Starting phenix.real_space_refine on Tue Oct 27 06:55:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t4u_55532/10_2026/9t4u_55532_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t4u_55532/10_2026/9t4u_55532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t4u_55532/10_2026/9t4u_55532_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t4u_55532/10_2026/9t4u_55532_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t4u_55532/10_2026/9t4u_55532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t4u_55532/10_2026/9t4u_55532.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 12 5.49 5 S 114 5.16 5 C 14694 2.51 5 N 4086 2.21 5 O 4398 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23304 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3856 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 471} Chain: "C" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3856 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 471} Chain: "B" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3856 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 471} Chain: "D" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3856 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 471} Chain: "E" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3856 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 471} Chain: "F" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3856 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 471} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.54, per 1000 atoms: 0.19 Number of scatterers: 23304 At special positions: 0 Unit cell: (112.887, 118.881, 162.837, 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 114 16.00 P 12 15.00 O 4398 8.00 N 4086 7.00 C 14694 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: 1.47 Conformation dependent library (CDL) restraints added in 1.1 seconds 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5364 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 14 sheets defined 56.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 8 through 29 removed outlier: 3.891A pdb=" N ILE A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 removed outlier: 3.528A pdb=" N ASN A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG A 44 " --> pdb=" O GLN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 117 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 137 through 155 removed outlier: 3.571A pdb=" N LYS A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 removed outlier: 3.816A pdb=" N MET A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 213 through 228 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 353 through 364 removed outlier: 3.961A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 398 through 422 removed outlier: 4.007A pdb=" N LYS A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 Processing helix chain 'A' and resid 444 through 472 removed outlier: 3.815A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 497 removed outlier: 3.602A pdb=" N TYR A 482 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 29 removed outlier: 3.936A pdb=" N ILE C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.638A pdb=" N ASN C 43 " --> pdb=" O GLU C 39 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG C 44 " --> pdb=" O GLN C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 117 Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 137 through 155 removed outlier: 3.646A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 removed outlier: 3.794A pdb=" N MET C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.537A pdb=" N CYS C 197 " --> pdb=" O ALA C 194 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL C 198 " --> pdb=" O HIS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 229 through 237 removed outlier: 3.529A pdb=" N MET C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 Processing helix chain 'C' and resid 287 through 299 Processing helix chain 'C' and resid 353 through 364 removed outlier: 3.926A pdb=" N LYS C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'C' and resid 375 through 391 Processing helix chain 'C' and resid 398 through 422 removed outlier: 3.924A pdb=" N LYS C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 442 Processing helix chain 'C' and resid 444 through 472 removed outlier: 3.812A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 497 removed outlier: 3.567A pdb=" N TYR C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 29 removed outlier: 3.911A pdb=" N ILE B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 38 through 53 removed outlier: 4.099A pdb=" N ARG B 44 " --> pdb=" O GLN B 40 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 117 Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 137 through 155 removed outlier: 3.597A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 removed outlier: 3.969A pdb=" N MET B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.507A pdb=" N MET B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 287 through 299 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 353 through 364 removed outlier: 3.864A pdb=" N LYS B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 375 through 391 Processing helix chain 'B' and resid 398 through 422 removed outlier: 3.939A pdb=" N LYS B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 442 Processing helix chain 'B' and resid 444 through 472 removed outlier: 3.852A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 497 removed outlier: 3.589A pdb=" N TYR B 482 " --> pdb=" O ARG B 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 29 removed outlier: 3.879A pdb=" N ILE D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 50 removed outlier: 4.097A pdb=" N ARG D 44 " --> pdb=" O GLN D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 117 Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 155 removed outlier: 3.602A pdb=" N LYS D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 228 Processing helix chain 'D' and resid 229 through 237 Processing helix chain 'D' and resid 253 through 266 Processing helix chain 'D' and resid 287 through 299 Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 353 through 364 removed outlier: 3.996A pdb=" N LYS D 358 " --> pdb=" O PRO D 354 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'D' and resid 375 through 391 Processing helix chain 'D' and resid 398 through 422 removed outlier: 3.942A pdb=" N LYS D 420 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 421 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 442 Processing helix chain 'D' and resid 444 through 472 removed outlier: 3.826A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 497 removed outlier: 3.633A pdb=" N TYR D 482 " --> pdb=" O ARG D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 29 removed outlier: 3.871A pdb=" N ILE E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 50 removed outlier: 4.040A pdb=" N ARG E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 117 Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 155 removed outlier: 3.551A pdb=" N LYS E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 