Starting phenix.real_space_refine on Sun Dec 29 01:46:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bl7_16102/12_2024/8bl7_16102.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bl7_16102/12_2024/8bl7_16102.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bl7_16102/12_2024/8bl7_16102.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bl7_16102/12_2024/8bl7_16102.map" model { file = "/net/cci-nas-00/data/ceres_data/8bl7_16102/12_2024/8bl7_16102.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bl7_16102/12_2024/8bl7_16102.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 42 5.49 5 S 280 5.16 5 C 33754 2.51 5 N 9408 2.21 5 O 10990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 54474 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3860 Classifications: {'peptide': 525} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 510} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.43, per 1000 atoms: 0.43 Number of scatterers: 54474 At special positions: 0 Unit cell: (153.6, 154.56, 160.32, 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 280 16.00 P 42 15.00 O 10990 8.00 N 9408 7.00 C 33754 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: 10.28 Conformation dependent library (CDL) restraints added in 5.7 seconds 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13300 Finding SS restraints... Secondary structure from input PDB file: 278 helices and 98 sheets defined 59.4% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.822A pdb=" N GLU A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 85 Processing helix chain 'A' and resid 88 through 108 Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 281 through 297 Processing helix chain 'A' and resid 338 through 356 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.797A pdb=" N GLY A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 409 removed outlier: 3.547A pdb=" N GLU A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 433 through 447 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 497 through 516 removed outlier: 3.728A pdb=" N THR A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.692A pdb=" N GLU B 59 " --> pdb=" O SER B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.559A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 255 through 269 Processing helix chain 'B' and resid 281 through 297 Processing helix chain 'B' and resid 338 through 356 Processing helix chain 'B' and resid 358 through 375 removed outlier: 3.933A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 409 removed outlier: 3.562A pdb=" N GLU B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 426 Processing helix chain 'B' and resid 433 through 447 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 461 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 removed outlier: 3.600A pdb=" N THR B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 29 Processing helix chain 'C' and resid 52 through 60 Processing helix chain 'C' and resid 64 through 85 Processing helix chain 'C' and resid 88 through 109 Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 removed outlier: 3.529A pdb=" N GLY C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 255 through 269 Processing helix chain 'C' and resid 281 through 297 Processing helix chain 'C' and resid 338 through 356 Processing helix chain 'C' and resid 358 through 375 removed outlier: 3.887A pdb=" N GLY C 375 " --> pdb=" O LYS C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 409 removed outlier: 3.554A pdb=" N GLU C 409 " --> pdb=" O ALA C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 425 Processing helix chain 'C' and resid 433 through 448 removed outlier: 3.859A pdb=" N GLU C 448 " --> pdb=" O LEU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'C' and resid 488 through 492 Processing helix chain 'C' and resid 497 through 516 removed outlier: 3.567A pdb=" N THR C 516 " --> pdb=" O GLY C 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 52 through 60 Processing helix chain 'D' and resid 64 through 85 Processing helix chain 'D' and resid 88 through 109 Processing helix chain 'D' and resid 112 through 134 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.541A pdb=" N GLY D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 281 through 297 Processing helix chain 'D' and resid 338 through 356 Processing helix chain 'D' and resid 358 through 375 removed outlier: 3.876A pdb=" N GLY D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 409 removed outlier: 3.509A pdb=" N GLU D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 426 Processing helix chain 'D' and resid 433 through 448 removed outlier: 3.904A pdb=" N GLU D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'D' and resid 461 through 472 Processing helix chain 'D' and resid 488 through 492 Processing helix chain 'D' and resid 497 through 516 removed outlier: 3.743A pdb=" N THR D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 29 Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.568A pdb=" N GLU E 59 " --> pdb=" O SER E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 85 Processing helix chain 'E' and resid 88 through 109 Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 removed outlier: 3.545A pdb=" N GLY E 159 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 255 through 269 Processing helix chain 'E' and resid 281 through 297 Processing helix chain 'E' and resid 338 through 356 Processing helix chain 'E' and resid 358 through 375 removed outlier: 3.888A pdb=" N GLY E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 409 Processing helix chain 'E' and resid 416 through 425 Processing helix chain 'E' and resid 433 through 448 removed outlier: 3.897A pdb=" N GLU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'E' and resid 461 through 472 Processing helix chain 'E' and resid 488 through 492 Processing helix chain 'E' and resid 497 through 516 removed outlier: 3.748A pdb=" N THR E 516 " --> pdb=" O GLY E 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.715A pdb=" N GLU F 59 " --> pdb=" O SER F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 85 Processing helix chain 'F' and resid 88 through 109 Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 removed outlier: 3.546A pdb=" N GLY F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 255 through 269 Processing helix chain 'F' and resid 281 through 297 Processing helix chain 'F' and resid 338 through 356 Processing helix chain 'F' and resid 358 through 375 removed outlier: 4.052A pdb=" N GLY F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 409 removed outlier: 3.514A pdb=" N GLU F 409 " --> pdb=" O ALA F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 426 Processing helix chain 'F' and resid 433 through 448 removed outlier: 3.956A pdb=" N GLU F 448 " --> pdb=" O LEU F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 459 Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'F' and resid 488 through 492 Processing helix chain 'F' and resid 497 through 516 removed outlier: 3.717A pdb=" N THR F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 29 Processing helix chain 'G' and resid 52 through 58 Processing helix chain 'G' and resid 64 through 85 Processing helix chain 'G' and resid 88 through 109 Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 removed outlier: 3.546A pdb=" N GLY G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 255 through 269 Processing helix chain 'G' and resid 281 through 297 Processing helix chain 'G' and resid 338 through 356 Processing helix chain 'G' and resid 358 through 375 removed outlier: 3.842A pdb=" N GLY G 375 " --> pdb=" O LYS G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 409 removed outlier: 3.529A