Starting phenix.real_space_refine on Sat Oct 11 12:33:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qi7_18436/10_2025/8qi7_18436.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qi7_18436/10_2025/8qi7_18436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qi7_18436/10_2025/8qi7_18436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qi7_18436/10_2025/8qi7_18436.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qi7_18436/10_2025/8qi7_18436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qi7_18436/10_2025/8qi7_18436.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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 4 5.49 5 S 64 5.16 5 C 9124 2.51 5 N 2596 2.21 5 O 2821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14609 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3623 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 438} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Restraints were copied for chains: D, B, C Time building chain proxies: 2.92, per 1000 atoms: 0.20 Number of scatterers: 14609 At special positions: 0 Unit cell: (124.7, 90.3, 100.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 4 15.00 O 2821 8.00 N 2596 7.00 C 9124 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: 0.95 Conformation dependent library (CDL) restraints added in 624.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 16 sheets defined 53.5% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 53 through 69 removed outlier: 3.610A pdb=" N LEU A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.794A pdb=" N ALA A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.623A pdb=" N ASN A 93 " --> pdb=" O SER A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 127 removed outlier: 4.105A pdb=" N GLU A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 removed outlier: 3.668A pdb=" N VAL A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 184 through 190 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.888A pdb=" N ARG A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.762A pdb=" N GLU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.635A pdb=" N ALA A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 261 " --> pdb=" O GLY A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.642A pdb=" N LYS A 269 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA A 271 " --> pdb=" O PHE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 320 removed outlier: 4.495A pdb=" N ARG A 314 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 removed outlier: 3.666A pdb=" N GLN A 341 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 369 removed outlier: 3.648A pdb=" N ARG A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 392 through 402 removed outlier: 3.527A pdb=" N LEU A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 437 through 459 removed outlier: 3.910A pdb=" N ARG A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 458 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 459 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.754A pdb=" N SER A 470 " --> pdb=" O GLN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 475 removed outlier: 3.653A pdb=" N LYS A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A 475 " --> pdb=" O PHE A 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 470 through 475' Processing helix chain 'A' and resid 475 through 494 removed outlier: 3.510A pdb=" N LEU A 485 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 53 through 69 removed outlier: 3.609A pdb=" N LEU D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.794A pdb=" N ALA D 87 " --> pdb=" O ALA D 83 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.623A pdb=" N ASN D 93 " --> pdb=" O SER D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 127 removed outlier: 4.105A pdb=" N GLU D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU D 124 " --> pdb=" O GLN D 120 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE D 127 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 155 removed outlier: 3.668A pdb=" N VAL D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 184 through 190 Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.888A pdb=" N ARG D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 215 " --> pdb=" O LEU D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 245 removed outlier: 3.762A pdb=" N GLU D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 261 removed outlier: 3.635A pdb=" N ALA D 260 " --> pdb=" O SER D 256 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 3.642A pdb=" N LYS D 269 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA D 271 " --> pdb=" O PHE D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 removed outlier: 4.495A pdb=" N ARG D 314 " --> pdb=" O THR D 310 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL D 319 " --> pdb=" O ILE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 342 removed outlier: 3.667A pdb=" N GLN D 341 " --> pdb=" O VAL D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 369 removed outlier: 3.648A pdb=" N ARG D 348 " --> pdb=" O THR D 344 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG D 368 " --> pdb=" O ALA D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 376 No H-bonds generated for 'chain 'D' and resid 374 through 376' Processing helix chain 'D' and resid 392 through 402 removed outlier: 3.527A pdb=" N LEU D 402 " --> pdb=" O ARG D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 435 Processing helix chain 'D' and resid 437 through 459 removed outlier: 3.910A pdb=" N ARG D 443 " --> pdb=" O ASP D 439 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 445 " --> pdb=" O PHE D 441 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP D 446 " --> pdb=" O ARG D 442 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 457 " --> pdb=" O ASN D 453 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL D 458 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS D 459 " --> pdb=" O GLY D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 470 removed outlier: 3.754A pdb=" N SER D 470 " --> pdb=" O GLN D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 475 removed outlier: 3.652A pdb=" N LYS D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP D 475 " --> pdb=" O PHE D 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 470 through 475' Processing helix chain 'D' and resid 475 through 494 removed outlier: 3.509A pdb=" N LEU D 485 " --> pdb=" O ARG D 481 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG D 488 " --> pdb=" O ASN D 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 53 through 69 removed outlier: 3.610A pdb=" N LEU B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.794A pdb=" N ALA B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.623A pdb=" N ASN B 93 " --> pdb=" O SER B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 127 removed outlier: 4.105A pdb=" N GLU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 155 removed outlier: 3.667A pdb=" N VAL B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 184 through 190 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.888A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.761A pdb=" N GLU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 261 removed outlier: 3.635A pdb=" N ALA B 260 " --> pdb=" O SER B 256 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B 261 " --> pdb=" O GLY B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.642A pdb=" N LYS B 269 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA B 271 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 320 removed outlier: 4.496A pdb=" N ARG B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 319 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 342 removed outlier: 3.666A pdb=" N GLN B 341 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 369 removed outlier: 3.648A pdb=" N ARG B 348 " --> pdb=" O THR B 344 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 392 through 402 removed outlier: 3.527A pdb=" N LEU B 402 " --> pdb=" O ARG B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 435 Processing helix chain 'B' and resid 437 through 459 removed outlier: 3.910A pdb=" N ARG B 443 " --> pdb=" O ASP B 439 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 457 " --> pdb=" O ASN B 453 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 459 " --> pdb=" O GLY B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 470 removed outlier: 3.755A pdb=" N SER B 470 " --> pdb=" O GLN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 475 removed outlier: 3.652A pdb=" N LYS B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 475 " --> pdb=" O PHE B 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 470 through 475' Processing helix chain 'B' and resid 475 through 494 removed outlier: 3.509A pdb=" N LEU B 485 " --> pdb=" O ARG B 481 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 53 through 69 removed outlier: 3.609A pdb=" N LEU C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.795A pdb=" N ALA C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.623A pdb=" N ASN C 93 " --> pdb=" O SER C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 127 removed outlier: 4.105A pdb=" N GLU C 114 " --> pdb=" O GLU C 110 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU C 124 " --> pdb=" O GLN C 120 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE C 127 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 155 removed outlier: 3.667A pdb=" N VAL C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 184 through 190 Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.887A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU C 215 " --> pdb=" O LEU C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.762A pdb=" N GLU C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 261 removed outlier: 3.635A pdb=" N ALA C 260 " --> pdb=" O SER C 256 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.643A pdb=" N LYS C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA C 271 " --> pdb=" O PHE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 320 removed outlier: 4.495A pdb=" N ARG C 314 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 319 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 342 removed outlier: 3.666A