Starting phenix.real_space_refine on Fri Jun 13 03:27:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qi7_18436/06_2025/8qi7_18436.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qi7_18436/06_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_18436/06_2025/8qi7_18436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qi7_18436/06_2025/8qi7_18436.map" model { file = "/net/cci-nas-00/data/ceres_data/8qi7_18436/06_2025/8qi7_18436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qi7_18436/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.86, per 1000 atoms: 0.54 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: 3.43 Conformation dependent library (CDL) restraints added in 1.8 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: 1.83 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: 4.42 Time building geometry restraints manager: 4.08 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: 0.10 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: 1.090 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: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 33.680 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- 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 : 1.773 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: 1.7685 time to fit residues: 343.6116 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 : 1.736 ------------------------------------------------------------------------------- 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: 3.78 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 : 2.030 Fit side-chains REVERT: A 128 ASP cc_start: 0.8578 (t0) cc_final: 0.8103 (t0) REVERT: A 457 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7685 (mm-30) REVERT: D 128 ASP cc_start: 0.8575 (t0) cc_final: 0.8115 (t0) REVERT: D 307 ILE cc_start: 0.7247 (OUTLIER) cc_final: 0.7038 (pt) REVERT: D 308 PRO cc_start: 0.8852 (Cg_endo) cc_final: 0.8645 (Cg_exo) REVERT: D 457 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 128 ASP cc_start: 0.8596 (t0) cc_final: 0.8136 (t0) REVERT: B 200 LYS cc_start: 0.8948 (mptp) cc_final: 0.8522 (mptt) REVERT: B 307 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.7039 (pt) REVERT: B 308 PRO cc_start: 0.8859 (Cg_endo) cc_final: 0.8643 (Cg_exo) REVERT: B 457 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7626 (mm-30) REVERT: C 128 ASP cc_start: 0.8586 (t0) cc_final: 0.8111 (t0) REVERT: C 307 ILE cc_start: 0.7240 (OUTLIER) cc_final: 0.7009 (pt) REVERT: C 308 PRO cc_start: 0.8860 (Cg_endo) cc_final: 0.8610 (Cg_exo) outliers start: 34 outliers final: 9 residues processed: 141 average time/residue: 1.2979 time to fit residues: 203.6002 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 : 1.690 ------------------------------------------------------------------------------- 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: 0.0070 chunk 48 optimal weight: 0.7980 chunk 21 optimal weight: 0.0980 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: 5.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- 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 = 0.3462 r_free = 0.3462 target = 0.126234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105918 restraints weight = 16952.827| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.81 r_work: 0.3170 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2207 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= 0.112 Angle : 0.540 7.070 20016 Z= 0.273 Chirality : 0.040 0.137 2196 Planarity : 0.005 0.071 2632 Dihedral : 6.304 81.754 2094 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % 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: -0.21 (0.17), residues: 824 sheet: -0.19 (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 D 57 HIS 0.003 0.001 HIS C 330 PHE 0.008 0.001 PHE D 311 TYR 0.013 0.001 TYR C 195 ARG 0.006 0.000 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.05609 ( 596) hydrogen bonds : angle 4.71186 ( 1680) covalent geometry : bond 0.00239 (14788) covalent geometry : angle 0.54025 (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 : 1.726 Fit side-chains REVERT: A 128 ASP cc_start: 0.8632 (t0) cc_final: 0.8193 (t0) REVERT: D 128 ASP cc_start: 0.8620 (t0) cc_final: 0.8197 (t0) REVERT: D 308 PRO cc_start: 0.8874 (Cg_endo) cc_final: 0.8639 (Cg_exo) REVERT: B 128 ASP cc_start: 0.8626 (t0) cc_final: 0.8192 (t0) REVERT: B 200 LYS cc_start: 0.8970 (mptp) cc_final: 0.8579 (mptt) REVERT: B 308 PRO cc_start: 0.8899 (Cg_endo) cc_final: 0.8655 (Cg_exo) REVERT: C 128 ASP cc_start: 0.8616 (t0) cc_final: 0.8200 (t0) REVERT: C 308 PRO cc_start: 0.8873 (Cg_endo) cc_final: 0.8606 (Cg_exo) outliers start: 14 outliers final: 0 residues processed: 126 average time/residue: 1.3621 time to fit residues: 188.3650 Evaluate side-chains 103 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 160 optimal weight: 0.5980 chunk 146 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.131363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111340 restraints weight = 