186 removed outlier: 3.801A pdb=" N MET E 176 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 228 Processing helix chain 'E' and resid 229 through 237 Processing helix chain 'E' and resid 253 through 266 Processing helix chain 'E' and resid 287 through 299 Processing helix chain 'E' and resid 313 through 317 Processing helix chain 'E' and resid 353 through 364 removed outlier: 3.903A pdb=" N LYS E 358 " --> pdb=" O PRO E 354 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'E' and resid 375 through 391 Processing helix chain 'E' and resid 398 through 422 removed outlier: 3.944A pdb=" N LYS E 420 " --> pdb=" O SER E 416 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 421 " --> pdb=" O LEU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 442 Processing helix chain 'E' and resid 444 through 472 removed outlier: 3.749A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 497 removed outlier: 3.628A pdb=" N TYR E 482 " --> pdb=" O ARG E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 29 removed outlier: 3.896A pdb=" N ILE F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 removed outlier: 3.629A pdb=" N ASN F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG F 44 " --> pdb=" O GLN F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 117 Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 137 through 155 removed outlier: 3.601A pdb=" N LYS F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 186 removed outlier: 3.812A pdb=" N MET F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 197 removed outlier: 3.796A pdb=" N ALA F 196 " --> pdb=" O ASN F 193 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS F 197 " --> pdb=" O ALA F 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 193 through 197' Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 213 through 229 removed outlier: 3.795A pdb=" N GLU F 229 " --> pdb=" O ASN F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 237 removed outlier: 3.598A pdb=" N MET F 233 " --> pdb=" O GLU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 Processing helix chain 'F' and resid 287 through 299 Processing helix chain 'F' and resid 313 through 317 Processing helix chain 'F' and resid 353 through 364 removed outlier: 4.059A pdb=" N LYS F 358 " --> pdb=" O PRO F 354 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE F 359 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 374 Processing helix chain 'F' and resid 375 through 391 removed outlier: 3.525A pdb=" N THR F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 422 removed outlier: 3.953A pdb=" N LYS F 420 " --> pdb=" O SER F 416 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE F 421 " --> pdb=" O LEU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 442 Processing helix chain 'F' and resid 444 through 472 removed outlier: 4.104A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 497 removed outlier: 3.607A pdb=" N TYR F 482 " --> pdb=" O ARG F 478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 167 removed outlier: 6.766A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LYS A 90 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA A 127 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLY A 92 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N VAL A 129 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG A 94 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 77 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY E 77 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY E 92 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 249 removed outlier: 7.345A pdb=" N PHE A 247 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N GLY A 274 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL A 249 " --> pdb=" O GLY A 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.230A pdb=" N LEU A 322 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.692A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LYS C 90 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ALA C 127 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLY C 92 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL C 129 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG C 94 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY C 77 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 77 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LYS F 90 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ALA F 127 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLY F 92 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL F 129 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG F 94 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 308 through 309 removed outlier: 7.805A pdb=" N PHE C 247 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N GLY C 274 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 249 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR C 246 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE C 323 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 248 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 322 " --> pdb=" O ALA C 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 163 through 167 removed outlier: 6.650A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 92 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 77 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY D 77 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LYS D 90 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA D 127 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY D 92 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL D 129 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG D 94 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 249 removed outlier: 7.350A pdb=" N PHE B 247 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N GLY B 274 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 249 " --> pdb=" O GLY B 274 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 321 through 322 removed outlier: 6.259A pdb=" N LEU B 322 " --> pdb=" O ALA B 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 246 through 249 removed outlier: 7.389A pdb=" N PHE D 247 " --> pdb=" O THR D 272 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N GLY D 274 " --> pdb=" O PHE D 247 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL D 249 " --> pdb=" O GLY D 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 321 through 322 removed outlier: 6.201A pdb=" N LEU D 322 " --> pdb=" O ALA D 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 246 through 249 removed outlier: 7.362A pdb=" N PHE E 247 " --> pdb=" O THR E 272 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLY E 274 " --> pdb=" O PHE E 247 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL E 249 " --> pdb=" O GLY E 274 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 321 through 322 removed outlier: 6.259A pdb=" N LEU E 322 " --> pdb=" O ALA E 345 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 246 through 249 removed outlier: 7.337A pdb=" N PHE F 247 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N GLY F 274 " --> pdb=" O PHE F 247 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL F 249 " --> pdb=" O GLY F 274 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 321 through 322 removed outlier: 6.044A pdb=" N LEU F 322 " --> pdb=" O ALA F 345 " (cutoff:3.500A) 1288 hydrogen bonds defined for protein. 