pdb=" N GLU G 409 " --> pdb=" O ALA G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 426 Processing helix chain 'G' and resid 433 through 447 Processing helix chain 'G' and resid 448 through 459 Processing helix chain 'G' and resid 461 through 472 Processing helix chain 'G' and resid 497 through 516 removed outlier: 3.868A pdb=" N THR G 516 " --> pdb=" O GLY G 512 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 29 Processing helix chain 'H' and resid 52 through 59 Processing helix chain 'H' and resid 64 through 85 Processing helix chain 'H' and resid 88 through 108 Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 233 through 244 Processing helix chain 'H' and resid 255 through 269 Processing helix chain 'H' and resid 281 through 297 Processing helix chain 'H' and resid 338 through 356 Processing helix chain 'H' and resid 358 through 375 removed outlier: 3.861A pdb=" N GLY H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 409 removed outlier: 3.546A pdb=" N GLU H 409 " --> pdb=" O ALA H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 426 Processing helix chain 'H' and resid 433 through 448 removed outlier: 3.930A pdb=" N GLU H 448 " --> pdb=" O LEU H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 459 Processing helix chain 'H' and resid 461 through 472 Processing helix chain 'H' and resid 488 through 492 Processing helix chain 'H' and resid 497 through 516 removed outlier: 3.893A pdb=" N THR H 516 " --> pdb=" O GLY H 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 29 Processing helix chain 'I' and resid 52 through 58 Processing helix chain 'I' and resid 64 through 85 Processing helix chain 'I' and resid 88 through 109 removed outlier: 3.518A pdb=" N ALA I 109 " --> pdb=" O LYS I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 removed outlier: 3.547A pdb=" N GLY I 159 " --> pdb=" O ASP I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 255 through 269 Processing helix chain 'I' and resid 281 through 297 Processing helix chain 'I' and resid 338 through 356 Processing helix chain 'I' and resid 358 through 375 removed outlier: 3.730A pdb=" N GLY I 375 " --> pdb=" O LYS I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 409 removed outlier: 3.541A pdb=" N GLU I 409 " --> pdb=" O ALA I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 426 Processing helix chain 'I' and resid 433 through 447 Processing helix chain 'I' and resid 448 through 459 Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'I' and resid 488 through 492 Processing helix chain 'I' and resid 497 through 516 removed outlier: 3.767A pdb=" N THR I 516 " --> pdb=" O GLY I 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 29 Processing helix chain 'J' and resid 52 through 60 removed outlier: 3.612A pdb=" N GLU J 59 " --> pdb=" O SER J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 85 Processing helix chain 'J' and resid 88 through 109 Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 155 through 170 removed outlier: 3.556A pdb=" N GLY J 159 " --> pdb=" O ASP J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 255 through 269 Processing helix chain 'J' and resid 281 through 297 Processing helix chain 'J' and resid 338 through 356 Processing helix chain 'J' and resid 358 through 375 removed outlier: 4.100A pdb=" N GLY J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 409 removed outlier: 3.527A pdb=" N GLU J 409 " --> pdb=" O ALA J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 416 through 425 Processing helix chain 'J' and resid 433 through 448 removed outlier: 3.845A pdb=" N GLU J 448 " --> pdb=" O LEU J 444 " (cutoff:3.500A) Processing helix chain 'J' and resid 448 through 459 Processing helix chain 'J' and resid 461 through 472 Processing helix chain 'J' and resid 488 through 492 Processing helix chain 'J' and resid 497 through 516 removed outlier: 3.536A pdb=" N THR J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 29 Processing helix chain 'K' and resid 52 through 60 removed outlier: 3.506A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 85 Processing helix chain 'K' and resid 88 through 109 Processing helix chain 'K' and resid 112 through 134 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 removed outlier: 3.516A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 255 through 269 Processing helix chain 'K' and resid 281 through 297 Processing helix chain 'K' and resid 338 through 356 Processing helix chain 'K' and resid 358 through 375 removed outlier: 3.947A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 409 Processing helix chain 'K' and resid 416 through 426 Processing helix chain 'K' and resid 433 through 448 removed outlier: 3.948A pdb=" N GLU K 448 " --> pdb=" O LEU K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 448 through 459 Processing helix chain 'K' and resid 461 through 472 Processing helix chain 'K' and resid 488 through 492 Processing helix chain 'K' and resid 497 through 516 removed outlier: 3.734A pdb=" N THR K 516 " --> pdb=" O GLY K 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 29 Processing helix chain 'L' and resid 52 through 60 removed outlier: 3.696A pdb=" N GLU L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 85 Processing helix chain 'L' and resid 88 through 109 Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 170 removed outlier: 3.554A pdb=" N GLY L 159 " --> pdb=" O ASP L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 255 through 269 Processing helix chain 'L' and resid 281 through 297 Processing helix chain 'L' and resid 338 through 356 Processing helix chain 'L' and resid 358 through 375 removed outlier: 3.989A pdb=" N GLY L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 409 removed outlier: 3.556A pdb=" N GLU L 409 " --> pdb=" O ALA L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 416 through 426 Processing helix chain 'L' and resid 433 through 448 removed outlier: 3.958A pdb=" N GLU L 448 " --> pdb=" O LEU L 444 " (cutoff:3.500A) Processing helix chain 'L' and resid 448 through 459 Processing helix chain 'L' and resid 461 through 472 Processing helix chain 'L' and resid 488 through 492 Processing helix chain 'L' and resid 497 through 516 removed outlier: 3.661A pdb=" N THR L 516 " --> pdb=" O GLY L 512 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 29 Processing helix chain 'M' and resid 52 through 59 removed outlier: 3.801A pdb=" N GLU M 59 " --> pdb=" O SER M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 85 Processing helix chain 'M' and resid 88 through 109 Processing helix chain 'M' and resid 112 through 134 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 removed outlier: 3.557A pdb=" N GLY M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 233 through 244 Processing helix chain 'M' and resid 255 through 269 Processing helix chain 'M' and resid 281 through 297 Processing helix chain 'M' and resid 338 through 356 Processing helix chain 'M' and resid 358 through 375 removed outlier: 3.857A pdb=" N GLY M 375 " --> pdb=" O LYS M 371 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 409 Processing helix chain 'M' and resid 416 through 426 Processing helix chain 'M' and resid 433 through 448 removed outlier: 3.955A pdb=" N GLU M 448 " --> pdb=" O LEU M 444 " (cutoff:3.500A) Processing helix chain 'M' and resid 448 through 459 Processing helix chain 'M' and resid 461 through 472 Processing helix chain 'M' and resid 488 through 492 Processing helix chain 'M' and resid 497 through 516 removed outlier: 3.703A pdb=" N THR M 516 " --> pdb=" O GLY M 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 29 removed outlier: 3.519A pdb=" N ARG N 13 " --> pdb=" O GLY N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 58 Processing