pdb=" N ARG G 394 " --> pdb=" O GLU G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 420 removed outlier: 3.556A pdb=" N LEU G 419 " --> pdb=" O GLY G 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 421 through 426 removed outlier: 4.166A pdb=" N LEU G 425 " --> pdb=" O CYS G 421 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP G 426 " --> pdb=" O ILE G 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 421 through 426' Processing helix chain 'G' and resid 432 through 446 Processing helix chain 'G' and resid 447 through 458 Processing helix chain 'G' and resid 460 through 470 Processing helix chain 'G' and resid 487 through 491 Processing helix chain 'G' and resid 496 through 514 removed outlier: 3.611A pdb=" N LEU G 512 " --> pdb=" O GLY G 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 96 removed outlier: 3.587A pdb=" N ILE I 96 " --> pdb=" O ASP I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'K' and resid 94 through 96 No H-bonds generated for 'chain 'K' and resid 94 through 96' Processing helix chain 'L' and resid 92 through 96 Processing helix chain 'N' and resid 92 through 96 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 6.103A pdb=" N THR B 35 " --> pdb=" O ALA A 516 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 518 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU A 522 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN B 40 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 48 removed outlier: 6.047A pdb=" N THR A 35 " --> pdb=" O ALA G 516 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL G 518 " --> pdb=" O THR A 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 6.408A pdb=" N VAL A 172 " --> pdb=" O ALA A 376 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU A 378 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR A 174 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL A 380 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LYS A 176 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192 removed outlier: 5.810A pdb=" N LYS A 318 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR A 217 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 320 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL A 246 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR A 217 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE A 248 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU A 219 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 191 through 192 removed outlier: 5.810A pdb=" N LYS A 318 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TYR A 217 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 320 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N PHE A 299 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU A 220 " --> pdb=" O PHE A 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.511A pdb=" N ASP A 483 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 2 through 6 removed outlier: 4.537A pdb=" N ALA B 516 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE C 37 " --> pdb=" O ALA B 516 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 518 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 172 through 177 removed outlier: 6.415A pdb=" N VAL B 172 " --> pdb=" O ALA B 376 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU B 378 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR B 174 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL B 380 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS B 176 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.613A pdb=" N LYS B 318 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR B 217 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY B 320 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 249 " --> pdb=" O VAL B 274 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.613A pdb=" N LYS B 318 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N TYR B 217 " --> pdb=" O LYS B 318 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY B 320 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N PHE B 299 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU B 220 " --> pdb=" O PHE B 299 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB4, first strand: chain 'C' and resid 2 through 6 removed outlier: 4.788A pdb=" N ALA C 516 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE D 37 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL C 518 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.416A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR C 217 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY C 320 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 249 " --> pdb=" O VAL C 274 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.416A pdb=" N LYS C 318 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR C 217 " --> pdb=" O LYS C 318 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY C 320 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N PHE C 299 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU C 220 " --> pdb=" O PHE C 299 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AB9, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.744A pdb=" N ASP C 483 " --> pdb=" O ASP C 478 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.409A pdb=" N ALA D 516 " --> pdb=" O THR E 35 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE E 37 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL D 518 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 172 through 177 removed outlier: 6.520A pdb=" N VAL D 172 " --> pdb=" O ALA D 376 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU D 378 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR D 174 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL D 380 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS D 176 " --> pdb=" O VAL D 380 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 191 through 192 removed outlier: 6.568A pdb=" N GLU D 321 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN D 214 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE D 323 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLU D 212 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N VAL D 246 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR D 217 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE D 248 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU D 219 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 191 through 192 removed outlier: 6.568A pdb=" N GLU D 321 " --> pdb=" O GLN D 214 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLN D 214 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ILE D 323 " --> pdb=" O GLU D 212 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N GLU D 212 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N PHE D 299 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU D 220 " --> pdb=" O PHE D 299 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AC6, first strand: chain 'D' and resid 475 through 478 removed outlier: 3.577A pdb=" N ASP D 483 " --> pdb=" O ASP D 478 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 2 through 6 removed outlier: 4.647A pdb=" N ALA E 516 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE F 37 " --> pdb=" O ALA E 516 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL E 518 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 172 through 