Starting phenix.real_space_refine on Tue Aug 26 03:42:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g7o_29818/08_2025/8g7o_29818.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g7o_29818/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8g7o_29818/08_2025/8g7o_29818.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g7o_29818/08_2025/8g7o_29818.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g7o_29818/08_2025/8g7o_29818.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g7o_29818/08_2025/8g7o_29818.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 7.05, per 1000 atoms: 0.21 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: 2.46 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.25 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: 6.68 Time building geometry restraints manager: 3.16 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: 0.02 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.980 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.140 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (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 ARG 0.012 0.000 ARG F 95 TYR 0.012 0.001 TYR A 64 PHE 0.006 0.001 PHE F 279 TRP 0.005 0.001 TRP E 42 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00310 (33362) covalent geometry : angle 0.57150 (45031) hydrogen bonds : bond 0.15529 ( 1852) hydrogen bonds : angle 6.05076 ( 5409) *********************** 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 : 1.352 Fit side-chains revert: symmetry clash 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: 0.8636 (mt) REVERT: A 290 MET cc_start: 0.8715 (mtm) cc_final: 0.8378 (mtt) REVERT: A 309 GLU cc_start: 0.7789 (tt0) cc_final: 0.7391 (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: 0.8897 (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: 0.8709 (tppt) REVERT: D 330 MET cc_start: 0.8270 (ttm) cc_final: 0.7983 (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: 0.8263 (mtp) REVERT: E 223 LYS cc_start: 0.8988 (pttt) cc_final: 0.8477 (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: 0.8368 (mm-40) REVERT: H 61 GLN cc_start: 0.7538 (tm-30) cc_final: 0.7330 (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: 0.7683 (mp10) REVERT: N 51 SER cc_start: 0.9239 (m) cc_final: 0.9014 (p) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.1812 time to fit residues: 125.5999 Evaluate side-chains 333 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN C 80 ASN D 80 ASN D 314 HIS E 340 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.103988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.072740 restraints weight = 64246.444| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.62 r_work: 0.2785 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 33362 Z= 0.226 Angle : 0.571 7.084 45031 Z= 0.305 Chirality : 0.045 0.201 5425 Planarity : 0.004 0.046 5768 Dihedral : 8.862 89.456 4837 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.70 % Allowed : 5.47 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.12), residues: 4361 helix: 2.36 (0.11), residues: 2023 sheet: 0.89 (0.21), residues: 553 loop : -0.63 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 7 TYR 0.015 0.001 TYR A 64 PHE 0.011 0.002 PHE N 6 TRP 0.003 0.001 TRP E 42 HIS 0.007 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00551 (33362) covalent geometry : angle 0.57122 (45031) hydrogen bonds : bond 0.06059 ( 1852) hydrogen bonds : angle 4.81455 ( 5409) *********************** 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 370 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 345 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8756 (t0) cc_final: 0.8257 (m-30) REVERT: A 215 ASP cc_start: 0.8271 (t0) cc_final: 0.7967 (t0) REVERT: A 257 LEU cc_start: 0.8886 (tt) cc_final: 0.8573 (mt) REVERT: A 290 MET cc_start: 0.8850 (mtm) cc_final: 0.8539 (mtt) REVERT: A 451 MET cc_start: 0.8907 (mtt) cc_final: 0.8684 (mtm) REVERT: B 3 ASP cc_start: 0.8745 (t0) cc_final: 0.8484 (t0) REVERT: B 281 ASP cc_start: 0.8695 (t70) cc_final: 0.8476 (t0) REVERT: C 330 MET cc_start: 0.8871 (ttm) cc_final: 0.8318 (ttm) REVERT: D 241 HIS cc_start: 0.8310 (m90) cc_final: 0.8038 (m-70) REVERT: D 321 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6769 (mm-30) REVERT: D 326 LYS cc_start: 0.9187 (tppt) cc_final: 0.8806 (tppt) REVERT: D 330 MET cc_start: 0.8680 (ttm) cc_final: 0.8256 (ttm) REVERT: D 358 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8178 (mm-30) REVERT: E 218 VAL cc_start: 0.9292 (t) cc_final: 0.8985 (p) REVERT: E 330 MET cc_start: 0.9009 (mtp) cc_final: 0.8574 (mmm) REVERT: G 218 VAL cc_start: 0.9279 (t) cc_final: 0.8882 (p) REVERT: G 290 MET