helix chain 'N' and resid 64 through 85 Processing helix chain 'N' and resid 88 through 108 Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 155 through 170 removed outlier: 3.562A pdb=" N GLY N 159 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 205 Processing helix chain 'N' and resid 233 through 244 Processing helix chain 'N' and resid 255 through 269 Processing helix chain 'N' and resid 281 through 297 Processing helix chain 'N' and resid 338 through 356 Processing helix chain 'N' and resid 358 through 375 removed outlier: 4.031A pdb=" N GLY N 375 " --> pdb=" O LYS N 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 409 removed outlier: 3.538A pdb=" N GLU N 409 " --> pdb=" O ALA N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 426 Processing helix chain 'N' and resid 433 through 447 Processing helix chain 'N' and resid 448 through 459 Processing helix chain 'N' and resid 461 through 472 Processing helix chain 'N' and resid 497 through 516 removed outlier: 3.897A pdb=" N THR N 516 " --> pdb=" O GLY N 512 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 4.273A pdb=" N THR A 517 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL B 39 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N CYS A 519 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.939A pdb=" N ASN A 37 " --> pdb=" O THR G 517 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N CYS G 519 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL G 521 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.349A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 192 through 195 removed outlier: 6.340A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 216 removed outlier: 9.340A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LEU A 222 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA9, first strand: chain 'B' and resid 4 through 7 removed outlier: 6.584A pdb=" N VAL C 39 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N MET B 520 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.667A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 192 through 195 removed outlier: 6.327A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 213 through 216 removed outlier: 9.386A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU B 222 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 226 through 227 Processing sheet with id=AB5, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AB6, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 7 removed outlier: 4.057A pdb=" N THR C 517 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL D 39 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N CYS C 519 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 174 through 179 removed outlier: 6.451A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU C 178 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 192 through 195 removed outlier: 6.340A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 213 through 216 removed outlier: 9.396A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU C 222 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AC3, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC4, first strand: chain 'C' and resid 476 through 479 Processing sheet with id=AC5, first strand: chain 'D' and resid 4 through 7 removed outlier: 4.189A pdb=" N THR D 517 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL E 39 " --> pdb=" O THR D 517 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N CYS D 519 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 175 through 179 removed outlier: 6.397A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.318A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 213 through 216 removed outlier: 9.324A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU D 222 " --> pdb=" O ILE D 301 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 226 through 227 Processing sheet with id=AD1, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AD2, first strand: chain 'D' and resid 476 through 479 Processing sheet with id=AD3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.514A pdb=" N LYS E 7 " --> pdb=" O MET E 520 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N THR E 517 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL F 39 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N CYS E 519 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 174 through 179 removed outlier: 6.372A pdb=" N VAL E 174 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE E 379 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR E 176 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL E 381 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLU E 178 " --> pdb=" O VAL E 381 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 192 through 195 removed outlier: 6.425A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 213 through 216 removed outlier: 9.343A pdb=" N ILE E 301 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LEU E 222 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 226 through 227 Processing sheet with id=AD8, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AD9, first strand: chain 'E' and resid 476 through 479 Processing sheet with id=AE1, first strand: chain 'F' and resid 4 through 7 removed outlier: 4.294A pdb=" N THR F 517 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL G 39 " --> pdb=" O THR F 517 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS F 519 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 174 through 179 removed outlier: 6.727A pdb=" N VAL F 174 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE F 379 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLU F 178 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 192 through 195 removed outlier: 6.330A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 213 through 216 removed outlier: 9.327A pdb=" N ILE F 301 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU F 222 " --> pdb=" O ILE F 301 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 226 through 227 Processing sheet with id=AE6, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AE7, first strand: chain 'F' and resid 476 through 479 Processing sheet with id=AE8, first strand: chain 'G' and resid 175 through 179 Processing sheet with id=AE9, first strand: chain 'G' and resid 192 through 195 removed outlier: 6.287A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 213 through 216 removed outlier: 9.360A pdb=" N ILE G 301 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU G 222 " --> pdb=" O ILE G 301 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 226 through 227 Processing sheet with id=AF3, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AF4, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AF5, first strand: chain 'H' and resid 4 through 7 removed outlier: 6.504A pdb=" N VAL I 39 " --> pdb=" O GLU H 518 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N MET H 520 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 48 through 50 removed outlier: 7.090A pdb=" N ASN H 37 " --> pdb=" O THR N 517 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N CYS N 519 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL H 39 " --> pdb=" O CYS N 519 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL N 521 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 174 through 179 removed outlier: 6.692A pdb=" N VAL H 174 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE H 379 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR H 176 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL H 381 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLU H 178 " --> pdb=" O VAL H 381 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 