16668.969| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.80 r_work: 0.3157 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2528 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= 0.091 Angle : 0.493 6.748 20016 Z= 0.250 Chirality : 0.038 0.129 2196 Planarity : 0.004 0.068 2632 Dihedral : 6.042 85.141 2080 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.12 % Allowed : 9.34 % Favored : 89.54 % 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: -0.26 (0.20), residues: 1828 helix: 0.72 (0.18), residues: 820 sheet: 0.00 (0.37), residues: 200 loop : -1.11 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 57 HIS 0.002 0.001 HIS C 171 PHE 0.007 0.001 PHE D 441 TYR 0.011 0.001 TYR B 195 ARG 0.005 0.000 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 596) hydrogen bonds : angle 4.35862 ( 1680) covalent geometry : bond 0.00193 (14788) covalent geometry : angle 0.49270 (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 135 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.645 Fit side-chains REVERT: A 128 ASP cc_start: 0.8607 (t0) cc_final: 0.8172 (t0) REVERT: D 128 ASP cc_start: 0.8598 (t0) cc_final: 0.8174 (t0) REVERT: B 128 ASP cc_start: 0.8621 (t0) cc_final: 0.8201 (t0) REVERT: B 200 LYS cc_start: 0.8932 (mptp) cc_final: 0.8540 (mptt) REVERT: C 128 ASP cc_start: 0.8570 (t0) cc_final: 0.8179 (t0) REVERT: C 200 LYS cc_start: 0.8942 (mptp) cc_final: 0.8577 (mptt) REVERT: C 308 PRO cc_start: 0.8894 (Cg_endo) cc_final: 0.8675 (Cg_exo) outliers start: 17 outliers final: 0 residues processed: 127 average time/residue: 1.3487 time to fit residues: 189.8388 Evaluate side-chains 95 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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: 5.9990 chunk 181 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 131 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 71 optimal weight: 0.1980 chunk 153 optimal weight: 0.0670 chunk 66 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.133196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113233 restraints weight = 16735.496| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.79 r_work: 0.3192 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2639 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= 0.089 Angle : 0.482 6.753 20016 Z= 0.245 Chirality : 0.038 0.129 2196 Planarity : 0.005 0.083 2632 Dihedral : 6.052 85.459 2080 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.59 % Allowed : 10.26 % Favored : 89.14 % 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: 0.15 (0.20), residues: 1828 helix: 1.24 (0.19), residues: 820 sheet: 0.21 (0.37), residues: 200 loop : -1.13 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 57 HIS 0.002 0.001 HIS B 247 PHE 0.007 0.001 PHE D 441 TYR 0.011 0.001 TYR A 195 ARG 0.002 0.000 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 596) hydrogen bonds : angle 4.21528 ( 1680) covalent geometry : bond 0.00192 (14788) covalent geometry : angle 0.48205 (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 114 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.967 Fit side-chains REVERT: A 98 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: A 128 ASP cc_start: 0.8587 (t0) cc_final: 0.8168 (t0) REVERT: D 98 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8096 (mt-10) REVERT: D 128 ASP cc_start: 0.8568 (t0) cc_final: 0.8154 (t0) REVERT: B 98 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: B 128 ASP cc_start: 0.8571 (t0) cc_final: 0.8155 (t0) REVERT: B 200 LYS cc_start: 0.8909 (mptp) cc_final: 0.8609 (mppt) REVERT: C 128 ASP cc_start: 0.8567 (t0) cc_final: 0.8163 (t0) REVERT: C 200 LYS cc_start: 0.8945 (mptp) cc_final: 0.8575 (mptt) outliers start: 9 outliers final: 1 residues processed: 113 average time/residue: 1.5071 time to fit residues: 186.2278 Evaluate side-chains 100 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain B residue 98 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 5 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.127252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107716 restraints weight = 16804.902| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.81 r_work: 0.3068 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14788 Z= 0.173 Angle : 0.622 7.859 20016 Z= 0.313 Chirality : 0.043 0.147 2196 Planarity : 0.005 0.084 2632 Dihedral : 6.214 84.353 2080 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.20 % Allowed : 11.45 % Favored : 88.36 % 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 (0.19), residues: 1828 helix: 1.05 (0.18), residues: 808 sheet: 0.49 (0.37), residues: 192 loop : -1.48 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 57 HIS 0.005 0.002 HIS B 330 PHE 0.011 0.002 PHE C 311 TYR 0.019 0.002 TYR D 195 ARG 0.003 0.000 ARG D 434 Details of bonding type rmsd hydrogen bonds : bond 0.06545 ( 596) hydrogen bonds : angle 4.64938 ( 1680) covalent geometry : bond 0.00427 (14788) covalent geometry : angle 0.62155 (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 108 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 