cc_start: 0.8867 (mtm) cc_final: 0.8143 (mpp) REVERT: G 330 MET cc_start: 0.8136 (ttm) cc_final: 0.7639 (ttm) REVERT: H 95 ASP cc_start: 0.9108 (m-30) cc_final: 0.8739 (m-30) REVERT: I 32 MET cc_start: 0.8827 (mpp) cc_final: 0.8594 (mpp) REVERT: I 43 GLN cc_start: 0.8592 (mp10) cc_final: 0.8328 (mp10) REVERT: J 93 ASP cc_start: 0.8844 (t70) cc_final: 0.8643 (t0) REVERT: K 15 ARG cc_start: 0.7980 (mtt90) cc_final: 0.7490 (mtt90) REVERT: L 4 GLN cc_start: 0.8257 (tp40) cc_final: 0.7344 (mp10) REVERT: L 32 MET cc_start: 0.8468 (ppp) cc_final: 0.8056 (ppp) REVERT: N 51 SER cc_start: 0.9195 (m) cc_final: 0.8987 (p) outliers start: 25 outliers final: 14 residues processed: 359 average time/residue: 0.1757 time to fit residues: 105.0910 Evaluate side-chains 326 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 312 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 307 ASN Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 371 LEU Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 84 ASP 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 337 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 394 optimal weight: 8.9990 chunk 203 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 401 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.106009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.074731 restraints weight = 64503.607| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.66 r_work: 0.2829 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33362 Z= 0.128 Angle : 0.487 8.011 45031 Z= 0.261 Chirality : 0.042 0.158 5425 Planarity : 0.003 0.042 5768 Dihedral : 8.242 79.983 4837 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.70 % Allowed : 7.30 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.13), residues: 4361 helix: 2.51 (0.11), residues: 2030 sheet: 0.80 (0.22), residues: 567 loop : -0.68 (0.13), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 92 TYR 0.011 0.001 TYR D 201 PHE 0.012 0.001 PHE F 193 TRP 0.005 0.001 TRP E 42 HIS 0.009 0.001 HIS D 314 Details of bonding type rmsd covalent geometry : bond 0.00299 (33362) covalent geometry : angle 0.48692 (45031) hydrogen bonds : bond 0.04738 ( 1852) hydrogen bonds : angle 4.40005 ( 5409) *********************** 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 363 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 338 time to evaluate : 1.602 Fit side-chains REVERT: A 74 ASP cc_start: 0.8735 (t0) cc_final: 0.8208 (m-30) REVERT: A 215 ASP cc_start: 0.8150 (t0) cc_final: 0.7795 (t0) REVERT: A 257 LEU cc_start: 0.8864 (tt) cc_final: 0.8557 (mt) REVERT: A 290 MET cc_start: 0.8782 (mtm) cc_final: 0.8469 (mtm) REVERT: B 3 ASP cc_start: 0.8690 (t0) cc_final: 0.8321 (t0) REVERT: C 251 ASP cc_start: 0.8422 (t0) cc_final: 0.8012 (t0) REVERT: C 330 MET cc_start: 0.8849 (ttm) cc_final: 0.8339 (ttm) REVERT: D 241 HIS cc_start: 0.8233 (m90) cc_final: 0.7943 (m-70) REVERT: D 321 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6773 (mm-30) REVERT: D 330 MET cc_start: 0.8662 (ttm) cc_final: 0.8261 (ttm) REVERT: D 358 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7708 (pm20) REVERT: E 218 VAL cc_start: 0.9193 (t) cc_final: 0.8914 (p) REVERT: E 282 ASN cc_start: 0.8844 (t0) cc_final: 0.8532 (t0) REVERT: E 330 MET cc_start: 0.8986 (mtp) cc_final: 0.8683 (mmm) REVERT: E 360 GLU cc_start: 0.8257 (tp30) cc_final: 0.7762 (tp30) REVERT: F 309 GLU cc_start: 0.8719 (mp0) cc_final: 0.8467 (mp0) REVERT: G 218 VAL cc_start: 0.9246 (t) cc_final: 0.8854 (p) REVERT: G 330 MET cc_start: 0.8078 (ttm) cc_final: 0.7574 (ttm) REVERT: H 35 GLU cc_start: 0.8055 (tp30) cc_final: 0.7759 (tp30) REVERT: H 95 ASP cc_start: 0.9080 (m-30) cc_final: 0.8698 (m-30) REVERT: I 43 GLN cc_start: 0.8606 (mp10) cc_final: 0.8386 (mp10) REVERT: I 69 ASP cc_start: 0.8062 (m-30) cc_final: 0.7765 (p0) REVERT: J 93 ASP cc_start: 0.8784 (t70) cc_final: 0.8549 (t0) REVERT: L 4 GLN cc_start: 0.8282 (tp40) cc_final: 0.7305 (mp10) REVERT: L 51 SER cc_start: 0.8514 (t) cc_final: 0.8235 (m) REVERT: N 24 GLU cc_start: 0.8354 (pm20) cc_final: 0.8103 (pm20) REVERT: N 51 SER cc_start: 0.9182 (m) cc_final: 0.8971 (p) outliers start: 25 outliers final: 12 residues processed: 352 average time/residue: 0.1998 time to fit residues: 116.5983 Evaluate side-chains 324 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 312 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU 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 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 J residue 66 LYS Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain M residue 51 SER Chi-restraints excluded: chain M residue 60 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 391 