177 removed outlier: 6.569A pdb=" N VAL E 172 " --> pdb=" O ALA E 376 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU E 378 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR E 174 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VAL E 380 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS E 176 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 191 through 192 removed outlier: 6.600A pdb=" N GLU E 321 " --> pdb=" O GLN E 214 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN E 214 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE E 323 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU E 212 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL E 246 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR E 217 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE E 248 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N LEU E 219 " --> pdb=" O ILE E 248 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 191 through 192 removed outlier: 6.600A pdb=" N GLU E 321 " --> pdb=" O GLN E 214 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN E 214 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE E 323 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLU E 212 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N PHE E 299 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU E 220 " --> pdb=" O PHE E 299 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 410 through 412 Processing sheet with id=AD3, first strand: chain 'E' and resid 475 through 478 Processing sheet with id=AD4, first strand: chain 'F' and resid 2 through 6 removed outlier: 4.753A pdb=" N ALA F 516 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ILE G 37 " --> pdb=" O ALA F 516 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL F 518 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 172 through 177 removed outlier: 6.532A pdb=" N VAL F 172 " --> pdb=" O ALA F 376 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU F 378 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR F 174 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL F 380 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYS F 176 " --> pdb=" O VAL F 380 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 191 through 192 removed outlier: 3.721A pdb=" N MET F 191 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU F 331 " --> pdb=" O MET F 191 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS F 318 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR F 217 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY F 320 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N VAL F 246 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR F 217 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE F 248 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU F 219 " --> pdb=" O ILE F 248 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA F 249 " --> pdb=" O VAL F 274 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 191 through 192 removed outlier: 3.721A pdb=" N MET F 191 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU F 331 " --> pdb=" O MET F 191 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS F 318 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N TYR F 217 " --> pdb=" O LYS F 318 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY F 320 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 9.058A pdb=" N PHE F 299 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU F 220 " --> pdb=" O PHE F 299 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 410 through 412 Processing sheet with id=AD9, first strand: chain 'F' and resid 475 through 478 removed outlier: 3.537A pdb=" N ASP F 483 " --> pdb=" O ASP F 478 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 172 through 177 removed outlier: 6.439A pdb=" N VAL G 172 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU G 378 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR G 174 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL G 380 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS G 176 " --> pdb=" O VAL G 380 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 191 through 192 removed outlier: 6.422A pdb=" N LYS G 318 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR G 217 " --> pdb=" O LYS G 318 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY G 320 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N VAL G 246 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N TYR G 217 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE G 248 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU G 219 " --> pdb=" O ILE G 248 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 191 through 192 removed outlier: 6.422A pdb=" N LYS G 318 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR G 217 " --> pdb=" O LYS G 318 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY G 320 " --> pdb=" O ASP G 215 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N PHE G 299 " --> pdb=" O VAL G 218 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU G 220 " --> pdb=" O PHE G 299 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 410 through 412 Processing sheet with id=AE5, first strand: chain 'G' and resid 475 through 478 removed outlier: 3.534A pdb=" N ASP G 483 " --> pdb=" O ASP G 478 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 9 through 11 removed outlier: 3.774A pdb=" N GLY N 98 " --> pdb=" O LEU N 72 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS N 70 " --> pdb=" O TYR N 100 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL N 46 " --> pdb=" O GLU N 19 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU N 19 " --> pdb=" O VAL N 46 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG N 20 " --> pdb=" O ASP N 87 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N ASP N 87 " --> pdb=" O ARG N 20 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 79 through 83 removed outlier: 8.600A pdb=" N ASP H 87 " --> pdb=" O ARG H 20 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ARG H 20 " --> pdb=" O ASP H 87 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU H 17 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N LYS H 70 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY H 98 " --> pdb=" O LEU H 72 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 79 through 83 removed outlier: 8.888A pdb=" N ASP I 87 " --> pdb=" O ARG I 20 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG I 20 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU I 17 " --> pdb=" O VAL I 47 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LYS I 70 " --> pdb=" O TYR I 100 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY I 98 " --> pdb=" O LEU I 72 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 79 through 83 removed outlier: 8.245A pdb=" N ASP J 87 " --> pdb=" O ARG J 20 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ARG J 20 " --> pdb=" O ASP J 87 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ARG J 15 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL J 49 " --> pdb=" O ARG J 15 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU J 17 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS J 70 " --> pdb=" O TYR J 100 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY J 98 " --> pdb=" O LEU J 72 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 79 through 83 