3717 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: 3.43 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7728 1.34 - 1.46: 4988 1.46 - 1.58: 10876 1.58 - 1.70: 18 1.70 - 1.82: 192 Bond restraints: 23802 Sorted by residual: bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.357 0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" C4 ADP C 601 " pdb=" C5 ADP C 601 " ideal model delta sigma weight residual 1.490 1.357 0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" C4 ADP F 601 " pdb=" C5 ADP F 601 " ideal model delta sigma weight residual 1.490 1.357 0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" C4 ADP E 601 " pdb=" C5 ADP E 601 " ideal model delta sigma weight residual 1.490 1.357 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C4 ADP D 601 " pdb=" C5 ADP D 601 " ideal model delta sigma weight residual 1.490 1.357 0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 23797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 31847 2.62 - 5.24: 237 5.24 - 7.86: 46 7.86 - 10.48: 18 10.48 - 13.10: 12 Bond angle restraints: 32160 Sorted by residual: angle pdb=" C1' ADP C 601 " pdb=" C2' ADP C 601 " pdb=" C3' ADP C 601 " ideal model delta sigma weight residual 111.00 97.90 13.10 3.00e+00 1.11e-01 1.91e+01 angle pdb=" C1' ADP F 601 " pdb=" C2' ADP F 601 " pdb=" C3' ADP F 601 " ideal model delta sigma weight residual 111.00 98.12 12.88 3.00e+00 1.11e-01 1.84e+01 angle pdb=" C1' ADP B 601 " pdb=" C2' ADP B 601 " pdb=" C3' ADP B 601 " ideal model delta sigma weight residual 111.00 98.21 12.79 3.00e+00 1.11e-01 1.82e+01 angle pdb=" C1' ADP E 601 " pdb=" C2' ADP E 601 " pdb=" C3' ADP E 601 " ideal model delta sigma weight residual 111.00 98.25 12.75 3.00e+00 1.11e-01 1.81e+01 angle pdb=" C1' ADP D 601 " pdb=" C2' ADP D 601 " pdb=" C3' ADP D 601 " ideal model delta sigma weight residual 111.00 98.29 12.71 3.00e+00 1.11e-01 1.79e+01 ... (remaining 32155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.01: 13052 26.01 - 52.01: 1064 52.01 - 78.02: 114 78.02 - 104.02: 2 104.02 - 130.03: 12 Dihedral angle restraints: 14244 sinusoidal: 5820 harmonic: 8424 Sorted by residual: dihedral pdb=" C5' ADP C 601 " pdb=" O5' ADP C 601 " pdb=" PA ADP C 601 " pdb=" O2A ADP C 601 " ideal model delta sinusoidal sigma weight residual -60.00 70.03 -130.03 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 69.80 -129.80 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" C5' ADP B 601 " pdb=" O5' ADP B 601 " pdb=" PA ADP B 601 " pdb=" O2A ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 68.10 -128.10 1 2.00e+01 2.50e-03 3.88e+01 ... (remaining 14241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2488 0.037 - 0.073: 688 0.073 - 0.110: 212 0.110 - 0.146: 85 0.146 - 0.183: 13 Chirality restraints: 3486 Sorted by residual: chirality pdb=" C3' ADP C 601 " pdb=" C2' ADP C 601 " pdb=" C4' ADP C 601 " pdb=" O3' ADP C 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" C2' ADP C 601 " pdb=" C1' ADP C 601 " pdb=" C3' ADP C 601 " pdb=" O2' ADP C 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" C2' ADP F 601 " pdb=" C1' ADP F 601 " pdb=" C3' ADP F 601 " pdb=" O2' ADP F 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 3483 not shown) Planarity restraints: 4158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 490 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C PHE C 490 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE C 490 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG C 491 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR E 353 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO E 354 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 354 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 354 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 304 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO E 305 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 305 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 305 " -0.021 5.00e-02 4.00e+02 ... (remaining 4155 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 562 2.68 - 3.23: 23662 3.23 - 3.79: 36837 3.79 - 4.34: 47020 4.34 - 4.90: 82172 Nonbonded interactions: 190253 Sorted by model distance: nonbonded pdb=" OG SER F 327 " pdb=" OE1 GLN F 330 " model vdw 2.122 3.040 nonbonded pdb=" OG SER B 83 " pdb=" ND1 HIS B 85 " model vdw 2.169 3.120 nonbonded pdb=" NH1 ARG F 217 " pdb=" OH TYR F 262 " model vdw 2.169 3.120 nonbonded pdb=" O GLY F 241 " pdb=" NZ LYS F 245 " model vdw 2.172 3.120 nonbonded pdb=" NH1 ARG D 217 " pdb=" OH TYR D 262 " model vdw 2.178 3.120 ... (remaining 190248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.220 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 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 0.133 23802 Z= 0.215 Angle : 0.674 13.103 32160 Z= 0.319 Chirality : 0.042 0.183 3486 Planarity : 0.003 0.057 4158 Dihedral : 17.547 130.028 8880 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % Rotamer: Outliers : 0.20 % Allowed : 24.13 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.16), residues: 2946 helix: 2.10 (0.14), residues: 1542 sheet: -1.22 (0.26), residues: 378 loop : -1.12 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 419 TYR 0.013 0.001 TYR C 310 PHE 0.011 0.001 PHE C 266 TRP 0.015 0.001 TRP F 385 HIS 0.004 0.001 HIS F 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 (23802) covalent geometry : angle 0.67360 / 0.32 (32160) hydrogen bonds : bond 0.12775 / 8.65 ( 1288) hydrogen bonds : angle 5.21947 / 3.70 ( 3717) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 224 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8523 (mt0) REVERT: A 250 GLN cc_start: 0.8390 (tm-30) cc_final: 0.7736 (tm-30) REVERT: C 72 TRP cc_start: 0.8755 (m100) cc_final: 0.8458 (m-10) REVERT: C 250 GLN cc_start: 0.8026 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 226 PHE cc_start: 0.8632 (m-80) cc_final: 0.8346 (m-10) REVERT: B 250 GLN cc_start: 0.8588 (tm-30) cc_final: 0.7976 (tm-30) REVERT: B 281 TRP cc_start: 0.8319 (t60) cc_final: 0.7805 (t60) REVERT: D 250 GLN cc_start: 0.8580 (tm-30) cc_final: 0.7823 (tm-30) REVERT: E 250 GLN cc_start: 0.8526 (tm-30) cc_final: 0.7890 (tm-30) REVERT: F 250 GLN cc_start: 0.8625 (tm-30) cc_final: 0.7782 (tm-30) REVERT: F 281 TRP cc_start: 0.8224 (t60) cc_final: 0.7788 (t60) outliers start: 5 outliers final: 1 residues processed: 228 average time/residue: 0.1661 time to fit residues: 59.7031 Evaluate side-chains 207 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 205 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 57 HIS A 193 ASN C 57 HIS B 57 HIS B 82 HIS B 193 ASN B 330 GLN D 57 HIS D 205 GLN E 57 HIS E 132 ASN F 57 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.109048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.077491 restraints weight = 46099.