1.690 Fit side-chains REVERT: A 128 ASP cc_start: 0.8554 (t0) cc_final: 0.8118 (t0) REVERT: D 128 ASP cc_start: 0.8528 (t0) cc_final: 0.8102 (t0) REVERT: B 128 ASP cc_start: 0.8545 (t0) cc_final: 0.8121 (t0) REVERT: B 200 LYS cc_start: 0.8930 (mptp) cc_final: 0.8609 (mppt) REVERT: C 128 ASP cc_start: 0.8546 (t0) cc_final: 0.8104 (t0) REVERT: C 200 LYS cc_start: 0.8925 (mptp) cc_final: 0.8639 (mppt) outliers start: 3 outliers final: 1 residues processed: 106 average time/residue: 1.5883 time to fit residues: 183.5050 Evaluate side-chains 105 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 180 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 129 optimal weight: 0.0070 chunk 146 optimal weight: 4.9990 chunk 152 optimal weight: 0.0970 chunk 178 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.131815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111847 restraints weight = 16743.706| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.80 r_work: 0.3143 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2742 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= 0.091 Angle : 0.491 6.686 20016 Z= 0.252 Chirality : 0.038 0.127 2196 Planarity : 0.005 0.076 2632 Dihedral : 6.090 83.292 2080 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.79 % Allowed : 10.66 % Favored : 88.55 % 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: 0.35 (0.20), residues: 1828 helix: 1.55 (0.19), residues: 824 sheet: 0.42 (0.39), residues: 200 loop : -1.26 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 57 HIS 0.002 0.000 HIS C 247 PHE 0.007 0.001 PHE D 441 TYR 0.009 0.001 TYR D 106 ARG 0.002 0.000 ARG C 359 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 596) hydrogen bonds : angle 4.24000 ( 1680) covalent geometry : bond 0.00194 (14788) covalent geometry : angle 0.49078 (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 122 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 1.751 Fit side-chains REVERT: A 98 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: A 128 ASP cc_start: 0.8522 (t0) cc_final: 0.8104 (t0) REVERT: A 498 MET cc_start: 0.8491 (tpp) cc_final: 0.8222 (ttp) REVERT: D 128 ASP cc_start: 0.8489 (t0) cc_final: 0.8073 (t0) REVERT: D 498 MET cc_start: 0.8526 (tpp) cc_final: 0.8166 (ttp) REVERT: B 128 ASP cc_start: 0.8521 (t0) cc_final: 0.8103 (t0) REVERT: B 200 LYS cc_start: 0.8898 (mptp) cc_final: 0.8585 (mppt) REVERT: B 498 MET cc_start: 0.8488 (tpp) cc_final: 0.8216 (ttp) REVERT: C 98 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: C 128 ASP cc_start: 0.8510 (t0) cc_final: 0.8099 (t0) REVERT: C 200 LYS cc_start: 0.8909 (mptp) cc_final: 0.8656 (mppt) REVERT: C 498 MET cc_start: 0.8526 (tpp) cc_final: 0.8155 (ttp) outliers start: 12 outliers final: 5 residues processed: 117 average time/residue: 1.4441 time to fit residues: 184.9657 Evaluate side-chains 112 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 211 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.8980 chunk 158 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.125990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106284 restraints weight = 16741.623| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.77 r_work: 0.3088 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14788 Z= 0.145 Angle : 0.588 7.371 20016 Z= 0.298 Chirality : 0.042 0.138 2196 Planarity : 0.005 0.073 2632 Dihedral : 6.149 83.385 2080 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.72 % Allowed : 10.79 % Favored : 88.49 % 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: 0.16 (0.20), residues: 1828 helix: 1.50 (0.18), residues: 808 sheet: 0.38 (0.39), residues: 200 loop : -1.44 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 134 HIS 0.004 0.001 HIS C 330 PHE 0.010 0.002 PHE A 291 TYR 0.017 0.002 TYR D 195 ARG 0.002 0.000 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.05884 ( 596) hydrogen bonds : angle 4.50225 ( 1680) covalent geometry : bond 0.00347 (14788) covalent geometry : angle 0.58777 (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 117 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.651 Fit side-chains REVERT: A 128 ASP cc_start: 0.8501 (t0) cc_final: 0.8073 (t0) REVERT: D 128 ASP cc_start: 0.8482 (t0) cc_final: 0.8054 (t0) REVERT: B 128 ASP cc_start: 0.8508 (t0) cc_final: 0.8079 (t0) REVERT: B 200 LYS cc_start: 0.8912 (mptp) cc_final: 0.8592 (mppt) REVERT: C 128 ASP cc_start: 0.8497 (t0) cc_final: 0.8070 (t0) REVERT: C 200 LYS cc_start: 0.8914 (mptp) cc_final: 0.8636 (mppt) outliers start: 11 outliers final: 5 residues processed: 114 average time/residue: 1.5245 time to fit residues: 191.1625 Evaluate side-chains 110 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain D residue 211 LEU 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: 3.9990 chunk 174 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 177 optimal weight: 0.3980 chunk 153 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 0.1980 chunk 86 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.126274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.106422 