Starting phenix.real_space_refine on Fri May 16 15:55:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qi7_18436/05_2025/8qi7_18436.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qi7_18436/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qi7_18436/05_2025/8qi7_18436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qi7_18436/05_2025/8qi7_18436.map" model { file = "/net/cci-nas-00/data/ceres_data/8qi7_18436/05_2025/8qi7_18436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qi7_18436/05_2025/8qi7_18436.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, D Time building chain proxies: 7.76, per 1000 atoms: 0.53 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: 3.26 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.76 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: 4.34 Time building geometry restraints manager: 3.83 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 1.320 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 32.030 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.610 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (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 TRP 0.004 0.001 TRP C 134 HIS 0.002 0.001 HIS B 279 PHE 0.008 0.001 PHE C 216 TYR 0.010 0.001 TYR A 195 ARG 0.002 0.000 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.38172 ( 596) hydrogen bonds : angle 9.29239 ( 1680) covalent geometry : bond 0.00412 (14788) covalent geometry : angle 0.65188 (20016) *********************** 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 : 1.752 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: 1.6587 time to fit residues: 322.8396 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 : 1.607 ------------------------------------------------------------------------------- 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 155 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 94 optimal weight: 0.0980 chunk 74 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 167 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.125395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.105322 restraints weight = 17125.922| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.82 r_work: 0.3022 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14788 Z= 0.148 Angle : 0.591 7.621 20016 Z= 0.307 Chirality : 0.040 0.140 2196 Planarity : 0.005 0.047 2632 Dihedral : 6.843 87.538 2094 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.24 % Allowed : 6.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.18), residues: 1828 helix: -1.65 (0.15), residues: 824 sheet: -0.80 (0.34), residues: 196 loop : -1.22 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 134 HIS 0.003 0.001 HIS A 247 PHE 0.006 0.001 PHE D 291 TYR 0.013 0.001 TYR A 195 ARG 0.006 0.000 ARG C 486 Details of bonding type rmsd hydrogen bonds : bond 0.07608 ( 596) hydrogen bonds : angle 5.38217 ( 1680) covalent geometry : bond 0.00269 (14788) covalent geometry : angle 0.59133 (20016) *********************** 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: 34 poor density : 119 time to evaluate : 1.798 Fit side-chains REVERT: A 128 ASP cc_start: 0.8577 (t0) cc_final: 0.8103 (t0) REVERT: A 457 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7682 (mm-30) REVERT: D 128 ASP cc_start: 0.8574 (t0) cc_final: 0.8115 (t0) REVERT: D 307 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.7047 (pt) REVERT: D 308 PRO cc_start: 0.8854 (Cg_endo) cc_final: 0.8646 (Cg_exo) REVERT: D 457 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7659 (mm-30) REVERT: B 128 ASP cc_start: 0.8594 (t0) cc_final: 0.8134 (t0) REVERT: B 200 LYS cc_start: 0.8947 (mptp) cc_final: 0.8523 (mptt) REVERT: B 307 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7047 (pt) REVERT: B 308 PRO cc_start: 0.8861 (Cg_endo) cc_final: 0.8644 (Cg_exo) REVERT: B 457 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7627 (mm-30) REVERT: C 128 ASP cc_start: 0.8585 (t0) cc_final: 0.8110 (t0) REVERT: C 307 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.7021 (pt) REVERT: C 308 PRO cc_start: 0.8863 (Cg_endo) cc_final: 0.8612 (Cg_exo) outliers start: 34 outliers final: 9 residues processed: 141 average time/residue: 1.1658 time to fit residues: 183.3345 Evaluate side-chains 116 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 307 ILE 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 54 