Starting phenix.real_space_refine on Sun Jul 21 14:12:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qi7_18436/07_2024/8qi7_18436.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qi7_18436/07_2024/8qi7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qi7_18436/07_2024/8qi7_18436.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qi7_18436/07_2024/8qi7_18436.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qi7_18436/07_2024/8qi7_18436.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qi7_18436/07_2024/8qi7_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 Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14609 Number of models: 1 Model: "" Number of chains: 8 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: "D" 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: "B" 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: "C" 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} Time building chain proxies: 8.76, per 1000 atoms: 0.60 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 - 3.50 Amino acid : False - 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: 5.27 Conformation dependent library (CDL) restraints added in 2.8 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: 1.93 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: 4.62 Time building geometry restraints manager: 5.71 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: 99.07 - 106.05: 389 106.05 - 113.04: 7792 113.04 - 120.02: 5439 120.02 - 127.00: 6236 127.00 - 133.99: 160 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 2.440 nonbonded pdb=" OG SER D 142 " pdb=" OP1 LLP D 280 " model vdw 2.275 2.440 nonbonded pdb=" OG SER B 142 " pdb=" OP1 LLP B 280 " model vdw 2.275 2.440 nonbonded pdb=" OG SER A 142 " pdb=" OP1 LLP A 280 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR D 96 " pdb=" OP3 LLP C 280 " model vdw 2.387 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.900 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: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 40.530 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.970 ------------------------------------------------------------------------------- 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= 0.281 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 173 time to evaluate : 1.621 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: 1.7241 time to fit residues: 334.8039 Evaluate side-chains 108 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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: 0.9990 chunk 139 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 167 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14788 Z= 0.175 Angle : 0.581 7.614 20016 Z= 0.302 Chirality : 0.040 0.149 2196 Planarity : 0.005 0.047 2632 Dihedral : 6.749 87.172 2094 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.24 % Allowed : 6.71 % Favored : 91.05 % 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: -2.10 (0.18), residues: 1828 helix: -1.56 (0.15), residues: 824 sheet: -0.78 (0.35), residues: 196 loop : -1.19 (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 0.007 0.001 PHE D 291 TYR 0.013 0.001 TYR A 195 ARG 0.006 0.000 ARG D 486 *********************** 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 154 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 120 time to evaluate : 1.698 Fit side-chains REVERT: A 128 ASP cc_start: 0.8462 (t0) cc_final: 0.8028 (t0) REVERT: A 457 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7588 (mm-30) REVERT: D 128 ASP cc_start: 0.8467 (t0) cc_final: 0.8032 (t0) REVERT: D 307 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.7046 (pt) REVERT: D 308 PRO cc_start: 0.8961 (Cg_endo) cc_final: 0.8683 (Cg_exo) REVERT: D 457 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7539 (mm-30) REVERT: B 128 ASP cc_start: 0.8473 (t0) cc_final: 0.8041 (t0) REVERT: B 200 LYS cc_start: 0.8888 (mptp) cc_final: 0.8462 (mptt) REVERT: B 307 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7078 (pt) REVERT: B 308 PRO cc_start: 0.8979 (Cg_endo) cc_final: 0.8695 (Cg_exo) REVERT: B 457 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7571 (mm-30) REVERT: C 128 ASP cc_start: 0.8487 (t0) cc_final: 