removed outlier: 8.803A pdb=" N ASP K 87 " --> pdb=" O ARG K 20 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ARG K 20 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ARG K 15 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL K 49 " --> pdb=" O ARG K 15 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU K 17 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA K 44 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LYS K 70 " --> pdb=" O TYR K 100 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY K 98 " --> pdb=" O LEU K 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 79 through 83 removed outlier: 8.532A pdb=" N ASP L 87 " --> pdb=" O ARG L 20 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ARG L 20 " --> pdb=" O ASP L 87 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU L 17 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS L 70 " --> pdb=" O TYR L 100 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY L 98 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 79 through 83 removed outlier: 8.749A pdb=" N ASP M 87 " --> pdb=" O ARG M 20 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ARG M 20 " --> pdb=" O ASP M 87 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ARG M 15 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N VAL M 49 " --> pdb=" O ARG M 15 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU M 17 " --> pdb=" O VAL M 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA M 44 " --> pdb=" O VAL M 71 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS M 70 " --> pdb=" O TYR M 100 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY M 98 " --> pdb=" O LEU M 72 " (cutoff:3.500A) 1911 hydrogen bonds defined for protein. 5409 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: 13.15 Time building geometry restraints manager: 9.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8842 1.33 - 1.45: 4234 1.45 - 1.57: 20063 1.57 - 1.69: 34 1.69 - 1.81: 189 Bond restraints: 33362 Sorted by residual: bond pdb=" ND1 HIS G 241 " pdb=" CE1 HIS G 241 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.76e+01 bond pdb=" ND1 HIS B 241 " pdb=" CE1 HIS B 241 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.75e+01 bond pdb=" ND1 HIS A 241 " pdb=" CE1 HIS A 241 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.74e+01 bond pdb=" ND1 HIS D 241 " pdb=" CE1 HIS D 241 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.71e+01 bond pdb=" CG ASN C 80 " pdb=" OD1 ASN C 80 " ideal model delta sigma weight residual 1.231 1.325 -0.094 1.90e-02 2.77e+03 2.44e+01 ... (remaining 33357 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 44784 3.12 - 6.24: 222 6.24 - 9.35: 22 9.35 - 12.47: 1 12.47 - 15.59: 2 Bond angle restraints: 45031 Sorted by residual: angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 124.28 15.59 1.00e+00 1.00e+00 2.43e+02 angle pdb=" PA ATP F 601 " pdb=" O3A ATP F 601 " pdb=" PB ATP F 601 " ideal model delta sigma weight residual 136.83 122.60 14.23 1.00e+00 1.00e+00 2.02e+02 angle pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " pdb=" O3G ATP F 601 " ideal model delta sigma weight residual 104.48 113.76 -9.28 1.14e+00 7.76e-01 6.69e+01 angle pdb=" CB HIS D 241 " pdb=" CG HIS D 241 " pdb=" CD2 HIS D 241 " ideal model delta sigma weight residual 131.20 122.60 8.60 1.30e+00 5.92e-01 4.37e+01 angle pdb=" CB HIS G 241 " pdb=" CG HIS G 241 " pdb=" CD2 HIS G 241 " ideal model delta sigma weight residual 131.20 122.61 8.59 1.30e+00 5.92e-01 4.37e+01 ... (remaining 45026 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 18987 17.90 - 35.80: 1413 35.80 - 53.70: 256 53.70 - 71.61: 91 71.61 - 89.51: 43 Dihedral angle restraints: 20790 sinusoidal: 8414 harmonic: 12376 Sorted by residual: dihedral pdb=" CA THR F 28 " pdb=" C THR F 28 " pdb=" N MET F 29 " pdb=" CA MET F 29 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASP B 337 " pdb=" CB ASP B 337 " pdb=" CG ASP B 337 " pdb=" OD1 ASP B 337 " ideal model delta sinusoidal sigma weight residual -30.00 -88.68 58.68 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA GLY A 7 " pdb=" C GLY A 7 " pdb=" N ALA A 8 " pdb=" CA ALA A 8 " ideal model delta harmonic sigma weight residual -180.00 -163.52 -16.48 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 20787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4694 0.063 - 0.126: 682 0.126 - 0.188: 27 0.188 - 0.251: 2 0.251 - 0.314: 20 Chirality restraints: 5425 Sorted by residual: chirality pdb=" C4' ATP F 601 " pdb=" C3' ATP F 601 " pdb=" C5' ATP F 601 " pdb=" O4' ATP F 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.81 0.31 2.00e-01 2.50e+01 2.46e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C2' ATP G 601 " pdb=" C1' ATP G 601 " pdb=" C3' ATP G 601 " pdb=" O2' ATP G 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 5422 not shown) Planarity restraints: 5768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP F 601 " 0.005 2.00e-02 2.50e+03 1.87e-02 9.59e+00 pdb=" C2 ATP F 601 " -0.003 2.00e-02 2.50e+03 pdb=" C4 ATP F 601 " -0.013 2.00e-02 2.50e+03 pdb=" C5 ATP F 601 " -0.033 2.00e-02 2.50e+03 pdb=" C6 ATP F 601 " -0.017 2.00e-02 2.50e+03 pdb=" C8 ATP F 601 " 0.016 2.00e-02 2.50e+03 pdb=" N1 ATP F 601 " 0.001 2.00e-02 2.50e+03 pdb=" N3 ATP F 601 " 0.012 2.00e-02 2.50e+03 pdb=" N6 ATP F 601 " 0.036 2.00e-02 2.50e+03 pdb=" N7 ATP F 601 " -0.017 2.00e-02 2.50e+03 pdb=" N9 ATP F 601 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 96 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C SER F 96 " -0.037 2.00e-02 2.50e+03 pdb=" O SER F 96 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE F 97 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 243 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO D 244 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 244 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 244 " 0.028 5.00e-02 4.00e+02 ... (remaining 5765 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 610 2.69 - 3.24: 32683 3.24 - 3.79: 48048 3.79 - 4.35: 63361 4.35 - 4.90: 109175 Nonbonded interactions: 253877 Sorted by model distance: nonbonded pdb=" OD1 ASP E 253 " pdb=" N GLY E 254 " model vdw 2.133 3.120 nonbonded pdb=" NH2 ARG A 115 " pdb=" OE1 GLU B 387 " model vdw 2.197 3.120 nonbonded pdb=" OD1 ASP G 177 " pdb=" NZ LYS G 392 " model vdw 2.199 3.120 nonbonded pdb=" OE1 GLU A 387 " pdb=" NH2 ARG G 115 " model vdw 2.221 3.120 nonbonded pdb=" OG SER A 44 " pdb=" OD2 ASP G 74 " model vdw 2.222 3.040 ... (remaining 253872 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.280 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 71.480 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 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 : 0.003 0.099 33362 Z= 0.184 Angle : 0.572 15.589 45031 Z= 0.350 Chirality : 0.045 0.314 5425 Planarity : 0.003 0.057 5768 Dihedral : 14.091 89.506 12852 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.72 (0.13), residues: 4361 helix: 2.62 (0.12), residues: 1995 sheet: 0.92 (0.21), residues: 553 loop : -0.51 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 42 HIS 0.003 0.001 HIS A 241 PHE 0.006 0.001 PHE F 279 TYR 0.012 0.001 TYR A 64 ARG 0.012 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.15529 ( 1852) hydrogen bonds : angle 6.05076 ( 5409) covalent geometry : bond 0.00310 (33362) covalent geometry : angle 0.57150 (45031) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8214 (t0) cc_final: 0.7871 (m-30) REVERT: A 215 ASP cc_start: 0.8289 (t0) cc_final: 0.8059 (t0) REVERT: A 257 LEU cc_start: 0.8887 (tt) cc_final: 0.8629 (mt) REVERT: A 290 MET cc_start: 0.8715 (mtm) cc_final: 0.8379 (mtt) REVERT: A 309 GLU cc_start: 0.7789 (tt0) cc_final: 0.7390 (tp30) REVERT: B 281 ASP cc_start: 0.8457 (t70) cc_final: 0.8158 (t0) REVERT: C 487 MET cc_start: 0.9124 (mmm) cc_final: 0.8902 (mmp) REVERT: D 241 HIS cc_start: 0.8369 (m90) cc_final: 0.8006 (m170) REVERT: D 321 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6293 (mm-30) REVERT: D 326 LYS cc_start: 0.8991 (tppt) cc_final: 0.8708 (tppt) REVERT: D 330 MET cc_start: 0.8270 (ttm) cc_final: 0.7982 (ttm) REVERT: D 358 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7635 (pm20) REVERT: E 191 MET cc_start: 0.8503 (mtp) cc_final: 0.8264 (mtp) REVERT: E 223 LYS cc_start: 0.8988 (pttt) cc_final: 0.8476 (mmtp) REVERT: G 218 VAL cc_start: 0.9188 (t) cc_final: 0.8817 (p) REVERT: G 330 MET cc_start: 0.7459 (ttm) cc_final: 0.7134 (ttm) REVERT: H 4 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8367 (mm-40) REVERT: H 61 GLN cc_start: 0.7538 (tm-30) cc_final: 0.7329 (tm-30) REVERT: H 95 ASP cc_start: 0.8928 (m-30) cc_final: 0.8671 (m-30) REVERT: J 84 ASP cc_start: 0.6780 (m-30) cc_final: 0.6488 (m-30) REVERT: J 93 ASP cc_start: 0.8823 (t0) cc_final: 0.8596 (t0) REVERT: K 15 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7654 (mtt90) REVERT: L 4 GLN cc_start: 0.8261 (tp40) cc_final: 0.7626 (mp10) REVERT: L 95 ASP cc_start: 0.9199 (m-30) cc_final: 0.8982 (m-30) REVERT: M 32 MET cc_start: 0.7933 (mmt) cc_final: 0.7569 (mmm) REVERT: M 43 GLN cc_start: 0.8083 (mp10) cc_final: 0.7682 (mp10) REVERT: N 51 SER cc_start: 0.9239 (m) cc_final: 0.9015 (p) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.4331 time to fit residues: 298.3638 Evaluate side-chains 331 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 366 optimal weight: 9.9990 chunk 328 optimal weight: 0.9980 chunk 182 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 340 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 206 optimal weight: 0.6980 chunk 253 optimal weight: 0.0020 chunk 394 optimal weight: 10.0000 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.077247 restraints weight = 63257.817| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.62 r_work: 0.2872 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33362 Z= 0.114 Angle : 0.499 7.546 45031 Z= 0.268 Chirality : 0.043 0.210 5425 Planarity : 0.003 0.045 5768 Dihedral : 8.399 87.235 4837 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.54 % Allowed : 4.79 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.13), residues: 4361 helix: 2.68 (0.11), residues: 2023 sheet: 0.95 (0.21), residues: 567 loop : -0.59 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 42 HIS 0.007 0.001 HIS D 314 PHE 0.011 0.001 PHE F 193 TYR 0.011 0.001 TYR A 64 ARG 0.007 0.000 ARG J 7 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 1852) hydrogen bonds : angle 4.55118 ( 5409) covalent geometry : bond 0.00241 (33362) covalent geometry : angle 0.49887 (45031) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 372 time to evaluate : 3.853 Fit side-chains REVERT: A 74 ASP cc_start: 0.8575 (t0) cc_final: 0.8205 (m-30) REVERT: A 215 ASP cc_start: 0.8238 (t0) cc_final: 0.7891 (t0) REVERT: A 257 LEU cc_start: 0.8786 (tt) cc_final: 0.8505 (mt) REVERT: A 290 MET cc_start: 0.8738 (mtm) cc_final: 0.8418 (mtt) REVERT: B 3 ASP cc_start: 0.8617 (t0) cc_final: 0.8356 (t0) REVERT: B 281 ASP cc_start: 0.8700 (t70) cc_final: 0.8471 (t0) REVERT: B 290 MET cc_start: 0.8924 (mtm) cc_final: 0.8292 (mtm) REVERT: B 326 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8690 (tppt) REVERT: C 242 ARG cc_start: 0.8872 (mmt90) cc_final: 0.8629 (mmm-85) REVERT: D 221 SER cc_start: 0.9009 (m) cc_final: 0.8407 (p) REVERT: D 241 HIS cc_start: 0.8249 (m90) cc_final: 0.7940 (m-70) REVERT: D 321 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6943 (mm-30) REVERT: D 326 LYS cc_start: 0.9168 (tppt) cc_final: 0.8834 (tppt) REVERT: D 330 MET cc_start: 0.8650 (ttm) cc_final: 0.8230 (ttm) REVERT: D 358 GLU cc_start: 0.8563 (mm-30) cc_final: 0.7695 (pm20) REVERT: E 282 ASN cc_start: 0.8817 (t0) cc_final: 0.8514 (t0) REVERT: E 330 MET cc_start: 0.8983 (mtp) cc_final: 0.8579 (mmm) REVERT: E 360 GLU cc_start: 0.8273 (tp30) cc_final: 0.7762 (tp30) REVERT: F 309 GLU cc_start: 0.8678 (mp0) cc_final: 0.8457 (mp0) REVERT: G 218 VAL cc_start: 0.9155 (t) cc_final: 0.8662 (p) REVERT: G 330 MET cc_start: 0.8115 (ttm) cc_final: 0.7603 (ttm) REVERT: H 4 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8427 (mm-40) REVERT: H 95 ASP cc_start: 0.9110 (m-30) cc_final: 0.8702 (m-30) REVERT: I 43 GLN cc_start: 0.8540 (mp10) cc_final: 0.8242 (mp10) REVERT: I 69 ASP cc_start: 0.8004 (m-30) cc_final: 0.7684 (p0) REVERT: K 15 ARG cc_start: 0.7878 (mtt90) cc_final: 0.7370 (mtt90) REVERT: L 4 GLN cc_start: 0.8249 (tp40) cc_final: 0.7325 (mp10) REVERT: L 32 MET cc_start: 0.8412 (ppp) cc_final: 0.8037 (ppp) REVERT: L 51 SER cc_start: 0.8500 (t) cc_final: 0.8219 (m) REVERT: M 32 MET cc_start: 0.8005 (mmt) cc_final: 0.7536 (mmm) REVERT: N 51 SER cc_start: 0.9177 (m) cc_final: 0.8936 (p) outliers start: 19 outliers final: 9 residues processed: 384 average time/residue: 0.4262 time to fit residues: 271.7200 Evaluate side-chains 327 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 318 time to evaluate : 3.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 38 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 318 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 326 optimal weight: 7.9990 chunk 317 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN D 80 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.105317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.074266 restraints weight = 63720.895| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.61 r_work: 0.2815 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33362 Z= 0.173 Angle : 0.513 7.555 45031 Z= 0.274 Chirality : 0.043 0.163 5425 Planarity : 0.003 0.040 5768 Dihedral : 8.218 78.743 4837 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.85 % Allowed : 6.76 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.13), residues: 4361 helix: 2.54 (0.11), residues: 2023 sheet: 0.95 (0.22), residues: 553 loop : -0.59 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 42 HIS 0.016 0.001 HIS D 314 PHE 0.010 0.001 PHE A 193 TYR 0.013 0.001 TYR A 64 ARG 0.005 0.000 ARG N 92 Details of bonding type rmsd hydrogen bonds : bond 0.05200 ( 1852) hydrogen bonds : angle 4.42218 ( 5409) covalent geometry : bond 0.00421 (33362) covalent geometry : angle 0.51324 (45031) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 328 time to evaluate : 4.098 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8721 (t0) cc_final: 0.8228 (m-30) REVERT: A 215 ASP cc_start: 0.8140 (t0) cc_final: 0.7783 (t0) REVERT: A 290 MET cc_start: 0.8801 (mtm) cc_final: 0.8505 (mtm) REVERT: B 3 ASP cc_start: 0.8751 (t0) cc_final: 0.8374 (t0) REVERT: B 326 LYS cc_start: 0.9087 (ttmt) cc_final: 0.8699 (tppt) REVERT: C 251 ASP cc_start: 0.8092 (t0) cc_final: 0.7873 (t0) REVERT: C 330 MET cc_start: 0.8862 (ttm) cc_final: 0.8431 (ttm) REVERT: D 241 HIS cc_start: 0.8280 (m90) cc_final: 0.7972 (m-70) REVERT: D 321 