restraints weight = 16759.656| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.78 r_work: 0.3140 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2719 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= 0.117 Angle : 0.543 7.079 20016 Z= 0.278 Chirality : 0.040 0.137 2196 Planarity : 0.005 0.071 2632 Dihedral : 6.158 82.802 2080 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.39 % Allowed : 10.99 % Favored : 88.62 % 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: 0.28 (0.20), residues: 1828 helix: 1.63 (0.19), residues: 812 sheet: 0.43 (0.39), residues: 200 loop : -1.42 (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 C 270 PHE 0.008 0.001 PHE B 291 TYR 0.013 0.001 TYR C 195 ARG 0.002 0.000 ARG C 359 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 596) hydrogen bonds : angle 4.39856 ( 1680) covalent geometry : bond 0.00271 (14788) covalent geometry : angle 0.54342 (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 112 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 1.609 Fit side-chains REVERT: A 128 ASP cc_start: 0.8510 (t0) cc_final: 0.8077 (t0) REVERT: A 498 MET cc_start: 0.8566 (tpp) cc_final: 0.8201 (ttp) REVERT: D 128 ASP cc_start: 0.8495 (t0) cc_final: 0.8061 (t0) REVERT: B 128 ASP cc_start: 0.8527 (t0) cc_final: 0.8092 (t0) REVERT: B 200 LYS cc_start: 0.8911 (mptp) cc_final: 0.8600 (mppt) REVERT: B 498 MET cc_start: 0.8564 (tpp) cc_final: 0.8195 (ttp) REVERT: C 128 ASP cc_start: 0.8508 (t0) cc_final: 0.8075 (t0) REVERT: C 200 LYS cc_start: 0.8906 (mptp) cc_final: 0.8646 (mppt) outliers start: 6 outliers final: 5 residues processed: 111 average time/residue: 1.5224 time to fit residues: 184.5090 Evaluate side-chains 111 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 211 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 57 optimal weight: 0.0970 chunk 21 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 173 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 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 = 0.3507 r_free = 0.3507 target = 0.128598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108991 restraints weight = 16638.104| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.83 r_work: 0.3067 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2729 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= 0.131 Angle : 0.567 7.335 20016 Z= 0.289 Chirality : 0.041 0.139 2196 Planarity : 0.005 0.071 2632 Dihedral : 6.228 83.023 2080 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % 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 (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: 0.23 (0.20), residues: 1828 helix: 1.57 (0.18), residues: 812 sheet: 0.37 (0.40), residues: 200 loop : -1.42 (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 D 330 PHE 0.009 0.001 PHE B 291 TYR 0.015 0.002 TYR D 195 ARG 0.002 0.000 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.05441 ( 596) hydrogen bonds : angle 4.45372 ( 1680) covalent geometry : bond 0.00312 (14788) covalent geometry : angle 0.56678 (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: 7 poor density : 107 time to evaluate : 1.801 Fit side-chains REVERT: A 128 ASP cc_start: 0.8513 (t0) cc_final: 0.8086 (t0) REVERT: D 128 ASP cc_start: 0.8491 (t0) cc_final: 0.8064 (t0) REVERT: B 128 ASP cc_start: 0.8532 (t0) cc_final: 0.8109 (t0) REVERT: B 200 LYS cc_start: 0.8907 (mptp) cc_final: 0.8595 (mppt) REVERT: C 128 ASP cc_start: 0.8511 (t0) cc_final: 0.8086 (t0) REVERT: C 200 LYS cc_start: 0.8903 (mptp) cc_final: 0.8645 (mppt) outliers start: 7 outliers final: 6 residues processed: 112 average time/residue: 1.5276 time to fit residues: 186.8498 Evaluate side-chains 114 residues out of total 1520 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 211 LEU 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: 3.9990 chunk 182 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 = 0.3431 r_free = 0.3431 target = 0.123247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103306 restraints weight = 16984.979| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.81 r_work: 0.2977 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14788 Z= 0.168 Angle : 0.626 7.562 20016 Z= 0.318 Chirality : 0.043 0.151 2196 Planarity : 0.005 0.070 2632 Dihedral : 6.425 82.970 2080 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.46 % Allowed : 10.72 % Favored : 88.82 % 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: 0.02 (0.20), residues: 1828 helix: 1.32 (0.18), residues: 812 sheet: 0.58 (0.40), residues: 192 loop : -1.51 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 134 HIS 0.005 0.002 HIS D 330 PHE 0.011 0.002 PHE B 291 TYR 0.019 0.002 TYR D 195 ARG 0.002 0.000 ARG D 387 Details of bonding type rmsd hydrogen bonds : bond 0.06533 ( 596) hydrogen bonds : angle 4.66276 ( 1680) covalent geometry : bond 0.00411 (14788) covalent geometry : angle 0.62571 (20016) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8290.07 seconds wall clock time: 143 minutes 36.56 seconds (8616.56 seconds total)