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 320 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 294 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 306 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 272 optimal weight: 0.9990 chunk 312 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.074751 restraints weight = 63448.691| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.59 r_work: 0.2825 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33362 Z= 0.140 Angle : 0.483 8.018 45031 Z= 0.258 Chirality : 0.042 0.143 5425 Planarity : 0.003 0.039 5768 Dihedral : 7.766 75.954 4837 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.10 % Allowed : 7.95 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.12), residues: 4361 helix: 2.54 (0.11), residues: 2030 sheet: 0.90 (0.22), residues: 546 loop : -0.75 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 92 TYR 0.010 0.001 TYR A 64 PHE 0.011 0.001 PHE D 279 TRP 0.006 0.001 TRP E 42 HIS 0.002 0.001 HIS G 241 Details of bonding type rmsd covalent geometry : bond 0.00332 (33362) covalent geometry : angle 0.48278 (45031) hydrogen bonds : bond 0.04686 ( 1852) hydrogen bonds : angle 4.26475 ( 5409) *********************** 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 362 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 323 time to evaluate : 1.300 Fit side-chains REVERT: A 74 ASP cc_start: 0.8745 (t0) cc_final: 0.8229 (m-30) REVERT: A 215 ASP cc_start: 0.8155 (t0) cc_final: 0.7814 (t0) REVERT: A 290 MET cc_start: 0.8765 (mtm) cc_final: 0.8461 (mtm) REVERT: D 241 HIS cc_start: 0.8215 (m90) cc_final: 0.7920 (m-70) REVERT: D 321 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6750 (mm-30) REVERT: D 330 MET cc_start: 0.8662 (ttm) cc_final: 0.8267 (ttm) REVERT: D 358 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7731 (pm20) REVERT: E 218 VAL cc_start: 0.9181 (t) cc_final: 0.8901 (p) REVERT: E 236 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8179 (pm20) REVERT: E 282 ASN cc_start: 0.8864 (t0) cc_final: 0.8574 (t0) REVERT: E 330 MET cc_start: 0.8961 (mtp) cc_final: 0.8716 (mmm) REVERT: E 360 GLU cc_start: 0.8281 (tp30) cc_final: 0.7792 (tp30) REVERT: G 218 VAL cc_start: 0.9273 (t) cc_final: 0.8806 (p) REVERT: G 330 MET cc_start: 0.8060 (ttm) cc_final: 0.7570 (ttm) REVERT: G 337 ASP cc_start: 0.6556 (t0) cc_final: 0.6330 (t0) REVERT: H 35 GLU cc_start: 0.8181 (tp30) cc_final: 0.7881 (tp30) REVERT: H 61 GLN cc_start: 0.7127 (tp40) cc_final: 0.6729 (tp40) REVERT: H 95 ASP cc_start: 0.9053 (m-30) cc_final: 0.8680 (m-30) REVERT: I 32 MET cc_start: 0.8847 (mpp) cc_final: 0.8635 (mpp) REVERT: K 76 TYR cc_start: 0.8030 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: L 4 GLN cc_start: 0.8331 (tp40) cc_final: 0.7306 (mp10) REVERT: L 51 SER cc_start: 0.8569 (t) cc_final: 0.8336 (m) REVERT: M 43 GLN cc_start: 0.8515 (mp10) cc_final: 0.8266 (mp10) REVERT: M 75 GLU cc_start: 0.8907 (pm20) cc_final: 0.8607 (pm20) REVERT: M 87 ASP cc_start: 0.8604 (p0) cc_final: 0.8071 (m-30) REVERT: N 24 GLU cc_start: 0.8439 (pm20) cc_final: 0.8229 (pm20) REVERT: N 51 SER cc_start: 0.9191 (m) cc_final: 0.8989 (p) outliers start: 39 outliers final: 20 residues processed: 349 average time/residue: 0.1896 time to fit residues: 111.2682 Evaluate side-chains 320 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 298 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 229 GLN 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 236 GLU 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 66 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 76 TYR Chi-restraints excluded: chain L residue 32 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 218 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 319 optimal weight: 0.5980 chunk 288 optimal weight: 0.6980 chunk 419 optimal weight: 0.9990 chunk 366 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 chunk 327 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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** H 4 GLN I 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.107508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.076541 restraints weight = 63605.406| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.63 r_work: 0.2859 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 33362 Z= 0.106 Angle : 0.461 8.907 45031 Z= 0.246 Chirality : 0.041 0.208 5425 Planarity : 0.003 0.038 5768 Dihedral : 7.063 71.712 4837 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.10 % Allowed : 8.65 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.13), residues: 4361 helix: 2.68 (0.11), residues: 2030 sheet: 0.99 (0.22), residues: 546 loop : -0.74 