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6787 (mm-30) REVERT: D 330 MET cc_start: 0.8697 (ttm) cc_final: 0.8276 (ttm) REVERT: D 358 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7699 (pm20) REVERT: E 218 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8838 (p) REVERT: E 330 MET cc_start: 0.8967 (mtp) cc_final: 0.8652 (mmm) REVERT: E 360 GLU cc_start: 0.8282 (tp30) cc_final: 0.7786 (tp30) REVERT: G 218 VAL cc_start: 0.9229 (t) cc_final: 0.8823 (p) REVERT: G 330 MET cc_start: 0.8079 (ttm) cc_final: 0.7577 (ttm) REVERT: H 35 GLU cc_start: 0.7958 (tp30) cc_final: 0.7743 (tp30) REVERT: H 61 GLN cc_start: 0.7286 (tp40) cc_final: 0.6806 (tp40) REVERT: H 95 ASP cc_start: 0.9083 (m-30) cc_final: 0.8677 (m-30) REVERT: I 43 GLN cc_start: 0.8629 (mp10) cc_final: 0.8413 (mp10) REVERT: I 69 ASP cc_start: 0.8078 (m-30) cc_final: 0.7825 (p0) REVERT: L 4 GLN cc_start: 0.8236 (tp40) cc_final: 0.7327 (mp10) REVERT: L 32 MET cc_start: 0.8368 (ppp) cc_final: 0.7951 (ppp) REVERT: L 51 SER cc_start: 0.8531 (t) cc_final: 0.8243 (m) REVERT: M 75 GLU cc_start: 0.8894 (pm20) cc_final: 0.8633 (pm20) REVERT: M 87 ASP cc_start: 0.8594 (p0) cc_final: 0.8067 (m-30) REVERT: N 51 SER cc_start: 0.9179 (m) cc_final: 0.8967 (p) REVERT: N 92 ARG cc_start: 0.7712 (tpp80) cc_final: 0.7508 (tpp80) outliers start: 30 outliers final: 15 residues processed: 346 average time/residue: 0.4137 time to fit residues: 239.1304 Evaluate side-chains 325 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 309 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 410 optimal weight: 8.9990 chunk 400 optimal weight: 3.9990 chunk 271 optimal weight: 0.7980 chunk 298 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 376 optimal weight: 0.0370 chunk 362 optimal weight: 0.8980 chunk 279 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.105772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.074785 restraints weight = 63653.937| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.61 r_work: 0.2827 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33362 Z= 0.147 Angle : 0.487 6.534 45031 Z= 0.260 Chirality : 0.042 0.168 5425 Planarity : 0.003 0.038 5768 Dihedral : 7.641 72.395 4837 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.18 % Allowed : 7.50 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.13), residues: 4361 helix: 2.57 (0.11), residues: 2023 sheet: 0.79 (0.22), residues: 567 loop : -0.71 (0.13), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 42 HIS 0.003 0.001 HIS D 314 PHE 0.018 0.001 PHE F 193 TYR 0.011 0.001 TYR A 64 ARG 0.004 0.000 ARG N 92 Details of bonding type rmsd hydrogen bonds : bond 0.04719 ( 1852) hydrogen bonds : angle 4.25672 ( 5409) covalent geometry : bond 0.00355 (33362) covalent geometry : angle 0.48654 (45031) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 331 time to evaluate : 3.550 Fit side-chains REVERT: A 74 ASP cc_start: 0.8715 (t0) cc_final: 0.8164 (m-30) REVERT: A 215 ASP cc_start: 0.8162 (t0) cc_final: 0.7769 (t0) REVERT: A 257 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8587 (mt) REVERT: A 290 MET cc_start: 0.8784 (mtm) cc_final: 0.8490 (mtm) REVERT: B 326 LYS cc_start: 0.9087 (ttmt) cc_final: 0.8704 (tppt) REVERT: C 286 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8743 (mt0) REVERT: C 330 MET cc_start: 0.8814 (ttm) cc_final: 0.8346 (ttm) REVERT: D 221 SER cc_start: 0.8974 (m) cc_final: 0.8322 (p) REVERT: D 241 HIS cc_start: 0.8206 (m90) cc_final: 0.7912 (m-70) REVERT: D 321 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6746 (mm-30) REVERT: D 330 MET cc_start: 0.8675 (ttm) cc_final: 0.8277 (ttm) REVERT: D 358 GLU cc_start: 0.8571 (mm-30) cc_final: 0.7729 (pm20) REVERT: E 218 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8845 (p) REVERT: E 236 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: E 282 ASN cc_start: 0.8840 (t0) cc_final: 0.8531 (t0) REVERT: E 330 MET cc_start: 0.8929 (mtp) cc_final: 0.8684 (mmm) REVERT: E 360 GLU cc_start: 0.8274 (tp30) cc_final: 0.7773 (tp30) REVERT: G 218 VAL cc_start: 0.9233 (t) cc_final: 0.8754 (p) REVERT: G 330 MET cc_start: 0.8056 (ttm) cc_final: 0.7560 (ttm) REVERT: G 337 ASP cc_start: 0.6563 (t0) cc_final: 0.6328 (t0) REVERT: H 19 GLU cc_start: 0.8492 (tt0) cc_final: 0.8264 (pt0) REVERT: H 35 GLU cc_start: 0.8043 (tp30) cc_final: 0.7802 (tp30) REVERT: H 95 ASP cc_start: 0.9067 (m-30) cc_final: 0.8657 (m-30) REVERT: I 32 MET cc_start: 0.8821 (mpp) cc_final: 0.8591 (mpp) REVERT: I 69 ASP cc_start: 0.8090 (m-30) cc_final: 0.7883 (p0) REVERT: L 4 GLN cc_start: 0.8327 (tp40) cc_final: 0.7307 (mp10) REVERT: L 51 SER cc_start: 0.8583 (t) cc_final: 0.8340 (m) REVERT: M 43 GLN cc_start: 0.8580 (mp10) cc_final: 0.8340 (mp10) REVERT: M 87 ASP cc_start: 0.8571 (p0) cc_final: 0.7984 (m-30) REVERT: N 51 SER cc_start: 0.9191 (m) cc_final: 0.8986 (p) outliers start: 42 outliers final: 19 residues processed: 357 average time/residue: 0.4054 time to fit residues: 241.0994 Evaluate side-chains 328 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 306 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain N residue 32 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 394 optimal weight: 0.0870 chunk 225 optimal weight: 0.8980 chunk 410 optimal weight: 8.9990 chunk 334 optimal weight: 10.0000 chunk 260 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 chunk 149 optimal weight: 0.6980 chunk 216 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 386 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.107229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.076312 restraints weight = 63371.724| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.61 r_work: 0.2856 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33362 Z= 0.111 Angle : 0.466 7.013 45031 Z= 0.249 Chirality : 0.042 0.216 5425 Planarity : 0.003 0.040 5768 Dihedral : 7.091 69.798 4837 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.24 % Allowed : 8.31 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.69 (0.13), residues: 4361 helix: 2.67 (0.11), residues: 2030 sheet: 0.86 (0.22), residues: 567 loop : -0.68 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 42 HIS 0.002 0.001 HIS C 241 PHE 0.011 0.001 PHE F 193 TYR 0.009 0.001 TYR A 64 ARG 0.004 0.000 ARG L 7 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 1852) hydrogen bonds : angle 4.11168 ( 5409) covalent geometry : bond 0.00251 (33362) covalent geometry : angle 0.46603 (45031) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 329 time to evaluate : 3.657 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8675 (t0) cc_final: 0.8122 (m-30) REVERT: A 215 ASP cc_start: 0.8107 (t0) cc_final: 0.7712 (t0) REVERT: A 257 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8567 (mt) REVERT: A 290 MET cc_start: 0.8749 (mtm) cc_final: 0.8421 (mtm) REVERT: B 326 LYS cc_start: 0.9099 (ttmt) cc_final: 0.8729 (tppt) REVERT: C 330 MET cc_start: 0.8733 (ttm) cc_final: 0.8271 (ttm) REVERT: D 221 SER cc_start: 0.8966 (m) cc_final: 0.8300 (p) REVERT: D 241 HIS cc_start: 0.8089 (m90) cc_final: 0.7754 (m-70) REVERT: D 321 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6716 (mm-30) REVERT: D 330 MET cc_start: 0.8648 (ttm) cc_final: 0.8243 (ttm) REVERT: D 358 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7782 (pm20) REVERT: E 218 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8812 (p) REVERT: E 236 