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.080121 restraints weight = 22692.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.081697 restraints weight = 15358.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.082595 restraints weight = 12494.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.082993 restraints weight = 11234.999| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23802 Z= 0.122 Angle : 0.561 6.407 32160 Z= 0.277 Chirality : 0.042 0.128 3486 Planarity : 0.003 0.032 4158 Dihedral : 7.661 112.069 3303 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.45 % Allowed : 23.20 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.16), residues: 2946 helix: 2.20 (0.13), residues: 1596 sheet: -0.62 (0.26), residues: 408 loop : -1.28 (0.19), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 419 TYR 0.017 0.001 TYR D 310 PHE 0.015 0.001 PHE C 421 TRP 0.009 0.001 TRP F 385 HIS 0.005 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (23802) covalent geometry : angle 0.56081 / 0.28 (32160) hydrogen bonds : bond 0.04125 / 2.80 ( 1288) hydrogen bonds : angle 4.21561 / 2.99 ( 3717) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8555 (mt0) REVERT: A 250 GLN cc_start: 0.8471 (tm-30) cc_final: 0.7837 (tm-30) REVERT: C 72 TRP cc_start: 0.8694 (m100) cc_final: 0.8493 (m-10) REVERT: C 150 MET cc_start: 0.8729 (mmm) cc_final: 0.8322 (mmm) REVERT: C 250 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7867 (tm-30) REVERT: B 250 GLN cc_start: 0.8634 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 415 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7278 (mm-30) REVERT: D 150 MET cc_start: 0.8703 (mmm) cc_final: 0.8330 (mmm) REVERT: D 250 GLN cc_start: 0.8508 (tm-30) cc_final: 0.7749 (tm-30) REVERT: D 415 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7273 (mm-30) REVERT: E 79 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8684 (ttt-90) REVERT: E 250 GLN cc_start: 0.8520 (tm-30) cc_final: 0.7890 (tm-30) REVERT: F 150 MET cc_start: 0.8768 (mmm) cc_final: 0.8372 (mmm) REVERT: F 226 PHE cc_start: 0.8697 (m-80) cc_final: 0.8363 (m-10) REVERT: F 250 GLN cc_start: 0.8606 (tm-30) cc_final: 0.7886 (tm-30) REVERT: F 281 TRP cc_start: 0.8015 (t60) cc_final: 0.7716 (t60) outliers start: 36 outliers final: 18 residues processed: 268 average time/residue: 0.1561 time to fit residues: 66.3949 Evaluate side-chains 229 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 72 TRP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 389 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [235, 93, 41, 114, 225, 148, 292, 173, 237, 37, 288] chunk 235 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 292 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 237 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 288 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 GLN B 193 ASN B 414 GLN D 205 GLN E 330 GLN F 330 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.077783 restraints weight = 46195.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.080440 restraints weight = 23112.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.082017 restraints weight = 15767.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.082918 restraints weight = 12930.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.083340 restraints weight = 11650.260| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23802 Z= 0.123 Angle : 0.550 6.728 32160 Z= 0.268 Chirality : 0.042 0.142 3486 Planarity : 0.003 0.025 4158 Dihedral : 6.953 102.588 3300 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.30 % Allowed : 23.24 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.16), residues: 2946 helix: 2.28 (0.13), residues: 1602 sheet: -0.43 (0.30), residues: 324 loop : -1.04 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 419 TYR 0.017 0.001 TYR B 310 PHE 0.014 0.001 PHE E 490 TRP 0.008 0.001 TRP D 72 HIS 0.003 0.001 HIS D 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (23802) covalent geometry : angle 0.54953 / 0.27 (32160) hydrogen bonds : bond 0.03910 / 2.64 ( 1288) hydrogen bonds : angle 3.96090 / 2.82 ( 3717) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8592 (mt0) REVERT: A 79 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8824 (ttt-90) REVERT: A 250 GLN cc_start: 0.8582 (tm-30) cc_final: 0.7893 (tm-30) REVERT: C 79 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8775 (ttt-90) REVERT: C 150 MET cc_start: 0.8734 (mmm) cc_final: 0.8299 (mmm) REVERT: C 151 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8058 (mm-30) REVERT: C 250 GLN cc_start: 0.8393 (tm-30) cc_final: 0.7972 (tm-30) REVERT: B 163 ASP cc_start: 0.8742 (t0) cc_final: 0.8505 (t0) REVERT: B 226 PHE cc_start: 0.8568 (m-80) cc_final: 0.8300 (m-10) REVERT: B 250 GLN cc_start: 0.8662 (tm-30) cc_final: 0.7656 (tm-30) REVERT: D 79 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8754 (ttm170) REVERT: D 150 MET cc_start: 0.8725 (mmm) cc_final: 0.8302 (mmm) REVERT: D 151 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8074 (mm-30) REVERT: D 250 GLN cc_start: 0.8554 (tm-30) cc_final: 0.7844 (tm-30) REVERT: E 79 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8737 (ttt-90) REVERT: E 111 MET cc_start: 0.9272 (tpp) cc_final: 0.8930 (tpp) REVERT: E 250 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8046 (tm-30) REVERT: F 79 ARG cc_start: 0.9259 (OUTLIER) cc_final: 0.7430 (ttm170) REVERT: F 150 MET cc_start: 0.8786 (mmm) cc_final: 0.8403 (mmm) REVERT: F 226 PHE cc_start: 0.8673 (m-80) cc_final: 0.8458 (m-10) REVERT: F 250 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8003 (tm-30) REVERT: F 269 LYS cc_start: 0.8549 (mtpt) cc_final: 0.8343 (ttmt) REVERT: F 281 TRP cc_start: 0.8034 (t60) cc_final: 0.7592 (t60) outliers start: 57 outliers final: 30 residues processed: 270 average time/residue: 0.1663 time to fit residues: 69.6475 Evaluate side-chains 244 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 193 ASN Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain D residue 72 TRP Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 389 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [45, 231, 102, 116, 182, 179, 53, 153, 95, 137, 172] chunk 45 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 182 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 494 ASN C 494 ASN B 139 ASN B 494 ASN D 139 ASN E 494 ASN F 494 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.075282 restraints weight = 46707.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.078116 restraints weight = 22863.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.080273 restraints weight = 14323.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.080153 restraints weight = 12465.