pdb=" N GLN C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 369 removed outlier: 3.649A pdb=" N ARG C 348 " --> pdb=" O THR C 344 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG C 368 " --> pdb=" O ALA C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 392 through 402 removed outlier: 3.527A pdb=" N LEU C 402 " --> pdb=" O ARG C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 437 through 459 removed outlier: 3.909A pdb=" N ARG C 443 " --> pdb=" O ASP C 439 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 445 " --> pdb=" O PHE C 441 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP C 446 " --> pdb=" O ARG C 442 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 457 " --> pdb=" O ASN C 453 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 458 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 459 " --> pdb=" O GLY C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 470 removed outlier: 3.755A pdb=" N SER C 470 " --> pdb=" O GLN C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 475 removed outlier: 3.653A pdb=" N LYS C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP C 475 " --> pdb=" O PHE C 471 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 470 through 475' Processing helix chain 'C' and resid 475 through 494 removed outlier: 3.510A pdb=" N LEU C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 removed outlier: 7.305A pdb=" N LEU A 71 " --> pdb=" O THR A 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.942A pdb=" N TYR A 100 " --> pdb=" O LYS A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 137 removed outlier: 3.652A pdb=" N ILE A 273 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE A 221 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP A 251 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ARG A 160 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ILE A 222 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N MET A 162 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY A 163 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 372 removed outlier: 3.918A pdb=" N SER A 371 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN A 408 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 71 through 72 removed outlier: 7.306A pdb=" N LEU D 71 " --> pdb=" O THR D 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.941A pdb=" N TYR D 100 " --> pdb=" O LYS D 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 134 through 137 removed outlier: 3.652A pdb=" N ILE D 273 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE D 221 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP D 251 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ARG D 160 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ILE D 222 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET D 162 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY D 163 " --> pdb=" O MET D 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 371 through 372 removed outlier: 3.918A pdb=" N SER D 371 " --> pdb=" O ASP D 385 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN D 408 " --> pdb=" O ARG D 425 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 removed outlier: 7.306A pdb=" N LEU B 71 " --> pdb=" O THR B 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.941A pdb=" N TYR B 100 " --> pdb=" O LYS B 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 134 through 137 removed outlier: 3.652A pdb=" N ILE B 273 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE B 221 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP B 251 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ARG B 160 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ILE B 222 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N MET B 162 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY B 163 " --> pdb=" O MET B 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 371 through 372 removed outlier: 3.918A pdb=" N SER B 371 " --> pdb=" O ASP B 385 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN B 408 " --> pdb=" O ARG B 425 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 removed outlier: 7.306A pdb=" N LEU C 71 " --> pdb=" O THR C 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.941A pdb=" N TYR C 100 " --> pdb=" O LYS C 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 134 through 137 removed outlier: 3.653A pdb=" N ILE C 273 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE C 221 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP C 251 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ARG C 160 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ILE C 222 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET C 162 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 163 " --> pdb=" O MET C 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 371 through 372 removed outlier: 3.918A pdb=" N SER C 371 " --> pdb=" O ASP C 385 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN C 408 " --> pdb=" O ARG C 425 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1680 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: 2.35 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2428 