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8178 (pm20) REVERT: E 282 ASN cc_start: 0.8835 (t0) cc_final: 0.8521 (t0) REVERT: E 330 MET cc_start: 0.8947 (mtp) cc_final: 0.8720 (mmm) REVERT: E 360 GLU cc_start: 0.8241 (tp30) cc_final: 0.7730 (tp30) REVERT: G 218 VAL cc_start: 0.9189 (t) cc_final: 0.8779 (p) REVERT: G 330 MET cc_start: 0.8028 (ttm) cc_final: 0.7535 (ttm) REVERT: H 19 GLU cc_start: 0.8483 (tt0) cc_final: 0.8276 (pt0) REVERT: H 35 GLU cc_start: 0.8113 (tp30) cc_final: 0.7831 (tp30) REVERT: H 61 GLN cc_start: 0.7162 (tp40) cc_final: 0.6742 (tp40) REVERT: H 95 ASP cc_start: 0.9017 (m-30) cc_final: 0.8635 (m-30) REVERT: I 69 ASP cc_start: 0.8153 (m-30) cc_final: 0.7881 (p0) REVERT: K 4 GLN cc_start: 0.8632 (tp-100) cc_final: 0.8320 (tp-100) REVERT: L 4 GLN cc_start: 0.8348 (tp40) cc_final: 0.7300 (mp10) REVERT: L 51 SER cc_start: 0.8651 (t) cc_final: 0.8406 (m) REVERT: M 7 ARG cc_start: 0.8412 (mtp85) cc_final: 0.8066 (mtp85) REVERT: M 43 GLN cc_start: 0.8548 (mp10) cc_final: 0.8281 (mp10) REVERT: M 69 ASP cc_start: 0.8994 (m-30) cc_final: 0.8700 (m-30) REVERT: M 87 ASP cc_start: 0.8587 (p0) cc_final: 0.8040 (m-30) REVERT: N 51 SER cc_start: 0.9192 (m) cc_final: 0.8987 (p) outliers start: 44 outliers final: 21 residues processed: 357 average time/residue: 0.4116 time to fit residues: 247.0406 Evaluate side-chains 332 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 308 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain N residue 32 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 323 optimal weight: 0.9990 chunk 134 optimal weight: 0.0270 chunk 212 optimal weight: 6.9990 chunk 365 optimal weight: 10.0000 chunk 363 optimal weight: 2.9990 chunk 400 optimal weight: 7.9990 chunk 137 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 334 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN C 40 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 HIS H 4 GLN K 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.071790 restraints weight = 64909.655| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.65 r_work: 0.2771 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 33362 Z= 0.232 Angle : 0.564 8.366 45031 Z= 0.299 Chirality : 0.044 0.192 5425 Planarity : 0.003 0.035 5768 Dihedral : 7.754 73.707 4837 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.13 % Allowed : 9.50 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.40 (0.12), residues: 4361 helix: 2.37 (0.11), residues: 2030 sheet: 0.91 (0.22), residues: 553 loop : -0.82 (0.13), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 42 HIS 0.007 0.001 HIS F 314 PHE 0.012 0.001 PHE F 193 TYR 0.013 0.001 TYR F 359 ARG 0.003 0.000 ARG D 420 Details of bonding type rmsd hydrogen bonds : bond 0.05877 ( 1852) hydrogen bonds : angle 4.39110 ( 5409) covalent geometry : bond 0.00571 (33362) covalent geometry : angle 0.56395 (45031) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 314 time to evaluate : 3.851 Fit side-chains REVERT: A 74 ASP cc_start: 0.8824 (t0) cc_final: 0.8277 (m-30) REVERT: A 215 ASP cc_start: 0.8203 (t0) cc_final: 0.7840 (t0) REVERT: A 257 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8604 (mt) REVERT: A 290 MET cc_start: 0.8807 (mtm) cc_final: 0.8524 (mtm) REVERT: B 326 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8712 (tppt) REVERT: C 330 MET cc_start: 0.8828 (ttm) cc_final: 0.8336 (ttm) REVERT: D 241 HIS cc_start: 0.8125 (m90) cc_final: 0.7814 (m-70) REVERT: D 321 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7067 (mm-30) REVERT: D 330 MET cc_start: 0.8680 (ttm) cc_final: 0.8290 (ttm) REVERT: E 236 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: E 282 ASN cc_start: 0.8781 (t0) cc_final: 0.8464 (t0) REVERT: E 330 MET cc_start: 0.8974 (mtp) cc_final: 0.8629 (mmm) REVERT: E 346 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8041 (mm-40) REVERT: E 360 GLU cc_start: 0.8239 (tp30) cc_final: 0.7754 (tp30) REVERT: G 330 MET cc_start: 0.8120 (ttm) cc_final: 0.7641 (ttm) REVERT: H 19 GLU cc_start: 0.8497 (tt0) cc_final: 0.8272 (pt0) REVERT: H 61 GLN cc_start: 0.7200 (tp40) cc_final: 0.6848 (tp40) REVERT: H 95 ASP cc_start: 0.8997 (m-30) cc_final: 0.8695 (m-30) REVERT: I 69 ASP cc_start: 0.8099 (m-30) cc_final: 0.7856 (p0) REVERT: K 32 MET cc_start: 0.8874 (ptm) cc_final: 0.8356 (ptp) REVERT: L 4 GLN cc_start: 0.8392 (tp40) cc_final: 0.7368 (mp10) REVERT: L 32 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7839 (ppp) REVERT: L 51 SER cc_start: 0.8617 (t) cc_final: 0.8369 (m) REVERT: M 43 GLN cc_start: 0.8682 (mp10) cc_final: 0.8421 (mp10) REVERT: M 69 ASP cc_start: 0.9031 (m-30) cc_final: 0.8712 (m-30) REVERT: M 87 ASP cc_start: 0.8596 (p0) cc_final: 0.8119 (m-30) outliers start: 40 outliers final: 25 residues processed: 338 average time/residue: 0.4304 time to fit residues: 242.0352 Evaluate side-chains 327 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 298 time to evaluate : 3.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain G residue 220 LEU Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain N residue 32 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 152 optimal weight: 0.8980 chunk 340 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 349 optimal weight: 6.9990 chunk 167 optimal weight: 0.9990 chunk 430 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 chunk 229 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 424 optimal weight: 0.0980 chunk 384 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN D 365 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.076897 restraints weight = 63550.305| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.62 r_work: 0.2863 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33362 Z= 0.103 Angle : 0.472 8.328 45031 Z= 0.251 Chirality : 0.042 0.176 5425 Planarity : 0.003 0.038 5768 Dihedral : 6.853 68.921 4837 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.93 % Allowed : 9.86 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.64 (0.13), residues: 4361 helix: 2.64 (0.11), residues: 2030 sheet: 0.84 (0.22), residues: 567 loop : -0.73 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 42 HIS 0.001 0.000 HIS B 314 PHE 0.012 0.001 PHE F 193 TYR 0.009 0.001 TYR F 359 ARG 0.004 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 1852) hydrogen bonds : angle 4.04266 ( 5409) covalent geometry : bond 0.00219 (33362) covalent geometry : angle 0.47213 (45031) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 326 time to evaluate : 3.817 Fit side-chains REVERT: A 74 ASP cc_start: 0.8691 (t0) cc_final: 0.8144 (m-30) REVERT: A 215 ASP cc_start: 0.8099 (t0) cc_final: 0.7671 (t0) REVERT: A 257 LEU cc_start: 0.8837 (tt) cc_final: 0.8566 (mt) REVERT: A 290 MET cc_start: 0.8755 (mtm) cc_final: 0.8435 (mtm) REVERT: B 262 LEU cc_start: 0.8525 (tt) cc_final: 0.7953 (mt) REVERT: B 326 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8772 (tppt) REVERT: C 330 MET cc_start: 0.8710 (ttm) cc_final: 0.8233 (ttm) REVERT: C 351 GLN cc_start: 0.7726 (mt0) cc_final: 0.7455 (mt0) REVERT: D 321 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7015 (mm-30) REVERT: D 330 MET cc_start: 0.8590 (ttm) cc_final: 0.8216 (ttm) REVERT: E 218 VAL cc_start: 0.9142 (OUTLIER) cc_final: 0.8842 (p) REVERT: E 235 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8683 (mm) REVERT: E 236 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8136 (pm20) REVERT: E 282 ASN cc_start: 0.8808 (t0) cc_final: 0.8503 (t0) REVERT: E 330 MET cc_start: 0.9020 (mtp) cc_final: 0.8758 (mmm) REVERT: E 360 GLU cc_start: 0.8232 (tp30) cc_final: 0.7744 (tp30) REVERT: G 290 MET cc_start: 0.8883 (mpp) cc_final: 0.8651 (mtt) REVERT: G 330 MET cc_start: 0.8031 (ttm) cc_final: 0.7543 (ttm) REVERT: H 61 GLN cc_start: 0.7022 (tp40) cc_final: 0.6820 (tp40) REVERT: H 95 ASP cc_start: 0.8966 (m-30) cc_final: 0.8657 (m-30) REVERT: I 14 ASP cc_start: 0.8699 (p0) cc_final: 0.8137 (p0) REVERT: I 19 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7961 (mm-30) REVERT: I 32 MET cc_start: 0.8804 (mpp) cc_final: 0.8544 (mpp) REVERT: I 61 GLN cc_start: 0.8644 (mp10) cc_final: 0.8164 (mp10) REVERT: K 4 GLN cc_start: 0.8650 (tp-100) cc_final: 0.8157 (tp-100) REVERT: K 32 MET cc_start: 0.8857 (ptm) cc_final: 0.8369 (ptp) REVERT: K 76 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7711 (m-80) REVERT: L 4 GLN cc_start: 0.8399 (tp40) cc_final: 0.7340 (mp10) REVERT: L 32 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7691 (ppp) REVERT: M 43 GLN cc_start: 0.8640 (mp10) cc_final: 0.8363 (mp10) REVERT: M 69 ASP cc_start: 0.9054 (m-30) cc_final: 0.8770 (m-30) REVERT: M 87 ASP cc_start: 0.8569 (p0) cc_final: 0.8072 (m-30) outliers start: 33 outliers final: 19 residues processed: 347 average time/residue: 0.4175 time to fit residues: 241.4736 Evaluate side-chains 325 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 301 time to evaluate : 3.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 76 TYR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain N residue 32 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 233 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 347 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 115 optimal weight: 0.6980 chunk 307 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 143 optimal weight: 4.9990 chunk 259 optimal weight: 0.7980 chunk 249 optimal weight: 0.0770 chunk 379 optimal weight: 0.0970 overall best weight: 1.1338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN D 241 HIS ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.076330 restraints weight = 63492.244| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.61 r_work: 0.2855 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33362 Z= 0.111 Angle : 0.477 8.732 45031 Z= 0.252 Chirality : 0.042 0.181 5425 Planarity : 0.003 0.038 5768 Dihedral : 6.641 68.091 4837 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.13 % Allowed : 10.17 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.69 (0.13), residues: 4361 helix: 2.69 (0.11), residues: 2030 sheet: 0.87 (0.22), residues: 567 loop : -0.72 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 42 HIS 0.002 0.000 HIS B 314 PHE 0.013 0.001 PHE F 279 TYR 0.010 0.001 TYR A 64 ARG 0.004 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 1852) hydrogen bonds : angle 4.00691 ( 5409) covalent geometry : bond 0.00253 (33362) covalent geometry : angle 0.47675 (45031) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 307 time to evaluate : 3.859 Fit side-chains REVERT: A 74 ASP cc_start: 0.8692 (t0) cc_final: 0.8118 (m-30) REVERT: A 201 TYR cc_start: 0.7970 (m-80) cc_final: 0.7600 (m-80) REVERT: A 215 ASP cc_start: 0.8122 (t0) cc_final: 0.7746 (t0) REVERT: A 257 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8577 (mt) REVERT: A 290 MET cc_start: 0.8752 (mtm) cc_final: 0.8429 (mtm) REVERT: B 262 LEU cc_start: 0.8487 (tt) cc_final: 0.7958 (mt) REVERT: B 326 LYS cc_start: 0.9120 (ttmt) cc_final: 0.8746 (tppt) REVERT: C 330 MET cc_start: 0.8728 (ttm) cc_final: 0.8259 (ttm) REVERT: C 351 GLN cc_start: 0.7690 (mt0) cc_final: 0.7458 (mt0) REVERT: D 221 SER cc_start: 0.8999 (m) cc_final: 0.8427 (p) REVERT: D 321 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6982 (mm-30) REVERT: D 330 MET cc_start: 0.8586 (ttm) cc_final: 0.8221 (ttm) REVERT: E 218 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8872 (p) REVERT: E 236 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: E 282 ASN cc_start: 0.8815 (t0) cc_final: 0.8519 (t0) REVERT: E 330 MET cc_start: 0.8944 (mtp) cc_final: 0.8738 (mmm) REVERT: E 360 GLU cc_start: 0.8238 (tp30) cc_final: 0.7741 (tp30) REVERT: G 290 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8660 (mtt) REVERT: G 330 MET cc_start: 0.8034 (ttm) cc_final: 0.7553 (ttm) REVERT: H 95 ASP cc_start: 0.8970 (m-30) cc_final: 0.8679 (m-30) REVERT: I 14 ASP cc_start: 0.8702 (p0) cc_final: 0.8110 (p0) REVERT: I 61 GLN cc_start: 0.8682 (mp10) cc_final: 0.8210 (mp10) REVERT: K 4 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8116 (tp-100) REVERT: K 32 MET cc_start: 0.8841 (ptm) cc_final: 0.8364 (ptp) REVERT: K 59 GLU cc_start: 0.7120 (tp30) cc_final: 0.6803 (tp30) REVERT: L 4 GLN cc_start: 0.8412 (tp40) cc_final: 0.7377 (mp10) REVERT: L 32 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7646 (ppp) REVERT: M 43 GLN cc_start: 0.8654 (mp10) cc_final: 0.8378 (mp10) REVERT: M 69 ASP cc_start: 0.9073 (m-30) cc_final: 0.8789 (m-30) REVERT: M 87 ASP cc_start: 0.8579 (p0) cc_final: 0.8083 (m-30) outliers start: 40 outliers final: 28 residues processed: 333 average time/residue: 0.4065 time to fit residues: 226.3444 Evaluate side-chains 328 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 295 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 432 ASN Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 191 MET Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain G residue 290 MET Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain N residue 32 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 246 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 293 optimal weight: 9.9990 chunk 209 optimal weight: 0.7980 chunk 267 optimal weight: 1.9990 chunk 323 optimal weight: 3.9990 chunk 386 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 260 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.107454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.076607 restraints weight = 63509.921| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.62 r_work: 0.2861 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33362 Z= 0.112 Angle : 0.480 12.186 45031 Z= 0.252 Chirality : 0.042 0.185 5425 Planarity : 0.003 0.038 5768 Dihedral : 6.504 66.335 4837 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.18 % Allowed : 10.23 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.69 (0.13), residues: 4361 helix: 2.68 (0.11), residues: 2030 sheet: 0.89 (0.22), residues: 567 loop : -0.73 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 42 HIS 0.002 0.000 HIS B 314 PHE 0.009 0.001 PHE A 279 TYR 0.011 0.001 TYR A 64 ARG 0.003 0.000 ARG N 92 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 1852) hydrogen bonds : angle 3.98783 ( 5409) covalent geometry : bond 0.00255 (33362) covalent geometry : angle 0.47962 (45031) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 313 time to evaluate : 3.733 Fit side-chains REVERT: A 74 ASP cc_start: 0.8686 (t0) cc_final: 0.8115 (m-30) REVERT: A 215 ASP cc_start: 0.8094 (t0) cc_final: 0.7695 (t0) REVERT: A 257 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8570 (mt) REVERT: A 290 MET cc_start: 0.8756 (mtm) cc_final: 0.8447 (mtm) REVERT: A 309 GLU cc_start: 0.8344 (tt0) cc_final: 0.7744 (tp30) REVERT: A 312 GLN cc_start: 0.8161 (mm110) cc_final: 0.7863 (mm110) REVERT: B 262 LEU