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.080014 restraints weight = 11356.579| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 23802 Z= 0.206 Angle : 0.596 8.120 32160 Z= 0.294 Chirality : 0.043 0.131 3486 Planarity : 0.003 0.023 4158 Dihedral : 6.899 99.937 3300 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.31 % Allowed : 23.28 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.16), residues: 2946 helix: 2.13 (0.13), residues: 1602 sheet: -0.40 (0.27), residues: 378 loop : -1.03 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 419 TYR 0.015 0.001 TYR C 310 PHE 0.014 0.001 PHE B 421 TRP 0.011 0.001 TRP F 385 HIS 0.004 0.001 HIS F 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (23802) covalent geometry : angle 0.59596 / 0.29 (32160) hydrogen bonds : bond 0.04813 / 3.24 ( 1288) hydrogen bonds : angle 4.05172 / 2.88 ( 3717) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 230 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8743 (tp40) REVERT: A 79 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8735 (ttt-90) REVERT: A 250 GLN cc_start: 0.8502 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 389 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9119 (mp) REVERT: C 79 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8853 (ttt-90) REVERT: C 250 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7901 (tm-30) REVERT: C 309 ILE cc_start: 0.9072 (mp) cc_final: 0.8750 (pt) REVERT: C 414 GLN cc_start: 0.7897 (tt0) cc_final: 0.7673 (tt0) REVERT: B 79 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.7888 (ttm170) REVERT: B 250 GLN cc_start: 0.8560 (tm-30) cc_final: 0.7545 (tm-30) REVERT: D 53 LYS cc_start: 0.9527 (OUTLIER) cc_final: 0.9237 (tttt) REVERT: D 79 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8838 (ttt-90) REVERT: D 150 MET cc_start: 0.8785 (mmm) cc_final: 0.8364 (mmm) REVERT: D 250 GLN cc_start: 0.8486 (tm-30) cc_final: 0.7781 (tm-30) REVERT: D 397 LEU cc_start: 0.9361 (mp) cc_final: 0.9137 (mp) REVERT: D 414 GLN cc_start: 0.7930 (tt0) cc_final: 0.7728 (tt0) REVERT: E 79 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8770 (ttt-90) REVERT: E 205 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8636 (mp10) REVERT: E 250 GLN cc_start: 0.8585 (tm-30) cc_final: 0.8039 (tm-30) REVERT: E 389 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9117 (mp) REVERT: F 79 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.7889 (ttm170) REVERT: F 250 GLN cc_start: 0.8670 (tm-30) cc_final: 0.7988 (tm-30) REVERT: F 269 LYS cc_start: 0.8639 (mtpt) cc_final: 0.8295 (ttmt) REVERT: F 281 TRP cc_start: 0.8109 (t60) cc_final: 0.7709 (t60) REVERT: F 308 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8232 (pptt) REVERT: F 309 ILE cc_start: 0.9315 (mp) cc_final: 0.9096 (mm) REVERT: F 414 GLN cc_start: 0.8033 (tt0) cc_final: 0.7808 (tt0) outliers start: 82 outliers final: 47 residues processed: 282 average time/residue: 0.1681 time to fit residues: 73.1171 Evaluate side-chains 267 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 209 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 72 TRP Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain D residue 420 LYS Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 197 CYS Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 308 LYS Chi-restraints excluded: chain F residue 389 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [123, 114, 126, 22, 39, 279, 43, 189, 10, 288, 115] chunk 123 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 279 optimal weight: 0.0980 chunk 43 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 288 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 205 GLN B 139 ASN E 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.109814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.077576 restraints weight = 46030.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.080259 restraints weight = 22709.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.081866 restraints weight = 15503.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.082772 restraints weight = 12665.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.083222 restraints weight = 11418.416| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 23802 Z= 0.116 Angle : 0.546 7.362 32160 Z= 0.266 Chirality : 0.042 0.168 3486 Planarity : 0.003 0.023 4158 Dihedral : 6.421 100.730 3300 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.62 % Allowed : 24.25 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.16), residues: 2946 helix: 2.34 (0.13), residues: 1596 sheet: -0.31 (0.32), residues: 282 loop : -0.94 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 419 TYR 0.020 0.001 TYR E 310 PHE 0.012 0.001 PHE C 421 TRP 0.010 0.001 TRP B 72 HIS 0.003 0.001 HIS F 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (23802) covalent geometry : angle 0.54618 / 0.27 (32160) hydrogen bonds : bond 0.03740 / 2.53 ( 1288) hydrogen bonds : angle 3.82747 / 2.71 ( 3717) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 244 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.9013 (ttm-80) REVERT: A 205 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8608 (mp10) REVERT: A 250 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8128 (tm-30) REVERT: C 79 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8782 (ttm170) REVERT: C 150 MET cc_start: 0.8781 (mmm) cc_final: 0.8401 (mmm) REVERT: C 151 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8054 (mm-30) REVERT: C 250 GLN cc_start: 0.8412 (tm-30) cc_final: 0.7681 (tm-30) REVERT: C 414 GLN cc_start: 0.7948 (tt0) cc_final: 0.7722 (tt0) REVERT: B 150 MET cc_start: 0.8784 (tpp) cc_final: 0.8453 (mmm) REVERT: B 163 ASP cc_start: 0.8773 (t0) cc_final: 0.8510 (t0) REVERT: B 250 GLN cc_start: 0.8664 (tm-30) cc_final: 0.7763 (tm-30) REVERT: D 53 LYS cc_start: 0.9518 (OUTLIER) cc_final: 0.9199 (tttt) REVERT: D 79 ARG cc_start: 0.9244 (OUTLIER) cc_final: 0.8830 (ttm170) REVERT: D 250 GLN cc_start: 0.8538 (tm-30) cc_final: 0.7859 (tm-30) REVERT: D 397 LEU cc_start: 0.9319 (mp) cc_final: 0.9077 (mp) REVERT: E 111 MET cc_start: 0.9278 (tpp) cc_final: 0.8897 (tpp) REVERT: E 250 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8216 (tm-30) REVERT: F 79 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.7530 (tpm170) REVERT: F 163 ASP cc_start: 0.8774 (t0) cc_final: 0.8238 (t0) REVERT: F 205 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8732 (mp10) REVERT: F 226 PHE cc_start: 0.8607 (m-80) cc_final: 0.8364 (m-10) REVERT: F 250 GLN cc_start: 0.8724 (tm-30) cc_final: 0.7685 (tm-30) REVERT: F 269 LYS cc_start: 0.8609 (mtpt) cc_final: 0.8358 (ttmt) REVERT: F 281 TRP cc_start: 0.7925 (t60) cc_final: 0.7648 (t60) REVERT: F 415 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7198 (mm-30) outliers start: 65 outliers final: 42 residues processed: 284 average time/residue: 0.1685 time to fit residues: 74.4435 Evaluate side-chains 265 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 216 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 53 LYS Chi-restraints excluded: chain D residue 72 TRP Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 389 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [18, 252, 234, 185, 233, 41, 235, 97, 194, 4, 87] chunk 18 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 235 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 4 optimal weight: 0.0000 chunk 87 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 139 ASN B 330 GLN E 414 GLN F 414 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.108350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.076757 restraints weight = 46011.