1.31 - 1.44: 3848 1.44 - 1.56: 8408 1.56 - 1.68: 4 1.68 - 1.81: 100 Bond restraints: 14788 Sorted by residual: bond pdb=" OP4 LLP B 280 " pdb=" P LLP B 280 " ideal model delta sigma weight residual 1.726 1.646 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C PRO D 429 " pdb=" O PRO D 429 " ideal model delta sigma weight residual 1.238 1.190 0.049 1.22e-02 6.72e+03 1.61e+01 bond pdb=" OP4 LLP D 280 " pdb=" P LLP D 280 " ideal model delta sigma weight residual 1.726 1.646 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" OP4 LLP A 280 " pdb=" P LLP A 280 " ideal model delta sigma weight residual 1.726 1.646 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" OP4 LLP C 280 " pdb=" P LLP C 280 " ideal model delta sigma weight residual 1.726 1.646 0.080 2.00e-02 2.50e+03 1.58e+01 ... (remaining 14783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 19522 1.74 - 3.48: 335 3.48 - 5.22: 119 5.22 - 6.97: 24 6.97 - 8.71: 16 Bond angle restraints: 20016 Sorted by residual: angle pdb=" CA ALA A 428 " pdb=" C ALA A 428 " pdb=" N PRO A 429 " ideal model delta sigma weight residual 118.44 125.35 -6.91 1.59e+00 3.96e-01 1.89e+01 angle pdb=" CA ALA B 428 " pdb=" C ALA B 428 " pdb=" N PRO B 429 " ideal model delta sigma weight residual 118.44 125.35 -6.91 1.59e+00 3.96e-01 1.89e+01 angle pdb=" CA ALA C 428 " pdb=" C ALA C 428 " pdb=" N PRO C 429 " ideal model delta sigma weight residual 118.44 125.34 -6.90 1.59e+00 3.96e-01 1.88e+01 angle pdb=" CA ALA D 428 " pdb=" C ALA D 428 " pdb=" N PRO D 429 " ideal model delta sigma weight residual 118.44 125.32 -6.88 1.59e+00 3.96e-01 1.87e+01 angle pdb=" CA GLY A 427 " pdb=" C GLY A 427 " pdb=" O GLY A 427 " ideal model delta sigma weight residual 121.19 117.38 3.81 9.10e-01 1.21e+00 1.75e+01 ... (remaining 20011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 8544 16.25 - 32.50: 376 32.50 - 48.75: 32 48.75 - 65.00: 4 65.00 - 81.25: 8 Dihedral angle restraints: 8964 sinusoidal: 3636 harmonic: 5328 Sorted by residual: dihedral pdb=" N HIS A 254 " pdb=" CA HIS A 254 " pdb=" CB HIS A 254 " pdb=" CG HIS A 254 " ideal model delta sinusoidal sigma weight residual -60.00 -113.75 53.75 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" N HIS B 254 " pdb=" CA HIS B 254 " pdb=" CB HIS B 254 " pdb=" CG HIS B 254 " ideal model delta sinusoidal sigma weight residual -60.00 -113.75 53.75 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" N HIS D 254 " pdb=" CA HIS D 254 " pdb=" CB HIS D 254 " pdb=" CG HIS D 254 " ideal model delta sinusoidal sigma weight residual -60.00 -113.75 53.75 3 1.50e+01 4.44e-03 9.23e+00 ... (remaining 8961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1734 0.045 - 0.091: 345 0.091 - 0.136: 103 0.136 - 0.181: 4 0.181 - 0.226: 10 Chirality restraints: 2196 Sorted by residual: chirality pdb=" CA PRO A 429 " pdb=" N PRO A 429 " pdb=" C PRO A 429 " pdb=" CB PRO A 429 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PRO B 429 " pdb=" N PRO B 429 " pdb=" C PRO B 429 " pdb=" CB PRO B 429 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA PRO C 429 " pdb=" N PRO C 429 " pdb=" C PRO C 429 " pdb=" CB PRO C 429 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2193 not shown) Planarity restraints: 2632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 167 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" C PRO D 167 " 0.044 2.00e-02 2.50e+03 pdb=" O PRO D 167 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP D 168 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 167 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C PRO A 167 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO A 167 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP A 168 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 167 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.55e+00 pdb=" C PRO C 167 " 0.044 2.00e-02 2.50e+03 pdb=" O PRO C 167 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP C 168 " -0.015 2.00e-02 2.50e+03 ... (remaining 2629 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3993 2.80 - 3.32: 12111 3.32 - 3.85: 21078 3.85 - 4.37: 27825 4.37 - 4.90: 48246 Nonbonded interactions: 113253 Sorted by model distance: nonbonded pdb=" OG SER C 142 " pdb=" OP1 LLP C 280 " model vdw 2.275 3.040 nonbonded pdb=" OG SER D 142 " pdb=" OP1 LLP D 280 " model vdw 2.275 3.040 nonbonded pdb=" OG SER B 142 " pdb=" OP1 LLP B 280 " model vdw 2.275 3.040 nonbonded pdb=" OG SER A 142 " pdb=" OP1 LLP A 280 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR D 96 " pdb=" OP3 LLP C 280 " model vdw 2.387 3.040 ... (remaining 113248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'B' selection = chain 'C' } 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: 1.760 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: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.400 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.004 0.080 14788 Z= 0.250 Angle : 0.652 8.707 20016 Z= 0.353 Chirality : 0.042 0.226 2196 Planarity : 0.004 0.039 2632 Dihedral : 9.145 81.253 5540 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.35 % Favored : 93.44 % Rotamer: Outliers : 0.79 % Allowed : 2.63 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.83 (0.16), residues: 1828 helix: -4.06 (0.09), residues: 700 sheet: -1.40 (0.35), residues: 188 loop : -1.41 (0.19), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 69 TYR 0.010 0.001 TYR A 195 PHE 0.008 0.001 PHE C 216 TRP 0.004 0.001 TRP C 134 HIS 0.002 0.001 HIS B 279 Details of bonding type rmsd covalent geometry : bond 0.00412 (14788) covalent geometry : angle 0.65188 (20016) hydrogen bonds : bond 0.38172 ( 596) hydrogen bonds : angle 9.29239 ( 1680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.581 Fit side-chains REVERT: A 128 ASP cc_start: 0.8421 (t0) cc_final: 0.7972 (t0) REVERT: D 128 ASP cc_start: 0.8442 (t0) cc_final: 0.8010 (t0) REVERT: D 307 ILE cc_start: 0.7256 (OUTLIER) cc_final: 0.7050 (pt) REVERT: B 128 ASP cc_start: 0.8444 (t0) cc_final: 0.8025 (t0) REVERT: B 307 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.7091 (pt) REVERT: C 128 ASP cc_start: 0.8452 (t0) cc_final: 0.8027 (t0) REVERT: C 307 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.6993 (pt) REVERT: C 475 ASP cc_start: 0.7353 (t0) cc_final: 0.7152 (t70) outliers start: 12 outliers final: 4 residues processed: 181 average time/residue: 0.8727 time to fit residues: 169.3193 Evaluate side-chains 108 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain D residue 254 HIS Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain B residue 254 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 254 HIS Chi-restraints excluded: chain C residue 307 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.0570 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS D 254 HIS B 254 HIS C 254 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106757 restraints weight = 17112.794| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.79 r_work: 0.3022 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14788 Z= 0.138 Angle : 0.581 7.412 20016 Z= 0.302 Chirality : 0.040 0.139 2196 Planarity : 0.005 0.046 2632 Dihedral : 6.876 88.562 2094 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.30 % Allowed : 6.05 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -2.14 (0.18), residues: 1828 helix: -1.61 (0.15), residues: 824 sheet: -0.79 (0.34), residues: 196 loop : -1.18 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 486 TYR 0.012 0.001 TYR A 195 PHE 0.007 0.001 PHE A 291 TRP 0.005 0.001 TRP A 134 HIS 0.002 0.001 HIS D 247 Details of bonding type rmsd covalent geometry : bond 0.00264 (14788) covalent geometry : angle 0.58082 (20016) hydrogen bonds : bond 0.08226 ( 596) hydrogen bonds : angle 5.45146 ( 1680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.566 Fit side-chains REVERT: A 128 ASP cc_start: 0.8571 (t0) cc_final: 0.8108 (t0) REVERT: A 252 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8147 (ptt) REVERT: A 457 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7679 (mm-30) REVERT: D 128 ASP cc_start: 0.8585 (t0) cc_final: 0.8120 (t0) REVERT: D 308 PRO cc_start: 0.8865 (Cg_endo) cc_final: 0.8658 (Cg_exo) REVERT: D 457 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7630 (mm-30) REVERT: B 128 ASP cc_start: 0.8580 (t0) cc_final: 0.8120 (t0) REVERT: B 200 LYS cc_start: 0.8955 (mptp) cc_final: 0.8535 (mptt) REVERT: B 307 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.7063 (pt) REVERT: B 308 PRO cc_start: 0.8894 (Cg_endo) cc_final: 0.8675 (Cg_exo) REVERT: B 457 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7618 (mm-30) REVERT: C 128 ASP cc_start: 0.8578 (t0) cc_final: 0.8117 (t0) REVERT: C 200 LYS cc_start: 0.8930 (mptp) cc_final: 0.8560 (mptt) REVERT: C 307 ILE cc_start: 0.7234 (OUTLIER) cc_final: 0.7013 (pt) REVERT: C 308 PRO cc_start: 0.8875 (Cg_endo) cc_final: 0.8625 (Cg_exo) outliers start: 35 outliers final: 9 residues processed: 140 average time/residue: 0.5572 time to fit residues: 86.8953 Evaluate side-chains 114 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain D residue 254 HIS Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain B residue 254 HIS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 254 HIS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 476 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 101 optimal weight: 0.0870 chunk 172 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 153 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107360 restraints weight = 16959.570| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.78 r_work: 0.3104 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14788 Z= 0.136 Angle : 0.589 7.633 20016 Z= 0.298 Chirality : 0.042 0.147 2196 Planarity : 0.005 0.077 2632 Dihedral : 6.395 82.205 2092 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.86 % Allowed : 7.76 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -1.20 (0.19), residues: 1828 helix: -0.33 (0.17), residues: 812 sheet: 0.04 (0.35), residues: 188 loop : -1.41 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 486 TYR 0.016 0.002 TYR B 195 PHE 0.010 0.002 PHE D 311 TRP 0.005 0.001 TRP C 134 HIS 0.004 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00312 (14788) covalent geometry : angle 0.58947 (20016) hydrogen bonds : bond 0.06709 ( 596) hydrogen bonds : angle 4.92419 ( 1680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.596 Fit side-chains REVERT: A 128 ASP cc_start: 0.8634 (t0) cc_final: 0.8159 (t0) REVERT: A 457 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7808 (mm-30) REVERT: D 128 ASP cc_start: 0.8633 (t0) cc_final: 0.8159 (t0) REVERT: D 457 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 128 ASP cc_start: 0.8662 (t0) cc_final: 0.8185 (t0) REVERT: B 200 LYS cc_start: 0.8950 (mptp) cc_final: 0.8554 (mptt) REVERT: B 308 PRO cc_start: 0.8852 (Cg_endo) cc_final: 0.8592 (Cg_exo) REVERT: B 457 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7789 (mm-30) REVERT: C 128 ASP cc_start: 0.8645 (t0) cc_final: 0.8198 (t0) REVERT: C 308 PRO cc_start: 0.8848 (Cg_endo) cc_final: 0.8574 (Cg_exo) outliers start: 13 outliers final: 1 residues processed: 122 average time/residue: 0.6889 time to fit residues: 91.8392 Evaluate side-chains 99 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107627 restraints weight = 16795.705| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.79 r_work: 0.3130 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14788 Z= 0.125 Angle : 0.558 7.143 20016 Z= 0.284 Chirality : 0.041 0.140 2196 Planarity : 0.005 0.080 2632 Dihedral : 6.212 84.759 2080 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.38 % Allowed : 7.83 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.19), residues: 1828 helix: 0.33 (0.18), residues: 812 sheet: 0.35 (0.36), residues: 188 loop : -1.46 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 486 TYR 0.014 0.001 TYR C 195 PHE 0.008 0.001 PHE D 311 TRP 0.005 0.001 TRP B 134 HIS 0.003 0.001 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.00284 (14788) covalent geometry : angle 0.55845 (20016) hydrogen bonds : bond 0.05773 ( 596) hydrogen bonds : angle 4.70820 ( 1680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.608 Fit side-chains REVERT: A 128 ASP cc_start: 0.8616 (t0) cc_final: 0.8168 (t0) REVERT: D 128 ASP cc_start: 0.8599 (t0) cc_final: 0.8144 (t0) REVERT: B 128 ASP cc_start: 0.8631 (t0) cc_final: 0.8173 (t0) REVERT: B 200 LYS cc_start: 0.8960 (mptp) cc_final: 0.8639 (mppt) REVERT: B 308 PRO cc_start: 0.8867 (Cg_endo) cc_final: 0.8619 (Cg_exo) REVERT: B 457 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7839 (mm-30) REVERT: C 128 ASP cc_start: 0.8615 (t0) cc_final: 0.8159 (t0) REVERT: C 308 PRO cc_start: 0.8857 (Cg_endo) cc_final: 0.8596 (Cg_exo) outliers start: 21 outliers final: 6 residues processed: 121 average time/residue: 0.6177 time to fit residues: 82.5429 Evaluate side-chains 104 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 439 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 161 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.102144 restraints weight = 16918.903| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.79 r_work: 0.3033 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14788 Z= 0.222 Angle : 0.697 8.505 20016 Z= 0.352 Chirality : 0.046 0.161 2196 Planarity : 0.006 0.072 2632 Dihedral : 6.441 84.689 2080 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.25 % Allowed : 8.68 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.19), residues: 1828 helix: 0.27 (0.18), residues: 808 sheet: 0.33 (0.37), residues: 188 loop : -1.76 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 434 TYR 0.022 0.002 TYR D 195 PHE 0.012 0.002 PHE C 291 TRP 0.007 0.002 TRP A 134 HIS 0.006 0.002 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00553 (14788) covalent geometry : angle 0.69656 (20016) hydrogen bonds : bond 0.08028 ( 596) hydrogen bonds : angle 5.02034 ( 1680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.616 Fit side-chains REVERT: A 128 ASP cc_start: 0.8592 (t0) cc_final: 0.8098 (t0) REVERT: D 128 ASP cc_start: 0.8572 (t0) cc_final: 0.8082 (t0) REVERT: B 128 ASP cc_start: 0.8581 (t0) cc_final: 0.8087 (t0) REVERT: B 200 LYS cc_start: 0.8935 (mptp) cc_final: 0.8596 (mppt) REVERT: B 308 PRO cc_start: 0.8830 (Cg_endo) cc_final: 0.8554 (Cg_exo) REVERT: B 457 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7851 (mm-30) REVERT: C 128 ASP cc_start: 0.8584 (t0) cc_final: 0.8093 (t0) outliers start: 19 outliers final: 14 residues processed: 110 average time/residue: 0.7255 time to fit residues: 87.0478 Evaluate side-chains 108 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 254 HIS Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 439 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 10 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106750 restraints weight = 16751.727| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.79 r_work: 0.3118 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14788 Z= 0.119 Angle : 0.554 7.218 20016 Z= 0.283 Chirality : 0.040 0.141 2196 Planarity : 0.005 0.066 2632 Dihedral : 6.282 82.712 2080 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.32 % Allowed : 9.08 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.20), residues: 1828 helix: 0.79 (0.19), residues: 808 sheet: 0.34 (0.38), residues: 192 loop : -1.60 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 