192 through 195 removed outlier: 6.255A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU H 247 " --> pdb=" O ALA H 274 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 213 through 216 removed outlier: 9.323A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 226 through 227 Processing sheet with id=AG2, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AG3, first strand: chain 'H' and resid 476 through 479 Processing sheet with id=AG4, first strand: chain 'I' and resid 4 through 7 removed outlier: 4.047A pdb=" N THR I 517 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL J 39 " --> pdb=" O THR I 517 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N CYS I 519 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 174 through 179 removed outlier: 6.401A pdb=" N VAL I 174 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE I 379 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR I 176 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL I 381 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLU I 178 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.348A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU I 247 " --> pdb=" O ALA I 274 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 213 through 216 removed outlier: 9.360A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 226 through 227 Processing sheet with id=AG9, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AH1, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AH2, first strand: chain 'J' and resid 4 through 8 removed outlier: 3.993A pdb=" N THR J 517 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL K 39 " --> pdb=" O THR J 517 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS J 519 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 174 through 179 removed outlier: 6.427A pdb=" N VAL J 174 " --> pdb=" O ALA J 377 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE J 379 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N THR J 176 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL J 381 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLU J 178 " --> pdb=" O VAL J 381 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 192 through 195 removed outlier: 6.327A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 213 through 216 removed outlier: 9.386A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU J 222 " --> pdb=" O ILE J 301 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 226 through 227 Processing sheet with id=AH7, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AH8, first strand: chain 'J' and resid 476 through 479 Processing sheet with id=AH9, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AI1, first strand: chain 'K' and resid 174 through 179 removed outlier: 6.686A pdb=" N VAL K 174 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE K 379 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR K 176 " --> pdb=" O ILE K 379 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N VAL K 381 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLU K 178 " --> pdb=" O VAL K 381 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.327A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 213 through 216 removed outlier: 9.355A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 226 through 227 Processing sheet with id=AI5, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AI6, first strand: chain 'K' and resid 476 through 479 Processing sheet with id=AI7, first strand: chain 'K' and resid 517 through 520 removed outlier: 3.527A pdb=" N GLU K 518 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL L 39 " --> pdb=" O GLU K 518 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N MET K 520 " --> pdb=" O VAL L 39 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 4 through 8 removed outlier: 4.110A pdb=" N THR L 517 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL M 39 " --> pdb=" O THR L 517 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N CYS L 519 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'L' and resid 174 through 179 removed outlier: 6.553A pdb=" N VAL L 174 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE L 379 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR L 176 " --> pdb=" O ILE L 379 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL L 381 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU L 178 " --> pdb=" O VAL L 381 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 192 through 195 removed outlier: 6.287A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 213 through 216 removed outlier: 9.367A pdb=" N ILE L 301 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU L 222 " --> pdb=" O ILE L 301 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AJ4, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AJ5, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.530A pdb=" N LYS M 7 " --> pdb=" O MET M 520 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR M 517 " --> pdb=" O ASN N 37 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL N 39 " --> pdb=" O THR M 517 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS M 519 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'M' and resid 174 through 179 removed outlier: 6.677A pdb=" N VAL M 174 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE M 379 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL M 381 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N GLU M 178 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'M' and resid 192 through 195 removed outlier: 6.334A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'M' and resid 213 through 216 removed outlier: 9.337A pdb=" N ILE M 301 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU M 222 " --> pdb=" O ILE M 301 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'M' and resid 226 through 227 Processing sheet with id=AK1, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AK2, first strand: chain 'M' and resid 476 through 479 Processing sheet with id=AK3, first strand: chain 'N' and resid 174 through 179 removed outlier: 6.781A pdb=" N VAL N 174 " --> pdb=" O ALA N 377 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ILE N 379 " --> pdb=" O VAL N 174 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR N 176 " --> pdb=" O ILE N 379 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL N 381 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU N 178 " --> pdb=" O VAL N 381 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'N' and resid 192 through 195 removed outlier: 6.287A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'N' and resid 213 through 216 removed outlier: 9.380A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'N' and resid 226 through 227 Processing sheet with id=AK7, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AK8, first strand: chain 'N' and resid 476 through 479 3767 hydrogen bonds defined for protein. 