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.079386 restraints weight = 22768.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.080949 restraints weight = 15378.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.081834 restraints weight = 12515.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.082095 restraints weight = 11252.810| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23802 Z= 0.131 Angle : 0.554 8.132 32160 Z= 0.270 Chirality : 0.042 0.153 3486 Planarity : 0.003 0.022 4158 Dihedral : 6.228 100.941 3300 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.87 % Allowed : 24.09 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.16), residues: 2946 helix: 2.35 (0.13), residues: 1596 sheet: -0.26 (0.32), residues: 282 loop : -0.92 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 419 TYR 0.022 0.001 TYR B 310 PHE 0.012 0.001 PHE B 421 TRP 0.008 0.001 TRP B 281 HIS 0.002 0.001 HIS F 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (23802) covalent geometry : angle 0.55392 / 0.27 (32160) hydrogen bonds : bond 0.03950 / 2.67 ( 1288) hydrogen bonds : angle 3.79209 / 2.69 ( 3717) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 237 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.9005 (ttt90) REVERT: A 205 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8611 (mp10) REVERT: A 250 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8169 (tm-30) REVERT: C 79 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8646 (ttt-90) REVERT: C 150 MET cc_start: 0.8762 (mmm) cc_final: 0.8400 (mmm) REVERT: C 163 ASP cc_start: 0.8815 (t0) cc_final: 0.8603 (t0) REVERT: C 250 GLN cc_start: 0.8405 (tm-30) cc_final: 0.7710 (tm-30) REVERT: C 414 GLN cc_start: 0.7972 (tt0) cc_final: 0.7747 (tt0) REVERT: B 79 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8819 (ttt90) REVERT: B 163 ASP cc_start: 0.8773 (t0) cc_final: 0.8380 (t0) REVERT: B 250 GLN cc_start: 0.8695 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 260 MET cc_start: 0.8821 (ttp) cc_final: 0.8581 (tmm) REVERT: D 79 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8808 (ttm170) REVERT: D 150 MET cc_start: 0.8780 (mmm) cc_final: 0.8467 (mmm) REVERT: D 250 GLN cc_start: 0.8545 (tm-30) cc_final: 0.7876 (tm-30) REVERT: D 397 LEU cc_start: 0.9322 (mp) cc_final: 0.9090 (mp) REVERT: E 111 MET cc_start: 0.9268 (tpp) cc_final: 0.8883 (tpp) REVERT: E 205 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8657 (mp10) REVERT: E 250 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8258 (tm-30) REVERT: F 79 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.7974 (ttm170) REVERT: F 163 ASP cc_start: 0.8814 (t0) cc_final: 0.8312 (t0) REVERT: F 205 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8682 (mp10) REVERT: F 250 GLN cc_start: 0.8751 (tm-30) cc_final: 0.7721 (tm-30) REVERT: F 269 LYS cc_start: 0.8569 (mtpt) cc_final: 0.8321 (ttmt) REVERT: F 281 TRP cc_start: 0.7931 (t60) cc_final: 0.7589 (t60) REVERT: F 415 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7281 (mm-30) outliers start: 71 outliers final: 49 residues processed: 284 average time/residue: 0.1671 time to fit residues: 73.5430 Evaluate side-chains 272 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain C residue 72 TRP Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 72 TRP Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 403 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [139, 135, 6, 69, 38, 276, 188, 293, 33, 288, 21] chunk 139 optimal weight: 0.0970 chunk 135 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 276 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 293 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 288 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.110477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.078376 restraints weight = 45870.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.081098 restraints weight = 22662.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.082708 restraints weight = 15334.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.083657 restraints weight = 12518.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.084065 restraints weight = 11242.706| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23802 Z= 0.106 Angle : 0.536 6.665 32160 Z= 0.261 Chirality : 0.042 0.166 3486 Planarity : 0.003 0.024 4158 Dihedral : 5.949 101.539 3300 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.46 % Allowed : 24.74 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.16), residues: 2946 helix: 2.46 (0.13), residues: 1584 sheet: -0.09 (0.33), residues: 282 loop : -0.80 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 419 TYR 0.015 0.001 TYR F 310 PHE 0.018 0.001 PHE B 17 TRP 0.009 0.001 TRP B 281 HIS 0.003 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (23802) covalent geometry : angle 0.53598 / 0.26 (32160) hydrogen bonds : bond 0.03484 / 2.37 ( 1288) hydrogen bonds : angle 3.69043 / 2.61 ( 3717) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 246 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7919 (mm-30) REVERT: A 205 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8616 (mp10) REVERT: A 250 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8227 (tm-30) REVERT: C 79 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8722 (ttm170) REVERT: C 150 MET cc_start: 0.8758 (mmm) cc_final: 0.8386 (mmm) REVERT: C 151 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8152 (mm-30) REVERT: C 250 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7693 (tm-30) REVERT: C 414 GLN cc_start: 0.7941 (tt0) cc_final: 0.7718 (tt0) REVERT: B 79 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.8902 (ttt90) REVERT: B 163 ASP cc_start: 0.8822 (t0) cc_final: 0.8456 (t0) REVERT: B 250 GLN cc_start: 0.8761 (tm-30) cc_final: 0.7980 (tm-30) REVERT: B 487 GLU cc_start: 0.8408 (tp30) cc_final: 0.7952 (tm-30) REVERT: D 79 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8735 (ttm170) REVERT: D 150 MET cc_start: 0.8819 (mmm) cc_final: 0.8542 (tpp) REVERT: D 163 ASP cc_start: 0.8764 (t0) cc_final: 0.8544 (t0) REVERT: D 250 GLN cc_start: 0.8549 (tm-30) cc_final: 0.7889 (tm-30) REVERT: D 309 ILE cc_start: 0.9210 (mp) cc_final: 0.8510 (tt) REVERT: E 111 MET cc_start: 0.9284 (tpp) cc_final: 0.8917 (tpp) REVERT: E 151 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7952 (mm-30) REVERT: E 205 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8662 (mp10) REVERT: E 250 GLN cc_start: 0.8685 (tm-30) cc_final: 0.8294 (tm-30) REVERT: F 79 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8812 (ttt180) REVERT: F 163 ASP cc_start: 0.8824 (t0) cc_final: 0.8054 (t0) REVERT: F 205 GLN cc_start: 0.9215 (OUTLIER) cc_final: 0.8674 (mp10) REVERT: F 250 GLN cc_start: 0.8761 (tm-30) cc_final: 0.7778 (tm-30) REVERT: F 269 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8392 (ttmt) REVERT: F 415 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7218 (mm-30) outliers start: 61 outliers final: 42 residues processed: 288 average time/residue: 0.1627 time to fit residues: 72.9555 Evaluate side-chains 271 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 222 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 403 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [260, 184, 128, 109, 179, 107, 34, 132, 62, 36, 200] chunk 260 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 128 optimal weight: 0.2980 chunk 109 optimal weight: 0.3980 chunk 179 optimal weight: 0.4980 chunk 107 optimal weight: 0.0970 chunk 34 optimal weight: 0.7980 chunk 132 optimal weight: 0.0570 chunk 62 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 overall best weight: 0.2696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN D 414 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.080542 restraints weight = 45842.