0.8049 (t0) REVERT: C 200 LYS cc_start: 0.8856 (mptp) cc_final: 0.8466 (mptt) REVERT: C 307 ILE cc_start: 0.7244 (OUTLIER) cc_final: 0.6940 (pt) REVERT: C 308 PRO cc_start: 0.8954 (Cg_endo) cc_final: 0.8643 (Cg_exo) outliers start: 34 outliers final: 7 residues processed: 142 average time/residue: 1.1995 time to fit residues: 189.9306 Evaluate side-chains 112 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 307 ILE Chi-restraints excluded: chain B residue 439 ASP Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 439 ASP 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 92 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 167 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14788 Z= 0.239 Angle : 0.612 8.062 20016 Z= 0.309 Chirality : 0.042 0.156 2196 Planarity : 0.005 0.074 2632 Dihedral : 6.413 86.584 2090 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.72 % Allowed : 8.29 % Favored : 90.99 % 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: -1.31 (0.19), residues: 1828 helix: -0.39 (0.17), residues: 812 sheet: 0.07 (0.35), residues: 188 loop : -1.53 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 134 HIS 0.005 0.001 HIS D 330 PHE 0.011 0.002 PHE D 311 TYR 0.017 0.002 TYR B 195 ARG 0.003 0.000 ARG D 486 *********************** 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 118 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 107 time to evaluate : 1.857 Fit side-chains REVERT: A 128 ASP cc_start: 0.8493 (t0) cc_final: 0.8052 (t0) REVERT: A 237 MET cc_start: 0.8382 (mtp) cc_final: 0.7815 (mmt) REVERT: A 457 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7658 (mm-30) REVERT: D 128 ASP cc_start: 0.8504 (t0) cc_final: 0.8051 (t0) REVERT: D 457 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7657 (mm-30) REVERT: B 128 ASP cc_start: 0.8512 (t0) cc_final: 0.8058 (t0) REVERT: B 237 MET cc_start: 0.8416 (mtp) cc_final: 0.7864 (mmt) REVERT: B 457 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7682 (mm-30) REVERT: C 128 ASP cc_start: 0.8509 (t0) cc_final: 0.8053 (t0) REVERT: C 237 MET cc_start: 0.8358 (mtp) cc_final: 0.7818 (mmt) outliers start: 11 outliers final: 0 residues processed: 118 average time/residue: 1.4380 time to fit residues: 185.2932 Evaluate side-chains 96 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 165 optimal weight: 0.7980 chunk 125 optimal weight: 0.0370 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 79 optimal weight: 0.0030 chunk 112 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.9672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2426 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= 0.151 Angle : 0.513 6.706 20016 Z= 0.262 Chirality : 0.039 0.127 2196 Planarity : 0.004 0.069 2632 Dihedral : 6.093 84.300 2080 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.18 % Allowed : 8.49 % Favored : 90.33 % 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: -0.54 (0.19), residues: 1828 helix: 0.41 (0.18), residues: 824 sheet: 0.52 (0.37), residues: 188 loop : -1.36 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 57 HIS 0.002 0.001 HIS C 247 PHE 0.007 0.001 PHE D 441 TYR 0.011 0.001 TYR C 195 ARG 0.006 0.000 ARG A 359 *********************** 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 136 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.653 Fit side-chains REVERT: A 128 ASP cc_start: 0.8448 (t0) cc_final: 0.8032 (t0) REVERT: A 237 MET cc_start: 0.8295 (mtp) cc_final: 0.7746 (mmt) REVERT: D 128 ASP cc_start: 0.8437 (t0) cc_final: 0.8030 (t0) REVERT: D 308 PRO cc_start: 0.8919 (Cg_endo) cc_final: 0.8636 (Cg_exo) REVERT: B 128 ASP cc_start: 0.8435 (t0) cc_final: 0.8036 (t0) REVERT: B 200 LYS cc_start: 0.8845 (mptp) cc_final: 0.8523 (mppt) REVERT: B 237 MET cc_start: 0.8337 (mtp) cc_final: 0.7796 (mmt) REVERT: B 308 PRO cc_start: 0.8936 (Cg_endo) cc_final: 0.8649 (Cg_exo) REVERT: C 128 ASP cc_start: 0.8449 (t0) cc_final: 0.8050 (t0) REVERT: C 200 LYS cc_start: 0.8837 (mptp) cc_final: 0.8468 (mptt) REVERT: C 237 MET cc_start: 0.8278 (mtp) cc_final: 0.7744 (mmt) REVERT: C 308 PRO cc_start: 0.8913 (Cg_endo) cc_final: 0.8610 (Cg_exo) outliers start: 18 outliers final: 3 residues processed: 130 average time/residue: 1.2714 time to fit