10878 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: 24.94 Time building geometry restraints manager: 12.17 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: 18543 1.34 - 1.46: 8010 1.46 - 1.58: 27768 1.58 - 1.70: 55 1.70 - 1.82: 518 Bond restraints: 54894 Sorted by residual: bond pdb=" CB VAL K 38 " pdb=" CG1 VAL K 38 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CG1 ILE N 60 " pdb=" CD1 ILE N 60 " ideal model delta sigma weight residual 1.513 1.451 0.062 3.90e-02 6.57e+02 2.54e+00 bond pdb=" CD GLU G 164 " pdb=" OE1 GLU G 164 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.33e+00 bond pdb=" CD GLU N 164 " pdb=" OE1 GLU N 164 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.26e+00 bond pdb=" CD GLU K 164 " pdb=" OE1 GLU K 164 " ideal model delta sigma weight residual 1.249 1.222 0.027 1.90e-02 2.77e+03 2.09e+00 ... (remaining 54889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 71817 1.97 - 3.94: 2022 3.94 - 5.90: 252 5.90 - 7.87: 104 7.87 - 9.84: 19 Bond angle restraints: 74214 Sorted by residual: angle pdb=" N GLU D 164 " pdb=" CA GLU D 164 " pdb=" CB GLU D 164 " ideal model delta sigma weight residual 110.16 116.92 -6.76 1.48e+00 4.57e-01 2.08e+01 angle pdb=" N GLU B 164 " pdb=" CA GLU B 164 " pdb=" CB GLU B 164 " ideal model delta sigma weight residual 110.16 116.85 -6.69 1.48e+00 4.57e-01 2.04e+01 angle pdb=" N GLU H 164 " pdb=" CA GLU H 164 " pdb=" CB GLU H 164 " ideal model delta sigma weight residual 110.16 116.83 -6.67 1.48e+00 4.57e-01 2.03e+01 angle pdb=" N GLU A 164 " pdb=" CA GLU A 164 " pdb=" CB GLU A 164 " ideal model delta sigma weight residual 110.16 116.77 -6.61 1.48e+00 4.57e-01 1.99e+01 angle pdb=" N GLU E 164 " pdb=" CA GLU E 164 " pdb=" CB GLU E 164 " ideal model delta sigma weight residual 110.16 116.65 -6.49 1.48e+00 4.57e-01 1.92e+01 ... (remaining 74209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 31200 17.97 - 35.93: 2516 35.93 - 53.90: 461 53.90 - 71.87: 98 71.87 - 89.83: 25 Dihedral angle restraints: 34300 sinusoidal: 13566 harmonic: 20734 Sorted by residual: dihedral pdb=" CA ASP D 41 " pdb=" C ASP D 41 " pdb=" N LYS D 42 " pdb=" CA LYS D 42 " ideal model delta harmonic sigma weight residual 180.00 148.44 31.56 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA ASP E 41 " pdb=" C ASP E 41 " pdb=" N LYS E 42 " pdb=" CA LYS E 42 " ideal model delta harmonic sigma weight residual 180.00 151.08 28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ASP F 41 " pdb=" C ASP F 41 " pdb=" N LYS F 42 " pdb=" CA LYS F 42 " ideal model delta harmonic sigma weight residual 180.00 152.32 27.68 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 34297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 5782 0.037 - 0.074: 2040 0.074 - 0.110: 852 0.110 - 0.147: 289 0.147 - 0.184: 39 Chirality restraints: 9002 Sorted by residual: chirality pdb=" CB VAL C 39 " pdb=" CA VAL C 39 " pdb=" CG1 VAL C 39 " pdb=" CG2 VAL C 39 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.47e-01 chirality pdb=" CA GLU G 164 " pdb=" N GLU G 164 " pdb=" C GLU G 164 " pdb=" CB GLU G 164 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA GLU L 164 " pdb=" N GLU L 164 " pdb=" C GLU L 164 " pdb=" CB GLU L 164 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 ... (remaining 8999 not shown) Planarity restraints: 9632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 311 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C LYS E 311 " 0.037 2.00e-02 2.50e+03 pdb=" O LYS E 311 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA E 312 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP M 41 " -0.008 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" CG ASP M 41 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP M 41 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP M 41 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET N 514 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C MET N 514 " 0.029 2.00e-02 2.50e+03 pdb=" O MET N 514 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE N 515 " -0.010 2.00e-02 2.50e+03 ... (remaining 9629 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 13280 2.80 - 3.32: 55846 3.32 - 3.85: 95819 3.85 - 4.37: 109401 4.37 - 4.90: 183366 Nonbonded interactions: 457712 Sorted by model distance: nonbonded pdb=" OD2 ASP H 41 " pdb=" NZ LYS N 4 " model vdw 2.270 3.120 nonbonded pdb=" OG1 THR E 90 " pdb=" O2B ATP E 601 " model vdw 2.290 3.040 nonbonded pdb=" NZ LYS L 4 " pdb=" OE1 GLU M 59 " model vdw 2.298 3.120 nonbonded pdb=" OG1 THR F 90 " pdb=" O2B ATP F 601 " model vdw 2.316 3.040 nonbonded pdb=" O GLU A 397 " pdb=" ND1 HIS A 401 " model vdw 2.321 3.120 ... (remaining 457707 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.680 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: 0.060 Extract box with map and model: 1.530 Check model and map are aligned: 0.290 Set scattering table: 0.420 Process input model: 99.010 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.370 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: 0.020 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 0.062 54894 Z= 0.259 Angle : 0.782 9.839 74214 Z= 0.434 Chirality : 0.048 0.184 9002 Planarity : 0.005 0.038 9632 Dihedral : 13.646 89.832 21000 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.09), residues: 7322 helix: 0.20 (0.07), residues: 4088 sheet: -0.29 (0.15), residues: 1050 loop : -0.81 (0.11), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 401 PHE 0.014 0.002 PHE G 195 TYR 0.020 0.001 TYR G 203 ARG 0.005 0.001 ARG D 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 597 time to evaluate : 4.530 Fit side-chains revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8568 (t) cc_final: 0.8346 (t) REVERT: A 517 THR cc_start: 0.9453 (m) cc_final: 0.9060 (p) REVERT: B 401 HIS cc_start: 0.8782 (m90) cc_final: 0.8534 (m90) REVERT: B 514 MET cc_start: 0.8404 (ttm) cc_final: 0.7556 (ttm) REVERT: B 517 THR cc_start: 0.9416 (m) cc_final: 0.8994 (p) REVERT: C 22 VAL cc_start: 0.8793 (t) cc_final: 0.8548 (t) REVERT: C 111 MET cc_start: 0.7140 (mmm) cc_final: 0.6520 (tpt) REVERT: C 307 MET cc_start: 0.8558 (pmm) cc_final: 0.8267 (pmm) REVERT: C 400 LEU cc_start: 0.9449 (tp) cc_final: 0.9129 (pp) REVERT: C 488 MET cc_start: 0.8094 (mmt) cc_final: 0.7445 (mmp) REVERT: F 111 MET cc_start: 0.7366 (mmm) cc_final: 0.6643 (mmt) REVERT: G 488 MET cc_start: 0.7753 (tpt) cc_final: 0.7231 (tpt) REVERT: H 22 VAL cc_start: 0.8550 (t) cc_final: 0.8316 (t) REVERT: H 69 MET cc_start: 0.8807 (mtp) cc_final: 0.8427 (mmm) REVERT: H 114 MET cc_start: 0.6610 (tmm) cc_final: 0.6372 (tmm) REVERT: H 488 MET cc_start: 0.7959 (mmp) cc_final: 0.7631 (mmt) REVERT: H 517 THR cc_start: 0.9409 (m) cc_final: 0.9049 (p) REVERT: I 64 ASP cc_start: 0.7973 (t0) cc_final: 0.7686 (t0) REVERT: I 166 MET cc_start: 0.9333 (tmm) cc_final: 0.9068 (tpt) REVERT: I 488 MET cc_start: 0.8254 (mmt) cc_final: 0.7846 (mmp) REVERT: J 307 MET cc_start: 0.8499 (pmm) cc_final: 0.8295 (pmm) REVERT: J 400 LEU cc_start: 0.9340 (tp) cc_final: 0.9133 (pp) REVERT: K 514 MET cc_start: 0.8547 (ttm) cc_final: 0.8297 (ttm) REVERT: K 517 THR cc_start: 0.9492 (m) cc_final: 0.9024 (p) REVERT: L 307 MET cc_start: 0.8132 (pmm) cc_final: 0.7778 (pmm) REVERT: L 400 LEU cc_start: 0.9319 (tp) cc_final: 0.9047 (pp) REVERT: L 514 MET cc_start: 0.8592 (ttm) cc_final: 0.8313 (ttm) REVERT: L 517 THR cc_start: 0.9348 (m) cc_final: 0.8960 (p) REVERT: M 267 MET cc_start: 0.6485 (mmm) cc_final: 0.5984 (ptt) REVERT: M 488 MET cc_start: 0.7970 (mmt) cc_final: 0.7051 (mmp) REVERT: N 114 MET cc_start: 0.6736 (tmm) cc_final: 0.6288 (tmm) REVERT: N 488 MET cc_start: 0.7626 (tpt) cc_final: 0.7164 (tpt) REVERT: N 520 MET cc_start: 0.6640 (ttt) cc_final: 0.6239 (ttt) outliers start: 0 outliers final: 0 residues processed: 597 average time/residue: 0.4906 time to fit residues: 521.1225 Evaluate side-chains 447 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 4.