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.083307 restraints weight = 22527.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.084970 restraints weight = 15233.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.085896 restraints weight = 12386.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.086295 restraints weight = 11135.700| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23802 Z= 0.096 Angle : 0.541 9.137 32160 Z= 0.261 Chirality : 0.041 0.174 3486 Planarity : 0.003 0.023 4158 Dihedral : 5.687 101.853 3300 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.30 % Allowed : 24.74 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.16), residues: 2946 helix: 2.52 (0.13), residues: 1596 sheet: 0.07 (0.31), residues: 336 loop : -0.95 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 419 TYR 0.021 0.001 TYR D 310 PHE 0.010 0.001 PHE B 421 TRP 0.010 0.001 TRP B 72 HIS 0.003 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (23802) covalent geometry : angle 0.54150 / 0.26 (32160) hydrogen bonds : bond 0.03139 / 2.15 ( 1288) hydrogen bonds : angle 3.58224 / 2.53 ( 3717) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 258 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8620 (mp10) REVERT: A 250 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8326 (tm-30) REVERT: C 150 MET cc_start: 0.8731 (mmm) cc_final: 0.8379 (mmm) REVERT: C 250 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 414 GLN cc_start: 0.7923 (tt0) cc_final: 0.7669 (tt0) REVERT: C 495 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7973 (mm-30) REVERT: B 79 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.7816 (ttm170) REVERT: B 150 MET cc_start: 0.8777 (tpp) cc_final: 0.8555 (mmm) REVERT: B 163 ASP cc_start: 0.8813 (t0) cc_final: 0.8285 (t0) REVERT: B 250 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8077 (tm-30) REVERT: B 260 MET cc_start: 0.8491 (tmm) cc_final: 0.8164 (tmm) REVERT: B 366 MET cc_start: 0.8205 (ttm) cc_final: 0.8000 (ttm) REVERT: B 487 GLU cc_start: 0.8387 (tp30) cc_final: 0.7947 (tm-30) REVERT: D 79 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8702 (ttm170) REVERT: D 150 MET cc_start: 0.8788 (mmm) cc_final: 0.8496 (tpp) REVERT: D 163 ASP cc_start: 0.8726 (t0) cc_final: 0.8477 (t0) REVERT: D 250 GLN cc_start: 0.8524 (tm-30) cc_final: 0.7940 (tm-30) REVERT: E 111 MET cc_start: 0.9274 (tpp) cc_final: 0.8909 (tpp) REVERT: E 205 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8640 (mp10) REVERT: E 250 GLN cc_start: 0.8683 (tm-30) cc_final: 0.7811 (tm-30) REVERT: F 79 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8585 (ttt-90) REVERT: F 163 ASP cc_start: 0.8818 (t0) cc_final: 0.8502 (t0) REVERT: F 205 GLN cc_start: 0.9209 (OUTLIER) cc_final: 0.8678 (mp10) REVERT: F 250 GLN cc_start: 0.8773 (tm-30) cc_final: 0.7843 (tm-30) REVERT: F 415 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7519 (mm-30) REVERT: F 487 GLU cc_start: 0.8377 (tp30) cc_final: 0.7934 (tm-30) outliers start: 57 outliers final: 36 residues processed: 294 average time/residue: 0.1666 time to fit residues: 75.7450 Evaluate side-chains 266 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 224 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain B residue 72 TRP Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain D residue 72 TRP Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 266 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [229, 193, 190, 90, 24, 129, 32, 213, 51, 59, 215] chunk 229 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 chunk 190 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 129 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 213 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 59 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN C 205 GLN C 297 GLN D 414 GLN F 330 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.079399 restraints weight = 45981.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.082091 restraints weight = 22599.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.083770 restraints weight = 15347.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.084682 restraints weight = 12461.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.084692 restraints weight = 11235.082| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23802 Z= 0.114 Angle : 0.563 8.509 32160 Z= 0.271 Chirality : 0.042 0.168 3486 Planarity : 0.003 0.034 4158 Dihedral : 5.692 102.441 3300 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.22 % Allowed : 25.42 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.16), residues: 2946 helix: 2.50 (0.13), residues: 1596 sheet: -0.02 (0.31), residues: 342 loop : -0.90 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 419 TYR 0.019 0.001 TYR D 310 PHE 0.016 0.001 PHE C 17 TRP 0.012 0.001 TRP F 281 HIS 0.002 0.001 HIS E 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (23802) covalent geometry : angle 0.56299 / 0.27 (32160) hydrogen bonds : bond 0.03526 / 2.40 ( 1288) hydrogen bonds : angle 3.65896 / 2.58 ( 3717) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8632 (mp10) REVERT: A 250 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8350 (tm-30) REVERT: C 150 MET cc_start: 0.8783 (mmm) cc_final: 0.8439 (mmm) REVERT: C 205 GLN cc_start: 0.9244 (mm110) cc_final: 0.8966 (mp10) REVERT: C 250 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 414 GLN cc_start: 0.7914 (tt0) cc_final: 0.7666 (tt0) REVERT: C 495 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7983 (mm-30) REVERT: B 79 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8131 (ttm170) REVERT: B 163 ASP cc_start: 0.8797 (t0) cc_final: 0.8319 (t0) REVERT: B 250 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8143 (tm-30) REVERT: B 487 GLU cc_start: 0.8400 (tp30) cc_final: 0.7960 (tm-30) REVERT: D 79 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8713 (ttm170) REVERT: D 150 MET cc_start: 0.8809 (mmm) cc_final: 0.8544 (tpp) REVERT: D 163 ASP cc_start: 0.8720 (t0) cc_final: 0.8501 (t0) REVERT: D 250 GLN cc_start: 0.8581 (tm-30) cc_final: 0.7968 (tm-30) REVERT: E 111 MET cc_start: 0.9275 (tpp) cc_final: 0.8879 (tpp) REVERT: E 205 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.8659 (mp10) REVERT: E 250 GLN cc_start: 0.8676 (tm-30) cc_final: 0.7825 (tm-30) REVERT: E 260 MET cc_start: 0.8938 (tmm) cc_final: 0.8632 (tmm) REVERT: F 79 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.8097 (ttm170) REVERT: F 163 ASP cc_start: 0.8810 (t0) cc_final: 0.8302 (t0) REVERT: F 205 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8690 (mp10) REVERT: F 250 GLN cc_start: 0.8796 (tm-30) cc_final: 0.7894 (tm-30) REVERT: F 415 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7315 (mm-30) REVERT: F 487 GLU cc_start: 0.8320 (tp30) cc_final: 0.7843 (tm-30) outliers start: 55 outliers final: 43 residues processed: 273 average time/residue: 0.1615 time to fit residues: 69.3213 Evaluate side-chains 270 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 221 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 260 MET Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 72 TRP Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain D residue 72 TRP Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 158 ILE Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 226 PHE Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [55, 5, 257, 130, 45, 33, 12, 190, 35, 15, 126] chunk 55 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 130 optimal weight: 0.0060 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.111793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.079807 restraints weight = 46162.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.082544 restraints weight = 22607.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.084192 restraints weight = 15293.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.085107 restraints weight = 12447.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085528 restraints weight = 11208.027| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23802 Z= 0.109 Angle : 0.561 9.483 32160 Z= 0.270 Chirality : 0.041 0.181 3486 Planarity : 0.003 0.033 4158 Dihedral : 5.663 103.287 3300 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.26 % Allowed : 25.67 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.16), residues: 2946 helix: 2.51 (0.13), residues: 1596 sheet: 0.11 (0.31), residues: 336 loop : -0.91 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 19 TYR 0.018 0.001 TYR D 310 PHE 0.018 0.001 PHE E 17 TRP 0.008 0.001 TRP B 72 HIS 0.002 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (23802) covalent geometry : angle 0.56135 / 0.27 (32160) hydrogen bonds : bond 0.03437 / 2.35 ( 1288) hydrogen bonds : angle 3.62853 / 2.56 ( 3717) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5892 Ramachandran restraints generated. 2946 Oldfield, 0 Emsley, 2946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 235 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8778 (mmm) cc_final: 0.8453 (mmm) REVERT: A 205 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8644 (mp10) REVERT: A 250 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8352 (tm-30) REVERT: A 411 MET cc_start: 0.7177 (tpp) cc_final: 0.6685 (mmt) REVERT: C 150 MET cc_start: 0.8812 (mmm) cc_final: 0.8487 (mmm) REVERT: C 250 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7746 (tm-30) REVERT: C 414 GLN cc_start: 0.7954 (tt0) cc_final: 0.7727 (tt0) REVERT: C 495 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7964 (mm-30) REVERT: B 79 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8153 (ttm170) REVERT: B 150 MET cc_start: 0.8811 (tpp) cc_final: 0.8541 (mmm) REVERT: B 163 ASP cc_start: 0.8797 (t0) cc_final: 0.8305 (t0) REVERT: B 250 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8094 (tm-30) REVERT: B 487 GLU cc_start: 0.8401 (tp30) cc_final: 0.7956 (tm-30) REVERT: D 79 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8714 (ttm170) REVERT: D 150 MET cc_start: 0.8824 (mmm) cc_final: 0.8588 (tpp) REVERT: D 163 ASP cc_start: 0.8705 (t0) cc_final: 0.8481 (t0) REVERT: D 250 GLN cc_start: 0.8570 (tm-30) cc_final: 0.7955 (tm-30) REVERT: E 111 MET cc_start: 0.9266 (tpp) cc_final: 0.8890 (tpp) REVERT: E 205 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.8652 (mp10) REVERT: E 250 GLN cc_start: 0.8741 (tm-30) cc_final: 0.7881 (tm-30) REVERT: E 260 MET cc_start: 0.8972 (tmm) cc_final: 0.8636 (tmm) REVERT: E 487 GLU cc_start: 0.8285 (tp30) cc_final: 0.7865 (tm-30) REVERT: F 79 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8141 (ttm170) REVERT: F 163 ASP cc_start: 0.8798 (t0) cc_final: 0.8306 (t0) REVERT: F 205 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8692 (mp10) REVERT: F 250 GLN cc_start: 0.8778 (tm-30) cc_final: 0.7887 (tm-30) REVERT: F 415 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7293 (mm-30) REVERT: F 487 GLU cc_start: 0.8334 (tp30) cc_final: 0.7868 (tm-30) outliers start: 56 outliers final: 44 residues processed: 274 average time/residue: 0.1569 time to fit residues: 67.5479 Evaluate side-chains 273 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 215 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 331 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain D residue 72 TRP Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain D residue 389 LEU Chi-restraints excluded: chain D residue 411 MET Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 244 ASP Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 344 ILE Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain F residue 79 ARG Chi-restraints excluded: chain F residue 205 GLN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 260 MET Chi-restraints excluded: chain F residue 344 ILE Chi-restraints excluded: chain F residue 389 LEU Chi-restraints excluded: chain F residue 403 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: [247, 106, 129, 55, 61, 42, 69, 285, 243, 150, 265] chunk 247 optimal weight: 0.0170 chunk 106 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 69 optimal weight: 0.4980 chunk 285 optimal weight: 0.9980 chunk 243 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 297 GLN B 264 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.112309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.080396 restraints weight = 45797.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.083122 restraints weight = 22471.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.084769 restraints weight = 15232.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085712 restraints weight = 12421.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.086118 restraints weight = 11156.978| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23802 Z= 0.104 Angle : 0.559 8.319 32160 Z= 0.268 Chirality : 0.041 0.183 3486 Planarity : 0.003 0.032 4158 Dihedral : 5.619 104.169 3300 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 25.63 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.16), residues: 2946 helix: 2.54 (0.13), residues: 1596 sheet: 0.15 (0.31), residues: 336 loop : -0.88 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 419 TYR 0.017 0.001 TYR D 310 PHE 0.015 0.001 PHE A 17 TRP 0.008 0.001 TRP B 72 HIS 0.002 0.001 HIS E 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (23802) covalent geometry : angle 0.55889 / 0.27 (32160) hydrogen bonds : bond 0.03318 / 2.26 ( 1288) hydrogen bonds : angle 3.60776 / 2.55 ( 3717) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3492.21 seconds wall clock time: 61 minutes 28.18 seconds (3688.18 seconds total)