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 21 optimal weight: 0.0020 chunk 138 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 71 optimal weight: 0.0000 overall best weight: 0.9596 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.129948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110291 restraints weight = 16727.975| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.76 r_work: 0.3174 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14788 Z= 0.110 Angle : 0.540 7.003 20016 Z= 0.273 Chirality : 0.040 0.136 2196 Planarity : 0.005 0.071 2632 Dihedral : 6.310 81.893 2094 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.92 % Allowed : 7.37 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 1828 helix: -0.22 (0.17), residues: 824 sheet: -0.20 (0.36), residues: 196 loop : -1.20 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 134 HIS 0.003 0.001 HIS C 247 PHE 0.008 0.001 PHE D 311 TYR 0.013 0.001 TYR B 195 ARG 0.004 0.000 ARG D 486 Details of bonding type rmsd hydrogen bonds : bond 0.05622 ( 596) hydrogen bonds : angle 4.73161 ( 1680) covalent geometry : bond 0.00237 (14788) covalent geometry : angle 0.54014 (20016) *********************** 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 127 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 1.791 Fit side-chains REVERT: A 128 ASP cc_start: 0.8611 (t0) cc_final: 0.8177 (t0) REVERT: D 128 ASP cc_start: 0.8604 (t0) cc_final: 0.8179 (t0) REVERT: D 308 PRO cc_start: 0.8877 (Cg_endo) cc_final: 0.8647 (Cg_exo) REVERT: D 457 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7838 (mm-30) REVERT: B 128 ASP cc_start: 0.8618 (t0) cc_final: 0.8192 (t0) REVERT: B 200 LYS cc_start: 0.8963 (mptp) cc_final: 0.8576 (mptt) REVERT: B 308 PRO cc_start: 0.8882 (Cg_endo) cc_final: 0.8642 (Cg_exo) REVERT: B 457 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7819 (mm-30) REVERT: C 128 ASP cc_start: 0.8585 (t0) cc_final: 0.8174 (t0) REVERT: C 308 PRO cc_start: 0.8867 (Cg_endo) cc_final: 0.8602 (Cg_exo) outliers start: 14 outliers final: 1 residues processed: 126 average time/residue: 1.3769 time to fit residues: 190.6707 Evaluate side-chains 102 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.129055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109079 restraints weight = 16696.215| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.79 r_work: 0.3125 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14788 Z= 0.103 Angle : 0.517 6.903 20016 Z= 0.261 Chirality : 0.039 0.134 2196 Planarity : 0.004 0.068 2632 Dihedral : 6.039 84.748 2080 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.12 % Allowed : 9.14 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 1828 helix: 0.54 (0.18), residues: 824 sheet: -0.05 (0.37), residues: 200 loop : -1.15 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 57 HIS 0.002 0.001 HIS A 247 PHE 0.007 0.001 PHE D 311 TYR 0.012 0.001 TYR B 195 ARG 0.004 0.000 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.04762 ( 596) hydrogen bonds : angle 4.48327 ( 1680) covalent geometry : bond 0.00224 (14788) covalent geometry : angle 0.51706 (20016) *********************** 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 132 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.409 Fit side-chains REVERT: A 128 ASP cc_start: 0.8586 (t0) cc_final: 0.8158 (t0) REVERT: D 128 ASP cc_start: 0.8582 (t0) cc_final: 0.8160 (t0) REVERT: D 308 PRO cc_start: 0.8860 (Cg_endo) cc_final: 0.8655 (Cg_exo) REVERT: B 128 ASP cc_start: 0.8598 (t0) cc_final: 0.8176 (t0) REVERT: B 200 LYS cc_start: 0.8959 (mptp) cc_final: 0.8553 (mptt) REVERT: B 308 PRO cc_start: 0.8870 (Cg_endo) cc_final: 0.8662 (Cg_exo) REVERT: C 128 ASP cc_start: 0.8574 (t0) cc_final: 0.8153 (t0) REVERT: C 200 LYS cc_start: 0.8916 (mptp) cc_final: 0.8568 (mptt) REVERT: C 308 PRO cc_start: 0.8865 (Cg_endo) cc_final: 0.8641 (Cg_exo) outliers start: 17 outliers final: 0 residues processed: 124 average time/residue: 1.3085 time to fit residues: 179.2906 Evaluate side-chains 100 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 78 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 109 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 131 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 480 GLN B 480 GLN C 480 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106739 restraints weight = 16870.536| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.80 