residues: 182.6006 Evaluate side-chains 105 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain C residue 211 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 132 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 151 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2551 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= 0.140 Angle : 0.503 7.042 20016 Z= 0.256 Chirality : 0.039 0.130 2196 Planarity : 0.004 0.062 2632 Dihedral : 6.075 87.734 2080 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.66 % Allowed : 9.74 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.18), residues: 824 sheet: 0.25 (0.38), residues: 200 loop : -1.31 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 57 HIS 0.002 0.001 HIS C 270 PHE 0.007 0.001 PHE D 441 TYR 0.012 0.001 TYR C 195 ARG 0.005 0.000 ARG A 359 *********************** 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 fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.664 Fit side-chains REVERT: A 128 ASP cc_start: 0.8441 (t0) cc_final: 0.8021 (t0) REVERT: D 128 ASP cc_start: 0.8431 (t0) cc_final: 0.8008 (t0) REVERT: D 308 PRO cc_start: 0.8957 (Cg_endo) cc_final: 0.8714 (Cg_exo) REVERT: D 498 MET cc_start: 0.8537 (tpp) cc_final: 0.8029 (ttp) REVERT: B 128 ASP cc_start: 0.8454 (t0) cc_final: 0.8043 (t0) REVERT: B 200 LYS cc_start: 0.8822 (mptp) cc_final: 0.8506 (mppt) REVERT: B 308 PRO cc_start: 0.8973 (Cg_endo) cc_final: 0.8725 (Cg_exo) REVERT: C 128 ASP cc_start: 0.8425 (t0) cc_final: 0.8032 (t0) REVERT: C 200 LYS cc_start: 0.8842 (mptp) cc_final: 0.8426 (mppt) REVERT: C 308 PRO cc_start: 0.8933 (Cg_endo) cc_final: 0.8670 (Cg_exo) outliers start: 10 outliers final: 4 residues processed: 113 average time/residue: 1.3915 time to fit residues: 172.9320 Evaluate side-chains 104 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain B residue 211 LEU 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 59 optimal weight: 7.9990 chunk 160 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14788 Z= 0.140 Angle : 0.495 6.834 20016 Z= 0.252 Chirality : 0.039 0.133 2196 Planarity : 0.004 0.059 2632 Dihedral : 6.084 87.313 2080 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.86 % Allowed : 9.67 % Favored : 89.47 % 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: 1.38 (0.19), residues: 820 sheet: 0.46 (0.39), residues: 200 loop : -1.34 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 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 0.004 0.000 ARG A 359 *********************** 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 119 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 1.734 Fit side-chains REVERT: A 98 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: A 128 ASP cc_start: 0.8395 (t0) cc_final: 0.7989 (t0) REVERT: D 98 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: D 128 ASP cc_start: 0.8404 (t0) cc_final: 0.8002 (t0) REVERT: D 308 PRO cc_start: 0.8972 (Cg_endo) cc_final: 0.8737 (Cg_exo) REVERT: B 98 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8163 (mt-10) REVERT: B 128 ASP cc_start: 0.8425 (t0) cc_final: 0.8019 (t0) REVERT: B 200 LYS cc_start: 0.8810 (mptp) cc_final: 0.8488 (mppt) REVERT: B 308 PRO cc_start: 0.8987 (Cg_endo) cc_final: 0.8750 (Cg_exo) REVERT: C 98 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: C 128 ASP cc_start: 0.8451 (t0) cc_final: 0.8045 (t0) REVERT: C 200 LYS cc_start: 0.8819 (mptp) cc_final: 0.8550 (mppt) REVERT: C 308 PRO cc_start: 0.8961 (Cg_endo) cc_final: 0.8712 (Cg_exo) REVERT: C 498 MET cc_start: 0.8428 (tpp) cc_final: 0.8127 (ttp) outliers start: 13 outliers final: 3 residues processed: 115 average time/residue: 1.4190 time to fit residues: 178.6966 Evaluate side-chains 115 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 108 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain B residue 98 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 130 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 177 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 108 optimal weight: 0.0770 chunk 81 optimal weight: 0.9990 overall best weight: 0.6542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2737 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= 0.130 Angle : 0.480 6.798 20016 