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 7 TYR 0.016 0.001 TYR B 197 PHE 0.013 0.001 PHE F 193 TRP 0.010 0.001 TRP B 42 HIS 0.002 0.001 HIS G 241 Details of bonding type rmsd covalent geometry : bond 0.00239 (33362) covalent geometry : angle 0.46083 (45031) hydrogen bonds : bond 0.03956 ( 1852) hydrogen bonds : angle 4.08908 ( 5409) *********************** 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 366 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 327 time to evaluate : 1.340 Fit side-chains REVERT: A 74 ASP cc_start: 0.8683 (t0) cc_final: 0.8113 (m-30) REVERT: A 215 ASP cc_start: 0.8122 (t0) cc_final: 0.7737 (t0) REVERT: A 290 MET cc_start: 0.8751 (mtm) cc_final: 0.8431 (mtm) REVERT: D 241 HIS cc_start: 0.8084 (m90) cc_final: 0.7760 (m-70) REVERT: D 330 MET cc_start: 0.8684 (ttm) cc_final: 0.8295 (ttm) REVERT: D 358 GLU cc_start: 0.8588 (mm-30) cc_final: 0.7788 (pm20) REVERT: E 236 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8167 (pm20) REVERT: E 282 ASN cc_start: 0.8856 (t0) cc_final: 0.8557 (t0) REVERT: E 330 MET cc_start: 0.8914 (mtp) cc_final: 0.8704 (mmm) REVERT: E 360 GLU cc_start: 0.8235 (tp30) cc_final: 0.7739 (tp30) REVERT: G 218 VAL cc_start: 0.9235 (t) cc_final: 0.8844 (p) REVERT: G 330 MET cc_start: 0.8027 (ttm) cc_final: 0.7543 (ttm) REVERT: H 35 GLU cc_start: 0.8175 (tp30) cc_final: 0.7816 (tp30) REVERT: H 61 GLN cc_start: 0.7319 (tp40) cc_final: 0.7108 (tp40) REVERT: H 95 ASP cc_start: 0.8991 (m-30) cc_final: 0.8638 (m-30) REVERT: K 4 GLN cc_start: 0.8554 (tp-100) cc_final: 0.8232 (tp-100) REVERT: K 76 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: L 4 GLN cc_start: 0.8369 (tp40) cc_final: 0.7322 (mp10) REVERT: L 32 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7751 (ppp) REVERT: L 51 SER cc_start: 0.8636 (t) cc_final: 0.8391 (m) REVERT: M 43 GLN cc_start: 0.8533 (mp10) cc_final: 0.8259 (mp10) REVERT: M 69 ASP cc_start: 0.9040 (m-30) cc_final: 0.8795 (m-30) REVERT: M 87 ASP cc_start: 0.8567 (p0) cc_final: 0.8051 (m-30) REVERT: N 51 SER cc_start: 0.9192 (m) cc_final: 0.8986 (p) outliers start: 39 outliers final: 18 residues processed: 351 average time/residue: 0.1733 time to fit residues: 102.7558 Evaluate side-chains 326 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 305 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 39 GLU 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 236 GLU Chi-restraints excluded: chain E residue 523 ILE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 97 LEU 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 N residue 32 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 107 optimal weight: 0.0770 chunk 129 optimal weight: 0.8980 chunk 85 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 299 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- 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** H 4 GLN K 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.105714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.074639 restraints weight = 63772.713| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.61 r_work: 0.2822 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33362 Z= 0.150 Angle : 0.490 8.287 45031 Z= 0.260 Chirality : 0.042 0.196 5425 Planarity : 0.003 0.037 5768 Dihedral : 7.102 70.155 4837 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.27 % Allowed : 8.99 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.13), residues: 4361 helix: 2.62 (0.11), residues: 2030 sheet: 0.96 (0.22), residues: 546 loop : -0.78 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 7 TYR 0.010 0.001 TYR A 64 PHE 0.016 0.001 PHE B 213 TRP 0.009 0.001 TRP B 42 HIS 0.008 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00361 (33362) covalent geometry : angle 0.48985 (45031) hydrogen bonds : bond 0.04637 ( 1852) hydrogen bonds : angle 4.15241 ( 5409) *********************** 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 364 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 319 time to evaluate : 0.995 Fit side-chains REVERT: A 74 ASP cc_start: 0.8730 (t0) cc_final: 0.8190 (m-30) REVERT: A 215 ASP cc_start: 0.8185 (t0) cc_final: 0.7825 (t0) REVERT: A 257 LEU cc_start: 0.8880 (tp) cc_final: 0.8618 (mt) REVERT: A 290 MET cc_start: 0.8780 (mtm) cc_final: 0.8463 (mtm) REVERT: A 312 GLN cc_start: 0.8185 (mm110) cc_final: 0.7881 (mm110) REVERT: D 241 HIS cc_start: 0.8075 (m90) cc_final: 0.7751 (m-70) REVERT: D 321 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6903 (mm-30) REVERT: D 330 MET cc_start: 0.8668 (ttm) cc_final: 0.8268 (ttm) REVERT: D 358 GLU cc_start: 0.8636 (mm-30) cc_final: 0.7801 (pm20) REVERT: E 236 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8174 (pm20) REVERT: E 282 ASN cc_start: 0.8827 (t0) cc_final: 0.8514 (t0) REVERT: E 330 MET cc_start: 0.8930 (mtp) cc_final: 0.8693 (mmm) REVERT: E 360 GLU cc_start: 0.8221 (tp30) cc_final: 0.7726 (tp30) REVERT: G 330 MET cc_start: 0.8042 (ttm) cc_final: 0.7562 (ttm) REVERT: H 95 ASP cc_start: 0.8984 (m-30) cc_final: 0.8654 (m-30) REVERT: I 32 MET cc_start: 0.8828 (mpp) cc_final: 0.8628 (mpp) REVERT: K 76 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7709 (m-80) REVERT: L 4 GLN cc_start: 0.8383 (tp40) cc_final: 0.7356 (mp10) REVERT: L 32 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7708 (ppp) REVERT: L 51 SER cc_start: 0.8664 (t) cc_final: 0.8417 (m) REVERT: M 7 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8063 (mtp85) REVERT: M 43 GLN cc_start: 0.8599 (mp10) cc_final: 0.8318 (mp10) REVERT: M 69 ASP cc_start: 0.9061 (m-30) cc_final: 0.8792 (m-30) REVERT: M 87 ASP cc_start: 0.8569 (p0) cc_final: 0.8067 (m-30) outliers start: 45 outliers final: 25 residues processed: 349 average time/residue: 0.1833 time to fit residues: 107.3838 Evaluate side-chains 330 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 302 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL 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 267 VAL 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 219 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL 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 66 LYS Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 76 TYR Chi-restraints excluded: chain K residue 84 ASP 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 300 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 396 optimal weight: 0.0870 chunk 321 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 337 optimal weight: 6.9990 chunk 253 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 375 optimal weight: 10.0000 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN 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 = 0.3513 r_free = 0.3513 target = 0.108411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.077536 restraints weight = 63541.123| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.62 r_work: 0.2879 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2034 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= 0.099 Angle : 0.465 8.186 45031 Z= 0.247 Chirality : 0.041 0.172 5425 Planarity : 0.003 0.038 5768 Dihedral : 6.563 67.526 4837 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.96 % Allowed : 9.81 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.13), residues: 4361 helix: 2.75 (0.11), residues: 2030 sheet: 1.06 (0.23), residues: 546 loop : -0.74 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 367 TYR 0.008 0.001 TYR A 64 PHE 0.017 0.001 PHE C 213 TRP 0.009 0.001 TRP E 42 HIS 0.008 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00214 (33362) covalent geometry : angle 0.46507 (45031) hydrogen bonds : bond 0.03624 ( 1852) hydrogen bonds : angle 3.98536 ( 5409) *********************** 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 357 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 323 time to evaluate : 1.322 Fit side-chains REVERT: A 74 ASP cc_start: 0.8672 (t0) cc_final: 0.8112 (m-30) REVERT: A 201 TYR cc_start: 0.7908 (m-80) cc_final: 0.7547 (m-80) REVERT: A 215 ASP cc_start: 0.8070 (t0) cc_final: 0.7697 (t0) REVERT: A 257 LEU cc_start: 0.8857 (tp) cc_final: 0.8614 (mt) REVERT: A 290 MET cc_start: 0.8735 (mtm) cc_final: 0.8406 (mtm) REVERT: A 312 GLN cc_start: 0.8162 (mm110) cc_final: 0.7834 (mm110) REVERT: B 290 MET cc_start: 0.8841 (mtt) cc_final: 0.8467 (mtm) REVERT: D 221 SER cc_start: 0.8998 (m) cc_final: 0.8415 (p) REVERT: D 330 MET cc_start: 0.8647 (ttm) cc_final: 0.8247 (ttm) REVERT: D 358 GLU cc_start: 0.8636 (mm-30) cc_final: 0.7861 (pm20) REVERT: E 236 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: E 282 ASN cc_start: 0.8848 (t0) cc_final: 0.8562 (t0) REVERT: E 330 MET cc_start: 0.8934 (mtp) cc_final: 0.8722 (mmm) REVERT: E 360 GLU cc_start: 0.8209 (tp30) cc_final: 0.7733 (tp30) REVERT: G 330 MET cc_start: 0.8019 (ttm) cc_final: 0.7514 (ttm) REVERT: H 19 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8279 (pt0) REVERT: H 61 GLN cc_start: 0.6926 (tp40) cc_final: 0.6563 (tp40) REVERT: H 95 ASP cc_start: 0.8968 (m-30) cc_final: 0.8650 (m-30) REVERT: I 19 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8043 (mm-30) REVERT: I 32 MET cc_start: 0.8829 (mpp) cc_final: 0.8623 (mpp) REVERT: K 4 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8361 (tp-100) REVERT: K 32 MET cc_start: 0.8641 (ptm) cc_final: 0.8283 (ptp) REVERT: K 76 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7708 (m-80) REVERT: L 4 GLN cc_start: 0.8417 (tp40) cc_final: 0.7381 (mp10) REVERT: L 32 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7617 (ppp) REVERT: M 7 ARG cc_start: 0.8291 (mtp85) cc_final: 0.8053 (mtp85) REVERT: M 43 GLN cc_start: 0.8615 (mp10) cc_final: 0.8322 (mp10) REVERT: M 69 ASP cc_start: 0.9080 (m-30) cc_final: 0.8846 (m-30) REVERT: M 87 ASP cc_start: 0.8559 (p0) cc_final: 0.8057 (m-30) outliers start: 34 outliers final: 22 residues processed: 344 average time/residue: 0.2001 time to fit residues: 116.0274 Evaluate side-chains 327 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 301 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 267 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain D residue 19 ASP 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 219 LEU 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 310 ASP Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 76 TYR Chi-restraints excluded: chain K residue 84 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 182 optimal weight: 5.9990 chunk 347 optimal weight: 5.9990 chunk 367 optimal weight: 7.9990 chunk 352 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 251 optimal weight: 0.0270 chunk 193 optimal weight: 3.9990 chunk 332 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 GLN D 80 ASN ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN F 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.076077 restraints weight = 63668.572| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.62 r_work: 0.2850 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2070 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= 0.121 Angle : 0.477 8.739 45031 Z= 0.252 Chirality : 0.042 0.168 5425 Planarity : 0.003 0.038 5768 Dihedral : 6.563 66.868 4837 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.24 % Allowed : 10.28 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.13), residues: 4361 helix: 2.72 (0.11), residues: 2030 sheet: 1.06 (0.23), residues: 546 loop : -0.75 (0.13), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 367 TYR 0.010 0.001 TYR A 64 PHE 0.010 0.001 PHE B 213 TRP 0.009 0.001 TRP E 42 HIS 0.008 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00283 (33362) covalent geometry : angle 0.47729 (45031) hydrogen bonds : bond 0.04105 ( 1852) hydrogen bonds : angle 4.00513 ( 5409) *********************** 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 348 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 1.074 Fit side-chains REVERT: A 74 ASP cc_start: 0.8686 (t0) cc_final: 0.8116 (m-30) REVERT: A 201 TYR cc_start: 0.7962 (m-80) cc_final: 0.7592 (m-80) REVERT: A 215 ASP cc_start: 0.8136 (t0) cc_final: 0.7796 (t0) REVERT: A 257 LEU cc_start: 0.8870 (tp) cc_final: 0.8634 (mt) REVERT: A 290 MET cc_start: 0.8769 (mtm) cc_final: 0.8443 (mtm) REVERT: A 312 GLN cc_start: 0.8175 (mm110) cc_final: 0.7835 (mm110) REVERT: D 221 SER cc_start: 0.9003 (m) cc_final: 0.8426 (p) REVERT: D 330 MET cc_start: 0.8652 (ttm) cc_final: 0.8247 (ttm) REVERT: D 358 GLU cc_start: 0.8639 (mm-30) cc_final: 0.7850 (pm20) REVERT: E 236 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8176 (pm20) REVERT: E 282 ASN cc_start: 0.8808 (t0) cc_final: 0.8507 (t0) REVERT: E 330 MET cc_start: 0.8922 (mtp) cc_final: 0.8709 (mmm) REVERT: E 360 GLU cc_start: 0.8253 (tp30) cc_final: 0.7732 (tp30) REVERT: G 330 MET cc_start: 0.8043 (ttm) cc_final: 0.7537 (ttm) REVERT: H 19 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8279 (pt0) REVERT: H 61 GLN cc_start: 0.6963 (tp40) cc_final: 0.6599 (tp40) REVERT: H 95 ASP cc_start: 0.8966 (m-30) cc_final: 0.8650 (m-30) REVERT: K 4 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8312 (tp-100) REVERT: K 32 MET cc_start: 0.8737 (ptm) cc_final: 0.8328 (ptp) REVERT: K 76 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7735 (m-80) REVERT: L 4 GLN cc_start: 0.8400 (tp40) cc_final: 0.7343 (mp10) REVERT: L 32 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7589 (ppp) REVERT: M 7 ARG cc_start: 0.8329 (mtp85) cc_final: 0.8108 (mtp85) REVERT: M 43 GLN cc_start: 0.8634 (mp10) cc_final: 0.8340 (mp10) REVERT: M 69 ASP cc_start: 0.9091 (m-30) cc_final: 0.8844 (m-30) REVERT: M 87 ASP cc_start: 0.8568 (p0) cc_final: 0.8065 (m-30) outliers start: 44 outliers final: 30 residues processed: 335 average time/residue: 0.1830 time to fit residues: 103.0469 Evaluate side-chains 334 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL 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 267 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 19 ASP 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 219 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 85 ASP 