r_work: 0.3097 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2478 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= 0.133 Angle : 0.577 7.366 20016 Z= 0.292 Chirality : 0.041 0.145 2196 Planarity : 0.005 0.062 2632 Dihedral : 6.089 83.980 2080 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.46 % Allowed : 10.46 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.20), residues: 1828 helix: 0.86 (0.18), residues: 812 sheet: 0.42 (0.37), residues: 192 loop : -1.43 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 134 HIS 0.004 0.001 HIS A 330 PHE 0.009 0.002 PHE D 311 TYR 0.016 0.002 TYR D 195 ARG 0.002 0.000 ARG A 359 Details of bonding type rmsd hydrogen bonds : bond 0.05879 ( 596) hydrogen bonds : angle 4.57761 ( 1680) covalent geometry : bond 0.00311 (14788) covalent geometry : angle 0.57669 (20016) *********************** 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 115 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 1.809 Fit side-chains REVERT: A 128 ASP cc_start: 0.8546 (t0) cc_final: 0.8112 (t0) REVERT: D 128 ASP cc_start: 0.8516 (t0) cc_final: 0.8074 (t0) REVERT: D 308 PRO cc_start: 0.8840 (Cg_endo) cc_final: 0.8623 (Cg_exo) REVERT: B 128 ASP cc_start: 0.8548 (t0) cc_final: 0.8101 (t0) REVERT: B 200 LYS cc_start: 0.8922 (mptp) cc_final: 0.8595 (mppt) REVERT: B 308 PRO cc_start: 0.8850 (Cg_endo) cc_final: 0.8631 (Cg_exo) REVERT: C 128 ASP cc_start: 0.8537 (t0) cc_final: 0.8091 (t0) REVERT: C 200 LYS cc_start: 0.8921 (mptp) cc_final: 0.8633 (mppt) REVERT: C 308 PRO cc_start: 0.8841 (Cg_endo) cc_final: 0.8616 (Cg_exo) outliers start: 7 outliers final: 1 residues processed: 114 average time/residue: 1.3833 time to fit residues: 173.3382 Evaluate side-chains 104 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 5 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.121457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.101881 restraints weight = 17084.267| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.77 r_work: 0.2960 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14788 Z= 0.228 Angle : 0.707 8.716 20016 Z= 0.356 Chirality : 0.047 0.164 2196 Planarity : 0.006 0.062 2632 Dihedral : 6.441 83.966 2080 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.25 % Allowed : 9.41 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.19), residues: 1828 helix: 0.52 (0.18), residues: 808 sheet: 0.32 (0.38), residues: 192 loop : -1.75 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 134 HIS 0.006 0.002 HIS C 270 PHE 0.012 0.002 PHE C 311 TYR 0.023 0.002 TYR C 195 ARG 0.003 0.000 ARG A 434 Details of bonding type rmsd hydrogen bonds : bond 0.08006 ( 596) hydrogen bonds : angle 4.95745 ( 1680) covalent geometry : bond 0.00573 (14788) covalent geometry : angle 0.70683 (20016) *********************** 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 123 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.613 Fit side-chains REVERT: A 128 ASP cc_start: 0.8534 (t0) cc_final: 0.8040 (t0) REVERT: D 128 ASP cc_start: 0.8526 (t0) cc_final: 0.8040 (t0) REVERT: D 308 PRO cc_start: 0.8829 (Cg_endo) cc_final: 0.8557 (Cg_exo) REVERT: B 128 ASP cc_start: 0.8541 (t0) cc_final: 0.8052 (t0) REVERT: B 200 LYS cc_start: 0.8922 (mptp) cc_final: 0.8571 (mppt) REVERT: B 308 PRO cc_start: 0.8841 (Cg_endo) cc_final: 0.8567 (Cg_exo) REVERT: C 128 ASP cc_start: 0.8526 (t0) cc_final: 0.8039 (t0) REVERT: C 200 LYS cc_start: 0.8907 (mptp) cc_final: 0.8587 (mppt) REVERT: C 308 PRO cc_start: 0.8838 (Cg_endo) cc_final: 0.8562 (Cg_exo) outliers start: 19 outliers final: 13 residues processed: 119 average time/residue: 1.4677 time to fit residues: 190.7999 Evaluate side-chains 115 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL 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 C residue 180 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 307 ILE 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 129 optimal weight: 2.9990 chunk 146 optimal weight: 0.0870 chunk 152 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.0970 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 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 = 0.3527 r_free = 0.3527 target = 0.130457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110584 restraints weight = 16818.921| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.80 r_work: 0.3101 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14788 Z= 0.098 Angle : 0.505 7.010 20016 Z= 0.260 Chirality : 0.039 0.129 2196 Planarity : 0.004 0.058 2632 Dihedral : 6.225 83.303 2080 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.38 % Allowed : 9.