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 614 optimal weight: 9.9990 chunk 551 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 570 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 346 optimal weight: 6.9990 chunk 424 optimal weight: 5.9990 chunk 661 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 457 ASN ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 54894 Z= 0.442 Angle : 0.676 7.625 74214 Z= 0.371 Chirality : 0.045 0.144 9002 Planarity : 0.004 0.038 9632 Dihedral : 8.758 71.260 8218 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.60 % Allowed : 5.83 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.09), residues: 7322 helix: 0.69 (0.08), residues: 4284 sheet: -0.37 (0.15), residues: 1050 loop : -0.86 (0.12), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 401 PHE 0.014 0.002 PHE C 8 TYR 0.013 0.002 TYR L 476 ARG 0.007 0.001 ARG N 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 473 time to evaluate : 4.587 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6973 (tmm) cc_final: 0.6725 (tmm) REVERT: B 419 LEU cc_start: 0.9325 (mt) cc_final: 0.9029 (mp) REVERT: C 111 MET cc_start: 0.7735 (mmm) cc_final: 0.7121 (mmm) REVERT: C 114 MET cc_start: 0.6999 (tmm) cc_final: 0.6693 (tmm) REVERT: C 307 MET cc_start: 0.8731 (pmm) cc_final: 0.8486 (pmm) REVERT: E 195 PHE cc_start: 0.8736 (p90) cc_final: 0.8516 (p90) REVERT: E 488 MET cc_start: 0.8197 (mmt) cc_final: 0.7627 (mmt) REVERT: E 519 CYS cc_start: 0.7269 (m) cc_final: 0.7060 (m) REVERT: F 114 MET cc_start: 0.7087 (tmm) cc_final: 0.6712 (tmm) REVERT: G 488 MET cc_start: 0.8149 (tpt) cc_final: 0.7648 (mmm) REVERT: G 519 CYS cc_start: 0.6933 (m) cc_final: 0.6005 (t) REVERT: H 114 MET cc_start: 0.7147 (tmm) cc_final: 0.6684 (tmm) REVERT: H 288 MET cc_start: 0.9533 (ppp) cc_final: 0.9323 (ppp) REVERT: H 488 MET cc_start: 0.8059 (mmp) cc_final: 0.7526 (mmt) REVERT: H 519 CYS cc_start: 0.6986 (m) cc_final: 0.6617 (t) REVERT: I 114 MET cc_start: 0.7146 (tmm) cc_final: 0.6778 (tmm) REVERT: I 488 MET cc_start: 0.8743 (mmt) cc_final: 0.8175 (mmt) REVERT: J 400 LEU cc_start: 0.9448 (tp) cc_final: 0.9234 (pp) REVERT: J 488 MET cc_start: 0.8204 (mmt) cc_final: 0.7728 (mmp) REVERT: K 114 MET cc_start: 0.7102 (tmm) cc_final: 0.6794 (tmm) REVERT: L 111 MET cc_start: 0.7084 (tpp) cc_final: 0.6543 (tpp) REVERT: L 114 MET cc_start: 0.7196 (tmm) cc_final: 0.6812 (tmm) REVERT: L 307 MET cc_start: 0.8252 (pmm) cc_final: 0.7914 (pmm) REVERT: L 488 MET cc_start: 0.8246 (mmt) cc_final: 0.7907 (mmt) REVERT: M 22 VAL cc_start: 0.8873 (t) cc_final: 0.8518 (t) REVERT: M 111 MET cc_start: 0.8012 (mmm) cc_final: 0.7771 (mmm) REVERT: M 114 MET cc_start: 0.7031 (tmm) cc_final: 0.6759 (tmm) REVERT: M 267 MET cc_start: 0.6412 (mmm) cc_final: 0.5881 (ptt) REVERT: M 488 MET cc_start: 0.8216 (mmt) cc_final: 0.7760 (mmt) REVERT: N 111 MET cc_start: 0.6801 (tpp) cc_final: 0.6503 (mmm) REVERT: N 114 MET cc_start: 0.6922 (tmm) cc_final: 0.6455 (tmm) REVERT: N 488 MET cc_start: 0.7986 (tpt) cc_final: 0.7446 (mmm) outliers start: 34 outliers final: 27 residues processed: 503 average time/residue: 0.4676 time to fit residues: 416.9372 Evaluate side-chains 415 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 388 time to evaluate : 4.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 550 optimal weight: 0.3980 chunk 450 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 662 optimal weight: 4.9990 chunk 715 optimal weight: 0.9990 chunk 589 optimal weight: 1.9990 chunk 656 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 531 optimal weight: 0.0970 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN ** F 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 ASN ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 54894 Z= 0.165 Angle : 0.524 6.918 74214 Z= 0.285 Chirality : 0.041 0.151 9002 Planarity : 0.003 0.049 9632 Dihedral : 8.417 69.805 8218 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.09), residues: 7322 helix: 1.11 (0.08), residues: 4312 sheet: -0.11 (0.17), residues: 910 loop : -0.74 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.013 0.001 PHE G 195 TYR 0.007 0.001 TYR I 476 ARG 0.007 0.000 ARG D 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 567 time to evaluate : 4.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6852 (tmm) cc_final: 0.6645 (tmm) REVERT: A 517 THR cc_start: 0.9447 (m) cc_final: 0.9208 (p) REVERT: B 114 MET cc_start: 0.6896 (tmm) cc_final: 0.6633 (tmm) REVERT: B 203 TYR cc_start: 0.8238 (m-80) cc_final: 0.8005 (m-80) REVERT: B 419 LEU cc_start: 0.9286 (mt) cc_final: 0.9056 (mp) REVERT: B 517 THR cc_start: 0.9470 (m) cc_final: 0.9207 (p) REVERT: C 111 MET cc_start: 0.7616 (mmm) cc_final: 0.6996 (mmm) REVERT: C 114 MET cc_start: 0.6986 (tmm) cc_final: 0.6635 (tmm) REVERT: C 307 MET cc_start: 0.8745 (pmm) cc_final: 0.8447 (pmm) REVERT: D 16 MET cc_start: 0.8347 (mtm) cc_final: 0.8133 (mtp) REVERT: D 517 THR cc_start: 0.9520 (m) cc_final: 0.9065 (p) REVERT: E 307 MET cc_start: 0.8874 (pmm) cc_final: 0.8647 (pmm) REVERT: E 488 MET cc_start: 0.7962 (mmt) cc_final: 0.7680 (mmt) REVERT: E 517 THR cc_start: 0.9432 (m) cc_final: 0.8975 (p) REVERT: E 519 CYS cc_start: 0.6791 (m) cc_final: 0.6579 (m) REVERT: F 517 THR cc_start: 0.9470 (m) cc_final: 0.8942 (p) REVERT: F 519 CYS cc_start: 0.5865 (t) cc_final: 0.5612 (t) REVERT: G 22 VAL cc_start: 0.8884 (t) cc_final: 0.8449 (t) REVERT: G 488 MET cc_start: 0.7972 (tpt) cc_final: 0.7530 (mmm) REVERT: H 69 MET cc_start: 0.8645 (mtp) cc_final: 0.8327 (mtt) REVERT: H 114 MET cc_start: 0.6931 (tmm) cc_final: 0.6544 (tmm) REVERT: H 488 MET cc_start: 0.7853 (mmp) cc_final: 0.7597 (mmt) REVERT: I 64 ASP cc_start: 0.8359 (t0) cc_final: 0.8044 (t0) REVERT: I 114 MET cc_start: 0.7070 (tmm) cc_final: 0.6696 (tmm) REVERT: I 400 LEU cc_start: 0.9347 (tp) cc_final: 0.9137 (pp) REVERT: I 488 MET cc_start: 0.8585 (mmt) cc_final: 0.8269 (mmt) REVERT: I 520 MET cc_start: 0.6775 (mtp) cc_final: 0.6333 (mtp) REVERT: J 5 ASP cc_start: 0.7663 (t0) cc_final: 0.7355 (m-30) REVERT: J 111 MET cc_start: 0.7382 (mmm) cc_final: 0.7182 (mmm) REVERT: J 307 MET cc_start: 0.8526 (pmm) cc_final: 0.8287 (pmm) REVERT: K 114 MET cc_start: 0.6965 (tmm) cc_final: 0.6665 (tmm) REVERT: K 517 THR cc_start: 0.9594 (m) cc_final: 0.9127 (p) REVERT: L 114 MET cc_start: 0.7106 (tmm) cc_final: 0.6730 (tmm) REVERT: L 307 MET cc_start: 0.8293 (pmm) cc_final: 0.7954 (pmm) REVERT: L 517 THR cc_start: 0.9401 (m) cc_final: 0.8942 (p) REVERT: M 22 VAL cc_start: 0.8731 (t) cc_final: 0.8324 (t) REVERT: M 267 MET cc_start: 0.6522 (mmm) cc_final: 0.5975 (ptp) REVERT: M 488 MET cc_start: 0.8168 (mmt) cc_final: 0.7957 (mmt) REVERT: M 517 THR cc_start: 0.9420 (m) cc_final: 0.8871 (p) REVERT: N 22 VAL cc_start: 0.8806 (t) cc_final: 0.8389 (t) REVERT: N 69 MET cc_start: 0.8722 (mtp) cc_final: 0.8430 (mtp) REVERT: N 114 MET cc_start: 0.6929 (tmm) cc_final: 0.6506 (tmm) REVERT: N 488 MET cc_start: 0.7747 (tpt) cc_final: 0.7339 (mmm) outliers start: 0 outliers final: 0 residues processed: 567 average time/residue: 0.4723 time to fit residues: 475.8075 Evaluate side-chains 440 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 4.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 0.5980 chunk 497 optimal weight: 20.0000 chunk 343 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 316 optimal weight: 0.0070 chunk 444 optimal weight: 9.9990 chunk 664 optimal weight: 6.9990 chunk 703 optimal weight: 30.0000 chunk 347 optimal weight: 40.0000 chunk 629 optimal weight: 3.9990 chunk 189 optimal weight: 0.0060 overall best weight: 1.1216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 HIS ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 ASN ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 54894 Z= 0.167 Angle : 0.511 7.342 74214 Z= 0.279 Chirality : 0.041 0.147 9002 Planarity : 0.003 0.027 9632 Dihedral : 8.115 68.629 8218 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 7322 helix: 1.25 (0.08), residues: 4312 sheet: -0.04 (0.17), residues: 910 loop : -0.69 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS I 401 PHE 0.012 0.001 PHE G 195 TYR 0.008 0.001 TYR I 476 ARG 0.006 0.000 ARG M 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 4.