Z= 0.245 Chirality : 0.038 0.132 2196 Planarity : 0.004 0.058 2632 Dihedral : 6.014 86.553 2080 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.05 % Allowed : 9.67 % Favored : 89.28 % 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: 0.51 (0.20), residues: 1828 helix: 1.77 (0.19), residues: 820 sheet: 0.57 (0.39), residues: 200 loop : -1.28 (0.21), residues: 808 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 A 441 TYR 0.010 0.001 TYR C 195 ARG 0.004 0.000 ARG A 359 *********************** 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 147 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.753 Fit side-chains REVERT: A 98 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: A 128 ASP cc_start: 0.8395 (t0) cc_final: 0.7995 (t0) REVERT: D 98 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: D 128 ASP cc_start: 0.8383 (t0) cc_final: 0.7993 (t0) REVERT: D 308 PRO cc_start: 0.8976 (Cg_endo) cc_final: 0.8747 (Cg_exo) REVERT: B 98 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: B 128 ASP cc_start: 0.8412 (t0) cc_final: 0.8020 (t0) REVERT: B 200 LYS cc_start: 0.8815 (mptp) cc_final: 0.8501 (mppt) REVERT: B 308 PRO cc_start: 0.8991 (Cg_endo) cc_final: 0.8761 (Cg_exo) REVERT: C 98 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: C 128 ASP cc_start: 0.8404 (t0) cc_final: 0.8016 (t0) REVERT: C 200 LYS cc_start: 0.8817 (mptp) cc_final: 0.8556 (mppt) REVERT: C 308 PRO cc_start: 0.8973 (Cg_endo) cc_final: 0.8740 (Cg_exo) REVERT: C 498 MET cc_start: 0.8361 (tpp) cc_final: 0.8129 (ttp) outliers start: 16 outliers final: 1 residues processed: 143 average time/residue: 1.4092 time to fit residues: 220.9672 Evaluate side-chains 118 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 113 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain D residue 98 GLU Chi-restraints excluded: chain B residue 98 GLU Chi-restraints excluded: chain C residue 98 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 0.6980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2631 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= 0.229 Angle : 0.586 7.354 20016 Z= 0.297 Chirality : 0.042 0.143 2196 Planarity : 0.005 0.056 2632 Dihedral : 6.239 86.307 2080 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.79 % Allowed : 10.26 % Favored : 88.95 % 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: 1.51 (0.18), residues: 812 sheet: 0.48 (0.40), residues: 200 loop : -1.51 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 134 HIS 0.004 0.001 HIS C 270 PHE 0.010 0.002 PHE C 291 TYR 0.017 0.002 TYR B 195 ARG 0.003 0.000 ARG A 359 *********************** 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 127 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.649 Fit side-chains REVERT: A 128 ASP cc_start: 0.8367 (t0) cc_final: 0.7954 (t0) REVERT: D 128 ASP cc_start: 0.8376 (t0) cc_final: 0.7967 (t0) REVERT: D 308 PRO cc_start: 0.8923 (Cg_endo) cc_final: 0.8657 (Cg_exo) REVERT: B 128 ASP cc_start: 0.8385 (t0) cc_final: 0.7977 (t0) REVERT: B 200 LYS cc_start: 0.8820 (mptp) cc_final: 0.8486 (mppt) REVERT: B 308 PRO cc_start: 0.8939 (Cg_endo) cc_final: 0.8675 (Cg_exo) REVERT: C 128 ASP cc_start: 0.8389 (t0) cc_final: 0.7959 (t0) REVERT: C 200 LYS cc_start: 0.8827 (mptp) cc_final: 0.8532 (mppt) REVERT: C 308 PRO cc_start: 0.8918 (Cg_endo) cc_final: 0.8651 (Cg_exo) REVERT: C 498 MET cc_start: 0.8442 (tpp) cc_final: 0.8126 (ttp) outliers start: 12 outliers final: 6 residues processed: 125 average time/residue: 1.4737 time to fit residues: 201.9023 Evaluate side-chains 122 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 254 HIS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain B residue 254 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 0.0670 chunk 50 optimal weight: 8.9990 chunk 149 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2700 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= 0.185 Angle : 0.548 7.124 20016 Z= 0.280 Chirality : 0.040 0.144 2196 Planarity : 0.004 0.056 2632 Dihedral : 6.197 84.849 2080 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.53 % Allowed : 10.66 % 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: 0.26 (0.20), residues: 1828 helix: 1.66 (0.18), residues: 812 sheet: 