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1828 helix: 1.13 (0.19), residues: 824 sheet: 0.32 (0.39), residues: 200 loop : -1.39 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 57 HIS 0.002 0.001 HIS B 247 PHE 0.007 0.001 PHE C 320 TYR 0.008 0.001 TYR A 195 ARG 0.002 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 596) hydrogen bonds : angle 4.33702 ( 1680) covalent geometry : bond 0.00204 (14788) covalent geometry : angle 0.50522 (20016) *********************** 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 130 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.700 Fit side-chains REVERT: A 128 ASP cc_start: 0.8538 (t0) cc_final: 0.8090 (t0) REVERT: D 128 ASP cc_start: 0.8493 (t0) cc_final: 0.8044 (t0) REVERT: D 308 PRO cc_start: 0.8839 (Cg_endo) cc_final: 0.8630 (Cg_exo) REVERT: B 128 ASP cc_start: 0.8528 (t0) cc_final: 0.8081 (t0) REVERT: B 200 LYS cc_start: 0.8879 (mptp) cc_final: 0.8559 (mppt) REVERT: B 308 PRO cc_start: 0.8843 (Cg_endo) cc_final: 0.8635 (Cg_exo) REVERT: C 128 ASP cc_start: 0.8513 (t0) cc_final: 0.8068 (t0) REVERT: C 200 LYS cc_start: 0.8911 (mptp) cc_final: 0.8625 (mppt) REVERT: C 308 PRO cc_start: 0.8839 (Cg_endo) cc_final: 0.8634 (Cg_exo) outliers start: 21 outliers final: 7 residues processed: 118 average time/residue: 1.3624 time to fit residues: 176.6506 Evaluate side-chains 114 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 180 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.128835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108969 restraints weight = 16660.762| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.79 r_work: 0.3152 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14788 Z= 0.105 Angle : 0.521 7.163 20016 Z= 0.266 Chirality : 0.039 0.130 2196 Planarity : 0.005 0.057 2632 Dihedral : 6.173 83.724 2080 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.86 % Allowed : 10.07 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.20), residues: 1828 helix: 1.50 (0.19), residues: 812 sheet: 0.41 (0.40), residues: 200 loop : -1.45 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 57 HIS 0.003 0.001 HIS C 330 PHE 0.007 0.001 PHE C 291 TYR 0.014 0.001 TYR C 195 ARG 0.002 0.000 ARG C 359 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 596) hydrogen bonds : angle 4.32280 ( 1680) covalent geometry : bond 0.00239 (14788) covalent geometry : angle 0.52056 (20016) *********************** 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 124 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 1.630 Fit side-chains REVERT: A 128 ASP cc_start: 0.8527 (t0) cc_final: 0.8091 (t0) REVERT: D 128 ASP cc_start: 0.8500 (t0) cc_final: 0.8066 (t0) REVERT: D 308 PRO cc_start: 0.8854 (Cg_endo) cc_final: 0.8653 (Cg_exo) REVERT: B 128 ASP cc_start: 0.8532 (t0) cc_final: 0.8096 (t0) REVERT: B 200 LYS cc_start: 0.8899 (mptp) cc_final: 0.8591 (mppt) REVERT: C 128 ASP cc_start: 0.8519 (t0) cc_final: 0.8090 (t0) REVERT: C 200 LYS cc_start: 0.8905 (mptp) cc_final: 0.8627 (mppt) outliers start: 13 outliers final: 6 residues processed: 117 average time/residue: 1.3560 time to fit residues: 174.8992 Evaluate side-chains 113 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 254 HIS Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 180 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 151 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 127 optimal weight: 5.9990 chunk 135 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.127505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107572 restraints weight = 16676.240| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.80 r_work: 0.3080 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2779 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= 0.126 Angle : 0.556 7.166 20016 Z= 0.283 Chirality : 0.041 0.141 2196 Planarity : 0.005 0.101 2632 Dihedral : 6.175 82.690 2080 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.99 % Allowed : 9.80 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1828 helix: 1.53 (0.19), residues: 812 sheet: 0.35 (0.40), residues: 200 loop : -1.47 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 