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6932 (tmm) cc_final: 0.6670 (tmm) REVERT: A 517 THR cc_start: 0.9453 (m) cc_final: 0.9172 (p) REVERT: B 114 MET cc_start: 0.6872 (tmm) cc_final: 0.6607 (tmm) REVERT: B 203 TYR cc_start: 0.8226 (m-80) cc_final: 0.8025 (m-80) REVERT: B 419 LEU cc_start: 0.9293 (mt) cc_final: 0.9051 (mp) REVERT: B 517 THR cc_start: 0.9515 (m) cc_final: 0.9174 (p) REVERT: C 111 MET cc_start: 0.7603 (mmm) cc_final: 0.7166 (mmm) REVERT: C 114 MET cc_start: 0.6921 (tmm) cc_final: 0.6579 (tmm) REVERT: C 307 MET cc_start: 0.8748 (pmm) cc_final: 0.8445 (pmm) REVERT: D 16 MET cc_start: 0.8289 (mtm) cc_final: 0.7817 (mtm) REVERT: D 520 MET cc_start: 0.6974 (ttt) cc_final: 0.6697 (mtp) REVERT: E 307 MET cc_start: 0.8890 (pmm) cc_final: 0.8672 (pmm) REVERT: E 488 MET cc_start: 0.7882 (mmt) cc_final: 0.7560 (mmt) REVERT: E 517 THR cc_start: 0.9453 (m) cc_final: 0.8977 (p) REVERT: F 16 MET cc_start: 0.8219 (mtm) cc_final: 0.7739 (mtp) REVERT: F 488 MET cc_start: 0.7797 (mmt) cc_final: 0.7503 (mmt) REVERT: F 514 MET cc_start: 0.8390 (ttm) cc_final: 0.7892 (ttm) REVERT: F 517 THR cc_start: 0.9389 (m) cc_final: 0.8934 (p) REVERT: G 22 VAL cc_start: 0.8820 (t) cc_final: 0.8415 (t) REVERT: G 111 MET cc_start: 0.7317 (mmm) cc_final: 0.6823 (mmm) REVERT: G 488 MET cc_start: 0.7991 (tpt) cc_final: 0.7544 (mmm) REVERT: G 520 MET cc_start: 0.6700 (mtp) cc_final: 0.6416 (mtp) REVERT: H 69 MET cc_start: 0.8708 (mtp) cc_final: 0.8394 (mtt) REVERT: H 111 MET cc_start: 0.7110 (mmm) cc_final: 0.6464 (mmt) REVERT: H 114 MET cc_start: 0.6858 (tmm) cc_final: 0.6471 (tmm) REVERT: H 488 MET cc_start: 0.7891 (mmp) cc_final: 0.7626 (mmt) REVERT: I 114 MET cc_start: 0.7053 (tmm) cc_final: 0.6684 (tmm) REVERT: I 488 MET cc_start: 0.8551 (mmt) cc_final: 0.8215 (mmt) REVERT: J 111 MET cc_start: 0.7400 (mmm) cc_final: 0.7081 (mmm) REVERT: J 307 MET cc_start: 0.8556 (pmm) cc_final: 0.8334 (pmm) REVERT: J 520 MET cc_start: 0.6958 (ttt) cc_final: 0.6621 (ttt) REVERT: K 63 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7110 (tm-30) REVERT: K 114 MET cc_start: 0.6991 (tmm) cc_final: 0.6700 (tmm) REVERT: K 203 TYR cc_start: 0.8086 (m-80) cc_final: 0.7796 (m-80) REVERT: K 517 THR cc_start: 0.9581 (m) cc_final: 0.9105 (p) REVERT: L 16 MET cc_start: 0.8544 (mtm) cc_final: 0.7878 (mtp) REVERT: L 114 MET cc_start: 0.7149 (tmm) cc_final: 0.6753 (tmm) REVERT: L 307 MET cc_start: 0.8369 (pmm) cc_final: 0.8023 (pmm) REVERT: L 517 THR cc_start: 0.9362 (m) cc_final: 0.8947 (p) REVERT: M 22 VAL cc_start: 0.8687 (t) cc_final: 0.8289 (t) REVERT: M 69 MET cc_start: 0.8472 (mtp) cc_final: 0.8228 (mtp) REVERT: M 111 MET cc_start: 0.7442 (mmm) cc_final: 0.7151 (mmm) REVERT: M 267 MET cc_start: 0.6324 (mmm) cc_final: 0.5822 (ptt) REVERT: M 517 THR cc_start: 0.9380 (m) cc_final: 0.8868 (p) REVERT: N 22 VAL cc_start: 0.8777 (t) cc_final: 0.8343 (t) REVERT: N 488 MET cc_start: 0.7766 (tpt) cc_final: 0.7354 (mmm) outliers start: 0 outliers final: 0 residues processed: 562 average time/residue: 0.4546 time to fit residues: 456.0213 Evaluate side-chains 440 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 4.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 10.0000 chunk 399 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 523 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 chunk 600 optimal weight: 5.9990 chunk 486 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 359 optimal weight: 0.0980 chunk 631 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 ASN ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 54894 Z= 0.277 Angle : 0.551 6.383 74214 Z= 0.300 Chirality : 0.042 0.143 9002 Planarity : 0.003 0.027 9632 Dihedral : 8.227 70.151 8218 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 7322 helix: 1.32 (0.08), residues: 4284 sheet: -0.24 (0.15), residues: 1050 loop : -0.73 (0.12), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 401 PHE 0.010 0.001 PHE L 195 TYR 0.010 0.001 TYR E 476 ARG 0.006 0.000 ARG D 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 4.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8538 (t) cc_final: 0.8337 (t) REVERT: A 114 MET cc_start: 0.7015 (tmm) cc_final: 0.6746 (tmm) REVERT: A 488 MET cc_start: 0.7785 (mmt) cc_final: 0.7302 (mmt) REVERT: B 114 MET cc_start: 0.7010 (tmm) cc_final: 0.6669 (tmm) REVERT: B 203 TYR cc_start: 0.8216 (m-80) cc_final: 0.8009 (m-80) REVERT: B 419 LEU cc_start: 0.9327 (mt) cc_final: 0.9079 (mp) REVERT: B 488 MET cc_start: 0.8304 (mmt) cc_final: 0.7867 (mmp) REVERT: B 517 THR cc_start: 0.9457 (m) cc_final: 0.9150 (p) REVERT: B 520 MET cc_start: 0.6964 (mtp) cc_final: 0.6678 (mtp) REVERT: C 114 MET cc_start: 0.6942 (tmm) cc_final: 0.6634 (tmm) REVERT: C 307 MET cc_start: 0.8749 (pmm) cc_final: 0.8445 (pmm) REVERT: D 16 MET cc_start: 0.8351 (mtm) cc_final: 0.7942 (mtp) REVERT: D 520 MET cc_start: 0.7094 (ttt) cc_final: 0.6716 (mtp) REVERT: E 307 MET cc_start: 0.8948 (pmm) cc_final: 0.8738 (pmm) REVERT: E 488 MET cc_start: 0.8102 (mmt) cc_final: 0.7587 (mmt) REVERT: F 16 MET cc_start: 0.8174 (mtm) cc_final: 0.7961 (mtp) REVERT: F 488 MET cc_start: 0.8041 (mmt) cc_final: 0.7712 (mmt) REVERT: F 519 CYS cc_start: 0.6273 (t) cc_final: 0.6033 (t) REVERT: G 22 VAL cc_start: 0.8897 (t) cc_final: 0.8437 (t) REVERT: G 111 MET cc_start: 0.7598 (mmm) cc_final: 0.7145 (mmm) REVERT: G 488 MET cc_start: 0.8280 (tpt) cc_final: 0.7717 (mmm) REVERT: G 514 MET cc_start: 0.8601 (ttm) cc_final: 0.8394 (ttm) REVERT: H 22 VAL cc_start: 0.8510 (t) cc_final: 0.8202 (t) REVERT: H 69 MET cc_start: 0.8735 (mtp) cc_final: 0.8418 (mtt) REVERT: H 111 MET cc_start: 0.7523 (mmm) cc_final: 0.7170 (mmm) REVERT: H 114 MET cc_start: 0.7001 (tmm) cc_final: 0.6532 (tmm) REVERT: H 488 MET cc_start: 0.7968 (mmp) cc_final: 0.7618 (mmt) REVERT: I 114 MET cc_start: 0.7130 (tmm) cc_final: 0.6714 (tmm) REVERT: I 488 MET cc_start: 0.8730 (mmt) cc_final: 0.8207 (mmt) REVERT: J 307 MET cc_start: 0.8566 (pmm) cc_final: 0.8347 (pmm) REVERT: J 520 MET cc_start: 0.7063 (ttt) cc_final: 0.6813 (ttt) REVERT: K 114 MET cc_start: 0.7057 (tmm) cc_final: 0.6721 (tmm) REVERT: L 16 MET cc_start: 0.8484 (mtm) cc_final: 0.8182 (mtp) REVERT: L 114 MET cc_start: 0.7093 (tmm) cc_final: 0.6695 (tmm) REVERT: L 307 MET cc_start: 0.8403 (pmm) cc_final: 0.8041 (pmm) REVERT: L 488 MET cc_start: 0.8158 (mmt) cc_final: 0.7781 (mmt) REVERT: M 22 VAL cc_start: 0.8744 (t) cc_final: 0.8305 (t) REVERT: M 111 MET cc_start: 0.7667 (mmm) cc_final: 0.7137 (mmm) REVERT: M 267 MET cc_start: 0.6353 (mmm) cc_final: 0.5835 (ptt) REVERT: M 488 MET cc_start: 0.8098 (mmt) cc_final: 0.7736 (mmt) REVERT: N 114 MET cc_start: 0.6965 (tmm) cc_final: 0.6543 (tmm) REVERT: N 488 MET cc_start: 0.8225 (tpt) cc_final: 0.7600 (mmm) outliers start: 0 outliers final: 0 residues processed: 516 average time/residue: 0.4681 time to fit residues: 429.6073 Evaluate side-chains 413 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 4.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 8.9990 chunk 633 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 413 optimal weight: 20.0000 chunk 173 optimal weight: 0.0670 chunk 704 optimal weight: 20.0000 chunk 584 optimal weight: 2.9990 chunk 326 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 232 optimal weight: 7.9990 chunk 369 optimal weight: 1.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 ASN ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 54894 Z= 0.181 Angle : 0.523 7.200 74214 Z= 0.285 Chirality : 0.041 0.145 9002 Planarity : 0.003 0.026 9632 Dihedral : 7.991 68.537 8218 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.09), residues: 7322 helix: 1.36 (0.08), residues: 4284 sheet: 0.01 (0.17), residues: 910 loop : -0.61 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 401 PHE 0.011 0.001 PHE L 195 TYR 0.008 0.001 TYR I 476 ARG 0.003 0.000 ARG D 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 4.