0.44 (0.40), residues: 200 loop : -1.49 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 134 HIS 0.003 0.001 HIS D 270 PHE 0.008 0.001 PHE A 291 TYR 0.014 0.001 TYR B 195 ARG 0.003 0.000 ARG A 359 *********************** 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 124 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.654 Fit side-chains REVERT: A 128 ASP cc_start: 0.8364 (t0) cc_final: 0.7956 (t0) REVERT: D 128 ASP cc_start: 0.8379 (t0) cc_final: 0.7953 (t0) REVERT: D 308 PRO cc_start: 0.8922 (Cg_endo) cc_final: 0.8659 (Cg_exo) REVERT: D 498 MET cc_start: 0.8461 (tpp) cc_final: 0.8093 (ttp) REVERT: B 128 ASP cc_start: 0.8380 (t0) cc_final: 0.7956 (t0) REVERT: B 200 LYS cc_start: 0.8813 (mptp) cc_final: 0.8487 (mppt) REVERT: B 308 PRO cc_start: 0.8939 (Cg_endo) cc_final: 0.8676 (Cg_exo) REVERT: C 128 ASP cc_start: 0.8378 (t0) cc_final: 0.7953 (t0) REVERT: C 200 LYS cc_start: 0.8807 (mptp) cc_final: 0.8530 (mppt) REVERT: C 308 PRO cc_start: 0.8916 (Cg_endo) cc_final: 0.8653 (Cg_exo) REVERT: C 498 MET cc_start: 0.8405 (tpp) cc_final: 0.8115 (ttp) outliers start: 8 outliers final: 7 residues processed: 123 average time/residue: 1.3897 time to fit residues: 187.8286 Evaluate side-chains 124 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 D residue 254 HIS Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 254 HIS 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 174 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2801 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= 0.144 Angle : 0.505 6.961 20016 Z= 0.259 Chirality : 0.039 0.139 2196 Planarity : 0.004 0.056 2632 Dihedral : 6.122 85.130 2080 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.33 % Allowed : 10.86 % 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: 0.54 (0.20), residues: 1828 helix: 1.94 (0.19), residues: 812 sheet: 0.50 (0.41), residues: 200 loop : -1.39 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 57 HIS 0.002 0.001 HIS A 247 PHE 0.007 0.001 PHE B 441 TYR 0.011 0.001 TYR B 195 ARG 0.003 0.000 ARG A 359 ********************** 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 122 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.608 Fit side-chains REVERT: A 128 ASP cc_start: 0.8358 (t0) cc_final: 0.7940 (t0) REVERT: D 128 ASP cc_start: 0.8359 (t0) cc_final: 0.7947 (t0) REVERT: D 308 PRO cc_start: 0.8950 (Cg_endo) cc_final: 0.8706 (Cg_exo) REVERT: D 498 MET cc_start: 0.8429 (tpp) cc_final: 0.8125 (ttp) REVERT: B 128 ASP cc_start: 0.8373 (t0) cc_final: 0.7961 (t0) REVERT: B 200 LYS cc_start: 0.8800 (mptp) cc_final: 0.8485 (mppt) REVERT: B 308 PRO cc_start: 0.8954 (Cg_endo) cc_final: 0.8718 (Cg_exo) REVERT: C 128 ASP cc_start: 0.8380 (t0) cc_final: 0.7973 (t0) REVERT: C 200 LYS cc_start: 0.8815 (mptp) cc_final: 0.8552 (mppt) REVERT: C 308 PRO cc_start: 0.8934 (Cg_endo) cc_final: 0.8696 (Cg_exo) REVERT: C 498 MET cc_start: 0.8364 (tpp) cc_final: 0.8088 (ttp) outliers start: 5 outliers final: 3 residues processed: 121 average time/residue: 1.4532 time to fit residues: 191.9850 Evaluate side-chains 117 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain D residue 254 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 21 optimal weight: 0.0170 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 = 0.130701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.110963 restraints weight = 16727.333| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.78 r_work: 0.3107 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2842 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= 0.140 Angle : 0.497 6.868 20016 Z= 0.254 Chirality : 0.039 0.138 2196 Planarity : 0.004 0.055 2632 Dihedral : 6.088 85.675 2080 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.20 % Allowed : 10.99 % 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: 0.68 (0.20), residues: 1828 helix: 2.09 (0.19), residues: 812 sheet: 0.54 (0.41), residues: 200 loop : -1.35 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 57 HIS 0.002 0.001 HIS C 247 PHE 0.007 0.001 PHE D 441 TYR 0.011 0.001 TYR B 195 ARG 0.003 0.000 ARG A 359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4184.48 seconds wall clock time: 74 minutes 28.76 seconds (4468.76 seconds total)