134 HIS 0.003 0.001 HIS B 270 PHE 0.009 0.001 PHE C 291 TYR 0.015 0.001 TYR B 195 ARG 0.002 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.05227 ( 596) hydrogen bonds : angle 4.40608 ( 1680) covalent geometry : bond 0.00296 (14788) covalent geometry : angle 0.55598 (20016) *********************** 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 123 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 1.567 Fit side-chains REVERT: A 128 ASP cc_start: 0.8513 (t0) cc_final: 0.8086 (t0) REVERT: D 128 ASP cc_start: 0.8489 (t0) cc_final: 0.8070 (t0) REVERT: D 308 PRO cc_start: 0.8832 (Cg_endo) cc_final: 0.8616 (Cg_exo) REVERT: B 128 ASP cc_start: 0.8508 (t0) cc_final: 0.8086 (t0) REVERT: B 200 LYS cc_start: 0.8885 (mptp) cc_final: 0.8569 (mppt) REVERT: C 128 ASP cc_start: 0.8497 (t0) cc_final: 0.8059 (t0) REVERT: C 200 LYS cc_start: 0.8894 (mptp) cc_final: 0.8614 (mppt) outliers start: 15 outliers final: 7 residues processed: 116 average time/residue: 1.3919 time to fit residues: 177.4336 Evaluate side-chains 115 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 180 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 57 optimal weight: 0.1980 chunk 21 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 119 optimal weight: 0.7980 chunk 173 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.126862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.106942 restraints weight = 16731.780| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.80 r_work: 0.3045 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2777 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= 0.129 Angle : 0.566 7.315 20016 Z= 0.289 Chirality : 0.041 0.143 2196 Planarity : 0.005 0.091 2632 Dihedral : 6.265 82.662 2080 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.53 % Allowed : 10.26 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.20), residues: 1828 helix: 1.54 (0.19), residues: 812 sheet: 0.36 (0.41), residues: 200 loop : -1.48 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 134 HIS 0.003 0.001 HIS A 270 PHE 0.009 0.001 PHE B 291 TYR 0.015 0.001 TYR B 195 ARG 0.002 0.000 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.05450 ( 596) hydrogen bonds : angle 4.46262 ( 1680) covalent geometry : bond 0.00305 (14788) covalent geometry : angle 0.56566 (20016) ********************** 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 114 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 106 time to evaluate : 1.548 Fit side-chains REVERT: A 128 ASP cc_start: 0.8485 (t0) cc_final: 0.8058 (t0) REVERT: D 128 ASP cc_start: 0.8453 (t0) cc_final: 0.8022 (t0) REVERT: D 308 PRO cc_start: 0.8842 (Cg_endo) cc_final: 0.8618 (Cg_exo) REVERT: B 128 ASP cc_start: 0.8474 (t0) cc_final: 0.8044 (t0) REVERT: B 200 LYS cc_start: 0.8897 (mptp) cc_final: 0.8574 (mppt) REVERT: C 128 ASP cc_start: 0.8470 (t0) cc_final: 0.8033 (t0) REVERT: C 200 LYS cc_start: 0.8877 (mptp) cc_final: 0.8593 (mppt) outliers start: 8 outliers final: 4 residues processed: 106 average time/residue: 1.3947 time to fit residues: 161.6608 Evaluate side-chains 110 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 180 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 146 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 137 optimal weight: 0.4980 chunk 182 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.129865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109947 restraints weight = 16774.188| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.80 r_work: 0.3137 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14788 Z= 0.098 Angle : 0.508 6.999 20016 Z= 0.261 Chirality : 0.039 0.134 2196 Planarity : 0.005 0.087 2632 Dihedral : 6.180 83.418 2080 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.26 % Allowed : 10.72 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1828 helix: 1.80 (0.19), residues: 812 sheet: 0.41 (0.41), residues: 200 loop : -1.38 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 57 HIS 0.002 0.001 HIS A 247 PHE 0.007 0.001 PHE D 441 TYR 0.011 0.001 TYR B 195 ARG 0.002 0.000 ARG B 359 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 596) hydrogen bonds : angle 4.24796 ( 1680) covalent geometry : bond 0.00217 (14788) covalent geometry : angle 0.50796 (20016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7669.02 seconds wall clock time: 133 minutes 5.99 seconds (7985.99 seconds total)