359 TYR 0.012 0.001 TYR A 195 PHE 0.007 0.001 PHE D 441 TRP 0.005 0.001 TRP D 134 HIS 0.003 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00270 (14788) covalent geometry : angle 0.55419 (20016) hydrogen bonds : bond 0.05439 ( 596) hydrogen bonds : angle 4.63403 ( 1680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.583 Fit side-chains REVERT: A 128 ASP cc_start: 0.8545 (t0) cc_final: 0.8114 (t0) REVERT: D 128 ASP cc_start: 0.8507 (t0) cc_final: 0.8074 (t0) REVERT: D 498 MET cc_start: 0.8614 (tpp) cc_final: 0.8150 (ttp) REVERT: B 128 ASP cc_start: 0.8531 (t0) cc_final: 0.8101 (t0) REVERT: B 200 LYS cc_start: 0.8908 (mptp) cc_final: 0.8590 (mppt) REVERT: B 308 PRO cc_start: 0.8848 (Cg_endo) cc_final: 0.8595 (Cg_exo) REVERT: B 498 MET cc_start: 0.8623 (tpp) cc_final: 0.8114 (ttp) REVERT: C 128 ASP cc_start: 0.8525 (t0) cc_final: 0.8079 (t0) REVERT: C 200 LYS cc_start: 0.8934 (mptp) cc_final: 0.8635 (mppt) REVERT: C 308 PRO cc_start: 0.8847 (Cg_endo) cc_final: 0.8590 (Cg_exo) REVERT: C 498 MET cc_start: 0.8615 (tpp) cc_final: 0.8152 (ttp) outliers start: 20 outliers final: 7 residues processed: 118 average time/residue: 0.7258 time to fit residues: 93.5175 Evaluate side-chains 105 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain D residue 439 ASP Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 439 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 119 optimal weight: 1.9990 chunk 160 optimal weight: 0.0020 chunk 99 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 156 optimal weight: 0.0030 chunk 13 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 110 optimal weight: 0.0770 chunk 101 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN D 480 GLN B 480 GLN C 480 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111338 restraints weight = 16742.897| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.78 r_work: 0.3185 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14788 Z= 0.085 Angle : 0.475 6.883 20016 Z= 0.244 Chirality : 0.038 0.129 2196 Planarity : 0.004 0.062 2632 Dihedral : 6.182 84.871 2080 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.72 % Allowed : 9.41 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.20), residues: 1828 helix: 1.47 (0.19), residues: 824 sheet: 0.37 (0.40), residues: 200 loop : -1.30 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 359 TYR 0.008 0.001 TYR B 195 PHE 0.007 0.001 PHE A 441 TRP 0.005 0.001 TRP B 57 HIS 0.002 0.000 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00183 (14788) covalent geometry : angle 0.47469 (20016) hydrogen bonds : bond 0.03490 ( 596) hydrogen bonds : angle 4.15961 ( 1680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.613 Fit side-chains REVERT: A 128 ASP cc_start: 0.8527 (t0) cc_final: 0.8106 (t0) REVERT: A 498 MET cc_start: 0.8486 (tpp) cc_final: 0.8244 (ttp) REVERT: D 128 ASP cc_start: 0.8513 (t0) cc_final: 0.8090 (t0) REVERT: D 498 MET cc_start: 0.8563 (tpp) cc_final: 0.8188 (ttp) REVERT: B 128 ASP cc_start: 0.8524 (t0) cc_final: 0.8100 (t0) REVERT: B 200 LYS cc_start: 0.8889 (mptp) cc_final: 0.8583 (mppt) REVERT: B 498 MET cc_start: 0.8548 (tpp) cc_final: 0.8155 (ttp) REVERT: C 128 ASP cc_start: 0.8522 (t0) cc_final: 0.8102 (t0) REVERT: C 200 LYS cc_start: 0.8922 (mptp) cc_final: 0.8662 (mppt) REVERT: C 498 MET cc_start: 0.8550 (tpp) cc_final: 0.8166 (ttp) outliers start: 11 outliers final: 2 residues processed: 136 average time/residue: 0.6785 time to fit residues: 100.9160 Evaluate side-chains 102 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain D residue 58 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 24 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 169 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 177 optimal weight: 0.9990 chunk 134 optimal weight: 0.4980 chunk 158 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.106850 restraints weight = 16879.129| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.80 r_work: 0.3143 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14788 Z= 0.114 Angle : 0.535 7.204 20016 Z= 0.272 Chirality : 0.040 0.136 2196 Planarity : 0.005 0.095 2632 Dihedral : 6.116 83.182 2080 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.59 % Allowed : 10.53 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.20), residues: 1828 helix: 1.63 (0.19), residues: 812 sheet: 0.44 (0.40), residues: 200 loop : -1.43 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 359 TYR 0.014 0.001 TYR B 195 PHE 0.008 0.001 PHE C 311 TRP 0.003 0.001 TRP A 134 HIS 0.003 0.001 HIS C 270 Details of bonding type rmsd covalent geometry : bond 0.00266 (14788) covalent geometry : angle 0.53545 (20016) hydrogen bonds : bond 0.04915 ( 596) hydrogen bonds : angle 4.30214 ( 1680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.510 Fit side-chains REVERT: A 128 ASP cc_start: 0.8522 (t0) cc_final: 0.8094 (t0) REVERT: D 128 ASP cc_start: 0.8502 (t0) cc_final: 0.8076 (t0) REVERT: B 128 ASP cc_start: 0.8525 (t0) cc_final: 0.8096 (t0) REVERT: B 200 LYS cc_start: 0.8891 (mptp) cc_final: 0.8586 (mppt) REVERT: C 128 ASP cc_start: 0.8517 (t0) cc_final: 0.8093 (t0) REVERT: C 