cc_start: 0.8471 (tt) cc_final: 0.7967 (mt) REVERT: B 326 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8767 (tppt) REVERT: C 82 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7884 (tm-30) REVERT: C 330 MET cc_start: 0.8675 (ttm) cc_final: 0.8206 (ttm) REVERT: C 351 GLN cc_start: 0.7690 (mt0) cc_final: 0.7458 (mt0) REVERT: D 221 SER cc_start: 0.9008 (m) cc_final: 0.8441 (p) REVERT: D 321 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6974 (mm-30) REVERT: D 330 MET cc_start: 0.8581 (ttm) cc_final: 0.8241 (ttm) REVERT: E 218 VAL cc_start: 0.9162 (OUTLIER) cc_final: 0.8865 (p) REVERT: E 236 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8166 (pm20) REVERT: E 282 ASN cc_start: 0.8797 (t0) cc_final: 0.8499 (t0) REVERT: E 330 MET cc_start: 0.8935 (mtp) cc_final: 0.8729 (mmm) REVERT: E 360 GLU cc_start: 0.8234 (tp30) cc_final: 0.7731 (tp30) REVERT: E 488 VAL cc_start: 0.8995 (t) cc_final: 0.8676 (p) REVERT: F 191 MET cc_start: 0.9075 (ptp) cc_final: 0.8840 (mtm) REVERT: G 330 MET cc_start: 0.8022 (ttm) cc_final: 0.7516 (ttm) REVERT: H 95 ASP cc_start: 0.8961 (m-30) cc_final: 0.8682 (m-30) REVERT: I 14 ASP cc_start: 0.8698 (p0) cc_final: 0.8095 (p0) REVERT: I 19 GLU cc_start: 0.8271 (mm-30) cc_final: 0.8009 (mm-30) REVERT: I 61 GLN cc_start: 0.8613 (mp10) cc_final: 0.8141 (mp10) REVERT: L 4 GLN cc_start: 0.8421 (tp40) cc_final: 0.7375 (mp10) REVERT: L 32 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7617 (ppp) REVERT: M 43 GLN cc_start: 0.8654 (mp10) cc_final: 0.8387 (mp10) REVERT: M 69 ASP cc_start: 0.9078 (m-30) cc_final: 0.8801 (m-30) REVERT: M 87 ASP cc_start: 0.8575 (p0) cc_final: 0.8086 (m-30) outliers start: 42 outliers final: 29 residues processed: 341 average time/residue: 0.4005 time to fit residues: 228.2279 Evaluate side-chains 334 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 301 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 432 ASN Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain N residue 32 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 22 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 326 optimal weight: 0.9990 chunk 315 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 370 optimal weight: 0.9980 chunk 289 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.076212 restraints weight = 64351.695| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.65 r_work: 0.2855 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33362 Z= 0.117 Angle : 0.491 12.382 45031 Z= 0.258 Chirality : 0.042 0.193 5425 Planarity : 0.003 0.037 5768 Dihedral : 6.463 65.989 4837 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.10 % Allowed : 10.34 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.69 (0.13), residues: 4361 helix: 2.69 (0.11), residues: 2030 sheet: 0.88 (0.22), residues: 567 loop : -0.72 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 42 HIS 0.002 0.001 HIS G 241 PHE 0.012 0.001 PHE F 279 TYR 0.011 0.001 TYR A 64 ARG 0.004 0.000 ARG B 367 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 1852) hydrogen bonds : angle 4.00420 ( 5409) covalent geometry : bond 0.00272 (33362) covalent geometry : angle 0.49115 (45031) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8722 Ramachandran restraints generated. 4361 Oldfield, 0 Emsley, 4361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 305 time to evaluate : 4.172 Fit side-chains REVERT: A 74 ASP cc_start: 0.8676 (t0) cc_final: 0.8106 (m-30) REVERT: A 201 TYR cc_start: 0.7959 (m-80) cc_final: 0.7591 (m-80) REVERT: A 215 ASP cc_start: 0.8090 (t0) cc_final: 0.7717 (t0) REVERT: A 257 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8557 (mt) REVERT: A 290 MET cc_start: 0.8761 (mtm) cc_final: 0.8448 (mtm) REVERT: A 309 GLU cc_start: 0.8342 (tt0) cc_final: 0.7749 (tp30) REVERT: B 262 LEU cc_start: 0.8462 (tt) cc_final: 0.7961 (mt) REVERT: B 290 MET cc_start: 0.8934 (mtm) cc_final: 0.8349 (mtm) REVERT: B 326 LYS cc_start: 0.9131 (ttmt) cc_final: 0.8785 (tppt) REVERT: C 82 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7869 (tm-30) REVERT: C 330 MET cc_start: 0.8673 (ttm) cc_final: 0.8202 (ttm) REVERT: C 351 GLN cc_start: 0.7673 (mt0) cc_final: 0.7452 (mt0) REVERT: D 221 SER cc_start: 0.9001 (m) cc_final: 0.8428 (p) REVERT: D 321 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6982 (mm-30) REVERT: D 330 MET cc_start: 0.8582 (ttm) cc_final: 0.8238 (ttm) REVERT: E 218 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8853 (p) REVERT: E 236 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8183 (pm20) REVERT: E 282 ASN cc_start: 0.8792 (t0) cc_final: 0.8495 (t0) REVERT: E 330 MET cc_start: 0.8934 (mtp) cc_final: 0.8721 (mmm) REVERT: E 360 GLU cc_start: 0.8233 (tp30) cc_final: 0.7729 (tp30) REVERT: E 488 VAL cc_start: 0.8959 (t) cc_final: 0.8636 (p) REVERT: G 330 MET cc_start: 0.8035 (ttm) cc_final: 0.7366 (tpp) REVERT: H 95 ASP cc_start: 0.8952 (m-30) cc_final: 0.8685 (m-30) REVERT: I 19 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8027 (mm-30) REVERT: I 61 GLN cc_start: 0.8581 (mp10) cc_final: 0.8104 (mp10) REVERT: K 32 MET cc_start: 0.8675 (ptm) cc_final: 0.8203 (ptp) REVERT: K 93 ASP cc_start: 0.9123 (t0) cc_final: 0.8898 (t0) REVERT: L 4 GLN cc_start: 0.8434 (tp40) cc_final: 0.7386 (mp10) REVERT: L 32 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7579 (ppp) REVERT: M 43 GLN cc_start: 0.8600 (mp10) cc_final: 0.8341 (mp10) REVERT: M 69 ASP cc_start: 0.9079 (m-30) cc_final: 0.8802 (m-30) REVERT: M 87 ASP cc_start: 0.8608 (p0) cc_final: 0.8103 (m-30) outliers start: 39 outliers final: 31 residues processed: 331 average time/residue: 0.4159 time to fit residues: 231.3379 Evaluate side-chains 338 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 303 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 432 ASN Chi-restraints excluded: chain D residue 246 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 87 ASP Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 60 ILE Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 60 ILE Chi-restraints excluded: chain N residue 32 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 78 optimal weight: 6.9990 chunk 389 optimal weight: 0.0270 chunk 4 optimal weight: 4.9990 chunk 354 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 387 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 213 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.077049 restraints weight = 63265.313| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.61 r_work: 0.2870 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 33362 Z= 0.108 Angle : 0.481 11.934 45031 Z= 0.253 Chirality : 0.042 0.189 5425 Planarity : 0.003 0.037 5768 Dihedral : 6.318 65.553 4837 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.04 % Allowed : 10.43 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.71 (0.13), residues: 4361 helix: 2.70 (0.11), residues: 2030 sheet: 0.90 (0.22), residues: 567 loop : -0.71 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 42 HIS 0.002 0.000 HIS B 314 PHE 0.009 0.001 PHE F 193 TYR 0.010 0.001 TYR A 64 ARG 0.004 0.000 ARG N 92 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 1852) hydrogen bonds : angle 3.97135 ( 5409) covalent geometry : bond 0.00247 (33362) covalent geometry : angle 0.48088 (45031) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15304.65 seconds wall clock time: 265 minutes 58.18 seconds (15958.18 seconds total)