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 N residue 32 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 157 optimal weight: 0.9980 chunk 340 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 386 optimal weight: 4.9990 chunk 389 optimal weight: 0.0050 chunk 112 optimal weight: 1.9990 chunk 211 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 414 optimal weight: 0.9980 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 = 0.3512 r_free = 0.3512 target = 0.108339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.077492 restraints weight = 63364.122| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.62 r_work: 0.2877 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33362 Z= 0.102 Angle : 0.468 8.799 45031 Z= 0.247 Chirality : 0.041 0.158 5425 Planarity : 0.003 0.038 5768 Dihedral : 6.319 65.959 4837 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.01 % Allowed : 10.57 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.13), residues: 4361 helix: 2.76 (0.11), residues: 2030 sheet: 0.82 (0.22), residues: 581 loop : -0.71 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 367 TYR 0.010 0.001 TYR A 64 PHE 0.010 0.001 PHE A 279 TRP 0.010 0.001 TRP E 42 HIS 0.009 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00228 (33362) covalent geometry : angle 0.46789 (45031) hydrogen bonds : bond 0.03652 ( 1852) hydrogen bonds : angle 3.93977 ( 5409) *********************** 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 354 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 318 time to evaluate : 0.804 Fit side-chains REVERT: A 74 ASP cc_start: 0.8651 (t0) cc_final: 0.8067 (m-30) REVERT: A 201 TYR cc_start: 0.7869 (m-80) cc_final: 0.7533 (m-80) REVERT: A 215 ASP cc_start: 0.8059 (t0) cc_final: 0.7685 (t0) REVERT: A 257 LEU cc_start: 0.8866 (tp) cc_final: 0.8630 (mt) REVERT: A 290 MET cc_start: 0.8737 (mtm) cc_final: 0.8416 (mtm) REVERT: A 312 GLN cc_start: 0.8153 (mm110) cc_final: 0.7796 (mm110) REVERT: D 221 SER cc_start: 0.9003 (m) cc_final: 0.8427 (p) REVERT: D 330 MET cc_start: 0.8631 (ttm) cc_final: 0.8222 (ttm) REVERT: D 358 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7882 (pm20) REVERT: E 236 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: E 282 ASN cc_start: 0.8812 (t0) cc_final: 0.8523 (t0) REVERT: E 360 GLU cc_start: 0.8235 (tp30) cc_final: 0.7744 (tp30) REVERT: G 330 MET cc_start: 0.8047 (ttm) cc_final: 0.7543 (ttm) REVERT: H 19 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8285 (pt0) REVERT: H 61 GLN cc_start: 0.7000 (tp40) cc_final: 0.6643 (tp40) REVERT: H 95 ASP cc_start: 0.8956 (m-30) cc_final: 0.8655 (m-30) REVERT: I 19 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8003 (mm-30) REVERT: K 4 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8302 (tp-100) REVERT: K 32 MET cc_start: 0.8705 (ptm) cc_final: 0.8305 (ptp) REVERT: K 76 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: K 93 ASP cc_start: 0.9116 (t0) cc_final: 0.8885 (t0) REVERT: L 4 GLN cc_start: 0.8408 (tp40) cc_final: 0.7352 (mp10) REVERT: L 32 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7527 (ppp) REVERT: M 43 GLN cc_start: 0.8657 (mp10) cc_final: 0.8363 (mp10) REVERT: M 69 ASP cc_start: 0.9135 (m-30) cc_final: 0.8906 (m-30) REVERT: M 87 ASP cc_start: 0.8589 (p0) cc_final: 0.8090 (m-30) outliers start: 36 outliers final: 29 residues processed: 341 average time/residue: 0.1702 time to fit residues: 97.0968 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 : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL 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 267 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain D residue 19 ASP 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 D residue 445 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain H residue 19 GLU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain J residue 85 ASP 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 N residue 32 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 330 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 chunk 316 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 408 optimal weight: 9.9990 chunk 400 optimal weight: 0.1980 chunk 199 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.106931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.075946 restraints weight = 63877.718| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.62 r_work: 0.2850 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33362 Z= 0.128 Angle : 0.491 10.892 45031 Z= 0.257 Chirality : 0.042 0.160 5425 Planarity : 0.003 0.037 5768 Dihedral : 6.437 65.880 4837 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.24 % Allowed : 10.76 