200 LYS cc_start: 0.8912 (mptp) cc_final: 0.8645 (mppt) outliers start: 9 outliers final: 3 residues processed: 108 average time/residue: 0.7554 time to fit residues: 88.7216 Evaluate side-chains 103 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain C residue 254 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 99 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 84 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.107027 restraints weight = 16920.115| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.81 r_work: 0.3120 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14788 Z= 0.128 Angle : 0.557 7.450 20016 Z= 0.283 Chirality : 0.041 0.144 2196 Planarity : 0.005 0.088 2632 Dihedral : 6.214 82.953 2080 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.59 % Allowed : 10.53 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.20), residues: 1828 helix: 1.55 (0.19), residues: 812 sheet: 0.38 (0.40), residues: 200 loop : -1.46 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 359 TYR 0.015 0.002 TYR B 195 PHE 0.009 0.001 PHE D 291 TRP 0.004 0.001 TRP A 134 HIS 0.004 0.001 HIS D 270 Details of bonding type rmsd covalent geometry : bond 0.00304 (14788) covalent geometry : angle 0.55699 (20016) hydrogen bonds : bond 0.05400 ( 596) hydrogen bonds : angle 4.42094 ( 1680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.575 Fit side-chains REVERT: A 128 ASP cc_start: 0.8524 (t0) cc_final: 0.8082 (t0) REVERT: D 128 ASP cc_start: 0.8500 (t0) cc_final: 0.8051 (t0) REVERT: B 128 ASP cc_start: 0.8524 (t0) cc_final: 0.8078 (t0) REVERT: B 200 LYS cc_start: 0.8913 (mptp) cc_final: 0.8597 (mppt) REVERT: B 498 MET cc_start: 0.8582 (tpp) cc_final: 0.8208 (ttp) REVERT: C 128 ASP cc_start: 0.8505 (t0) cc_final: 0.8061 (t0) REVERT: C 200 LYS cc_start: 0.8896 (mptp) cc_final: 0.8619 (mppt) outliers start: 9 outliers final: 3 residues processed: 107 average time/residue: 0.7499 time to fit residues: 87.3197 Evaluate side-chains 105 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 254 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 82 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 114 optimal weight: 0.0970 chunk 153 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 166 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 149 optimal weight: 0.0020 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.130557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.110958 restraints weight = 16673.738| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.78 r_work: 0.3179 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14788 Z= 0.092 Angle : 0.493 7.072 20016 Z= 0.253 Chirality : 0.038 0.127 2196 Planarity : 0.005 0.084 2632 Dihedral : 6.146 83.631 2080 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.13 % Allowed : 10.99 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.20), residues: 1828 helix: 1.88 (0.19), residues: 812 sheet: 0.52 (0.41), residues: 200 loop : -1.31 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 359 TYR 0.010 0.001 TYR B 195 PHE 0.007 0.001 PHE B 441 TRP 0.005 0.001 TRP D 57 HIS 0.002 0.001 HIS B 247 Details of bonding type rmsd covalent geometry : bond 0.00202 (14788) covalent geometry : angle 0.49301 (20016) hydrogen bonds : bond 0.03953 ( 596) hydrogen bonds : angle 4.17887 ( 1680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3656 Ramachandran restraints generated. 1828 Oldfield, 0 Emsley, 1828 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.525 Fit side-chains REVERT: A 128 ASP cc_start: 0.8530 (t0) cc_final: 0.8116 (t0) REVERT: D 128 ASP cc_start: 0.8481 (t0) cc_final: 0.8060 (t0) REVERT: B 128 ASP cc_start: 0.8504 (t0) cc_final: 0.8084 (t0) REVERT: B 200 LYS cc_start: 0.8900 (mptp) cc_final: 0.8592 (mppt) REVERT: B 498 MET cc_start: 0.8505 (tpp) cc_final: 0.8210 (ttp) REVERT: C 128 ASP cc_start: 0.8476 (t0) cc_final: 0.8071 (t0) REVERT: C 200 LYS cc_start: 0.8894 (mptp) cc_final: 0.8646 (mppt) outliers start: 2 outliers final: 1 residues processed: 108 average time/residue: 0.7641 time to fit residues: 89.6814 Evaluate side-chains 101 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110086 restraints weight = 16699.003| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.80 r_work: 0.3163 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14788 Z= 0.100 Angle : 0.508 7.192 20016 Z= 0.259 Chirality : 0.039 0.132 2196 Planarity : 0.005 0.080 2632 Dihedral : 6.148 83.660 2080 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.46 % Allowed : 10.79 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.20), residues: 1828 helix: 1.95 (0.19), residues: 812 sheet: 0.54 (0.41), residues: 200 loop : -1.31 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 359 TYR 0.012 0.001 TYR B 195 PHE 0.007 0.001 PHE B 441 TRP 0.004 0.001 TRP A 57 HIS 0.002 0.001 HIS C 247 Details of bonding type rmsd covalent geometry : bond 0.00229 (14788) covalent geometry : angle 0.50789 (20016) hydrogen bonds : bond 0.04294 ( 596) hydrogen bonds : angle 4.19377 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4070.77 seconds wall clock time: 70 minutes 15.06 seconds (4215.06 seconds total)