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.13), residues: 4361 helix: 2.72 (0.11), residues: 2030 sheet: 0.79 (0.22), residues: 581 loop : -0.73 (0.13), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 367 TYR 0.011 0.001 TYR A 64 PHE 0.010 0.001 PHE A 279 TRP 0.010 0.001 TRP B 42 HIS 0.009 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00304 (33362) covalent geometry : angle 0.49067 (45031) hydrogen bonds : bond 0.04178 ( 1852) hydrogen bonds : angle 4.00759 ( 5409) ********************** 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 348 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 304 time to evaluate : 1.078 Fit side-chains REVERT: A 74 ASP cc_start: 0.8685 (t0) cc_final: 0.8116 (m-30) REVERT: A 201 TYR cc_start: 0.7958 (m-80) cc_final: 0.7592 (m-80) REVERT: A 215 ASP cc_start: 0.8069 (t0) cc_final: 0.7737 (t0) REVERT: A 257 LEU cc_start: 0.8879 (tp) cc_final: 0.8638 (mt) REVERT: A 290 MET cc_start: 0.8763 (mtm) cc_final: 0.8450 (mtm) REVERT: B 290 MET cc_start: 0.8937 (mtm) cc_final: 0.8349 (mtm) REVERT: D 221 SER cc_start: 0.9016 (m) cc_final: 0.8450 (p) REVERT: D 330 MET cc_start: 0.8637 (ttm) cc_final: 0.8227 (ttm) REVERT: E 236 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: E 282 ASN cc_start: 0.8818 (t0) cc_final: 0.8525 (t0) REVERT: E 330 MET cc_start: 0.8544 (mmm) cc_final: 0.8225 (tpp) REVERT: E 360 GLU cc_start: 0.8257 (tp30) cc_final: 0.7762 (tp30) REVERT: G 330 MET cc_start: 0.8067 (ttm) cc_final: 0.7563 (ttm) REVERT: H 19 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8289 (pt0) REVERT: H 61 GLN cc_start: 0.7062 (tp40) cc_final: 0.6701 (tp40) REVERT: H 95 ASP cc_start: 0.8959 (m-30) cc_final: 0.8678 (m-30) REVERT: I 19 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8013 (mm-30) REVERT: K 32 MET cc_start: 0.8732 (ptm) cc_final: 0.8309 (ptp) REVERT: K 76 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: K 93 ASP cc_start: 0.9162 (t0) cc_final: 0.8949 (t0) REVERT: L 4 GLN cc_start: 0.8410 (tp40) cc_final: 0.7346 (mp10) REVERT: L 32 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7563 (ppp) REVERT: M 43 GLN cc_start: 0.8625 (mp10) cc_final: 0.8344 (mp10) REVERT: M 69 ASP cc_start: 0.9141 (m-30) cc_final: 0.8906 (m-30) REVERT: M 87 ASP cc_start: 0.8575 (p0) cc_final: 0.8081 (m-30) outliers start: 44 outliers final: 35 residues processed: 332 average time/residue: 0.1936 time to fit residues: 107.8613 Evaluate side-chains 339 residues out of total 3549 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 300 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL 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 267 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain D residue 19 ASP 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 D residue 445 THR Chi-restraints excluded: chain E residue 50 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 310 ASP Chi-restraints excluded: chain H residue 19 GLU 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 25 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 51 SER Chi-restraints excluded: chain K residue 76 TYR Chi-restraints excluded: chain K residue 84 ASP 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 75 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 434 random chunks: chunk 219 optimal weight: 0.9980 chunk 391 optimal weight: 0.2980 chunk 281 optimal weight: 7.9990 chunk 256 optimal weight: 1.9990 chunk 388 optimal weight: 3.9990 chunk 339 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 411 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 374 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.106674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.075439 restraints weight = 64129.573| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.65 r_work: 0.2842 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33362 Z= 0.131 Angle : 0.492 10.346 45031 Z= 0.258 Chirality : 0.042 0.159 5425 Planarity : 0.003 0.037 5768 Dihedral : 6.555 66.055 4837 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.21 % Allowed : 10.59 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.13), residues: 4361 helix: 2.71 (0.11), residues: 2023 sheet: 0.78 (0.22), residues: 581 loop : -0.74 (0.13), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 367 TYR 0.011 0.001 TYR A 64 PHE 0.013 0.001 PHE F 279 TRP 0.010 0.001 TRP B 42 HIS 0.009 0.001 HIS F 314 Details of bonding type rmsd covalent geometry : bond 0.00311 (33362) covalent geometry : angle 0.49166 (45031) hydrogen bonds : bond 0.04285 ( 1852) hydrogen bonds : angle 4.02225 ( 5409) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7643.26 seconds wall clock time: 131 minutes 33.09 seconds (7893.09 seconds total)