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6941 (tmm) cc_final: 0.6698 (tmm) REVERT: A 488 MET cc_start: 0.7854 (mmt) cc_final: 0.7467 (mmt) REVERT: A 517 THR cc_start: 0.9418 (m) cc_final: 0.9138 (p) REVERT: B 114 MET cc_start: 0.6850 (tmm) cc_final: 0.6536 (tmm) REVERT: B 419 LEU cc_start: 0.9306 (mt) cc_final: 0.9068 (mp) REVERT: B 514 MET cc_start: 0.8536 (ttm) cc_final: 0.8257 (ttm) REVERT: B 517 THR cc_start: 0.9434 (m) cc_final: 0.9184 (p) REVERT: C 22 VAL cc_start: 0.8563 (t) cc_final: 0.8332 (t) REVERT: C 111 MET cc_start: 0.7625 (mmm) cc_final: 0.7328 (mmm) REVERT: C 114 MET cc_start: 0.6936 (tmm) cc_final: 0.6642 (tmm) REVERT: C 307 MET cc_start: 0.8788 (pmm) cc_final: 0.8510 (pmm) REVERT: D 16 MET cc_start: 0.8291 (mtm) cc_final: 0.7968 (mtp) REVERT: E 307 MET cc_start: 0.8960 (pmm) cc_final: 0.8741 (pmm) REVERT: E 488 MET cc_start: 0.8008 (mmt) cc_final: 0.7602 (mmt) REVERT: F 519 CYS cc_start: 0.6106 (t) cc_final: 0.5791 (t) REVERT: G 22 VAL cc_start: 0.8866 (t) cc_final: 0.8420 (t) REVERT: G 111 MET cc_start: 0.7457 (mmm) cc_final: 0.7075 (mmm) REVERT: G 488 MET cc_start: 0.8148 (tpt) cc_final: 0.7651 (mmm) REVERT: H 16 MET cc_start: 0.8421 (mtm) cc_final: 0.8125 (mtp) REVERT: H 69 MET cc_start: 0.8764 (mtp) cc_final: 0.8455 (mtp) REVERT: H 111 MET cc_start: 0.7391 (mmm) cc_final: 0.7032 (mmm) REVERT: H 114 MET cc_start: 0.6888 (tmm) cc_final: 0.6463 (tmm) REVERT: H 488 MET cc_start: 0.7919 (mmp) cc_final: 0.7682 (mmt) REVERT: I 114 MET cc_start: 0.6954 (tmm) cc_final: 0.6606 (tmm) REVERT: I 400 LEU cc_start: 0.9345 (tp) cc_final: 0.9120 (pp) REVERT: I 488 MET cc_start: 0.8610 (mmt) cc_final: 0.8208 (mmt) REVERT: J 111 MET cc_start: 0.7511 (mmm) cc_final: 0.7256 (mmm) REVERT: J 307 MET cc_start: 0.8495 (pmm) cc_final: 0.8237 (pmm) REVERT: K 114 MET cc_start: 0.6834 (tmm) cc_final: 0.6528 (tmm) REVERT: K 517 THR cc_start: 0.9604 (m) cc_final: 0.9157 (p) REVERT: L 16 MET cc_start: 0.8367 (mtm) cc_final: 0.7870 (mtm) REVERT: L 114 MET cc_start: 0.6941 (tmm) cc_final: 0.6619 (tmm) REVERT: L 307 MET cc_start: 0.8426 (pmm) cc_final: 0.8057 (pmm) REVERT: L 488 MET cc_start: 0.8067 (mmt) cc_final: 0.7815 (mmt) REVERT: L 517 THR cc_start: 0.9456 (m) cc_final: 0.9038 (p) REVERT: M 22 VAL cc_start: 0.8671 (t) cc_final: 0.8244 (t) REVERT: M 267 MET cc_start: 0.6406 (mmm) cc_final: 0.5853 (ptt) REVERT: M 488 MET cc_start: 0.8131 (mmt) cc_final: 0.7920 (mmt) REVERT: M 514 MET cc_start: 0.8572 (ttm) cc_final: 0.8141 (ttm) REVERT: M 517 THR cc_start: 0.9442 (m) cc_final: 0.9037 (p) REVERT: N 111 MET cc_start: 0.6836 (mmm) cc_final: 0.6571 (mmm) REVERT: N 488 MET cc_start: 0.8205 (tpt) cc_final: 0.7601 (mmm) REVERT: N 520 MET cc_start: 0.6745 (mtp) cc_final: 0.6457 (mtp) outliers start: 0 outliers final: 0 residues processed: 540 average time/residue: 0.4558 time to fit residues: 437.0227 Evaluate side-chains 425 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 401 optimal weight: 4.9990 chunk 514 optimal weight: 0.7980 chunk 398 optimal weight: 10.0000 chunk 592 optimal weight: 9.9990 chunk 393 optimal weight: 1.9990 chunk 701 optimal weight: 8.9990 chunk 439 optimal weight: 20.0000 chunk 427 optimal weight: 0.9990 chunk 323 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 401 HIS ** F 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 401 HIS ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 ASN ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 54894 Z= 0.205 Angle : 0.532 7.455 74214 Z= 0.289 Chirality : 0.041 0.143 9002 Planarity : 0.003 0.025 9632 Dihedral : 7.864 68.761 8218 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.10), residues: 7322 helix: 1.40 (0.08), residues: 4284 sheet: -0.15 (0.15), residues: 1050 loop : -0.66 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 401 PHE 0.013 0.001 PHE F 44 TYR 0.009 0.001 TYR H 476 ARG 0.004 0.000 ARG D 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 4.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.6947 (tmm) cc_final: 0.6710 (tmm) REVERT: A 517 THR cc_start: 0.9431 (m) cc_final: 0.9140 (p) REVERT: A 520 MET cc_start: 0.7760 (mtp) cc_final: 0.7431 (mtp) REVERT: B 114 MET cc_start: 0.6898 (tmm) cc_final: 0.6591 (tmm) REVERT: B 419 LEU cc_start: 0.9324 (mt) cc_final: 0.9083 (mp) REVERT: B 520 MET cc_start: 0.6803 (mtp) cc_final: 0.6352 (mtp) REVERT: C 22 VAL cc_start: 0.8599 (t) cc_final: 0.8371 (t) REVERT: C 114 MET cc_start: 0.6995 (tmm) cc_final: 0.6658 (tmm) REVERT: C 307 MET cc_start: 0.8704 (pmm) cc_final: 0.8374 (pmm) REVERT: D 520 MET cc_start: 0.6730 (mtp) cc_final: 0.6211 (mtp) REVERT: E 307 MET cc_start: 0.8959 (pmm) cc_final: 0.8737 (pmm) REVERT: E 488 MET cc_start: 0.8032 (mmt) cc_final: 0.7576 (mmt) REVERT: F 111 MET cc_start: 0.7411 (mmm) cc_final: 0.7179 (mmm) REVERT: F 488 MET cc_start: 0.7754 (mmt) cc_final: 0.6972 (mmt) REVERT: F 519 CYS cc_start: 0.6111 (t) cc_final: 0.5879 (t) REVERT: G 22 VAL cc_start: 0.8858 (t) cc_final: 0.8433 (t) REVERT: G 111 MET cc_start: 0.7591 (mmm) cc_final: 0.7078 (mmm) REVERT: G 488 MET cc_start: 0.8212 (tpt) cc_final: 0.7699 (mmm) REVERT: H 69 MET cc_start: 0.8703 (mtp) cc_final: 0.8432 (mtp) REVERT: H 111 MET cc_start: 0.7413 (mmm) cc_final: 0.6977 (mmm) REVERT: H 114 MET cc_start: 0.6917 (tmm) cc_final: 0.6472 (tmm) REVERT: H 488 MET cc_start: 0.7977 (mmp) cc_final: 0.7713 (mmt) REVERT: H 520 MET cc_start: 0.7237 (mtp) cc_final: 0.6829 (mtp) REVERT: I 114 MET cc_start: 0.6984 (tmm) cc_final: 0.6598 (tmm) REVERT: I 488 MET cc_start: 0.8634 (mmt) cc_final: 0.8165 (mmt) REVERT: J 111 MET cc_start: 0.7513 (mmm) cc_final: 0.7242 (mmm) REVERT: J 307 MET cc_start: 0.8516 (pmm) cc_final: 0.8269 (pmm) REVERT: K 114 MET cc_start: 0.6846 (tmm) cc_final: 0.6541 (tmm) REVERT: K 203 TYR cc_start: 0.8176 (m-80) cc_final: 0.7934 (m-80) REVERT: K 514 MET cc_start: 0.8365 (ttm) cc_final: 0.8049 (ttm) REVERT: K 517 THR cc_start: 0.9594 (m) cc_final: 0.9191 (p) REVERT: L 114 MET cc_start: 0.6960 (tmm) cc_final: 0.6617 (tmm) REVERT: L 307 MET cc_start: 0.8421 (pmm) cc_final: 0.8029 (pmm) REVERT: M 22 VAL cc_start: 0.8665 (t) cc_final: 0.8209 (t) REVERT: M 111 MET cc_start: 0.7583 (mmm) cc_final: 0.7347 (mmm) REVERT: M 267 MET cc_start: 0.6384 (mmm) cc_final: 0.5840 (ptt) REVERT: M 517 THR cc_start: 0.9428 (m) cc_final: 0.8979 (p) REVERT: M 520 MET cc_start: 0.7647 (mtp) cc_final: 0.7205 (mtp) REVERT: N 111 MET cc_start: 0.6964 (mmm) cc_final: 0.6523 (mmm) REVERT: N 114 MET cc_start: 0.6763 (tmm) cc_final: 0.6435 (tmm) REVERT: N 488 MET cc_start: 0.8247 (tpt) cc_final: 0.7612 (mmm) REVERT: N 520 MET cc_start: 0.6779 (mtp) cc_final: 0.6510 (mtp) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.4672 time to fit residues: 435.2015 Evaluate side-chains 423 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 40.0000 chunk 280 optimal weight: 10.0000 chunk 419 optimal weight: 4.9990 chunk 211 optimal weight: 6.9990 chunk 137 optimal weight: 30.0000 chunk 135 optimal weight: 4.9990 chunk 446 optimal weight: 30.0000 chunk 478 optimal weight: 1.9990 chunk 346 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 551 optimal weight: 0.0010 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 ASN ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 54894 Z= 0.300 Angle : 0.568 7.107 74214 Z= 0.309 Chirality : 0.042 0.142 9002 Planarity : 0.003 0.026 9632 Dihedral : 7.974 70.130 8218 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.10), residues: 7322 helix: 1.37 (0.08), residues: 4270 sheet: -0.20 (0.15), residues: 1050 loop : -0.75 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 401 PHE 0.013 0.001 PHE F 44 TYR 0.010 0.001 TYR D 476 ARG 0.011 0.000 ARG C 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 4.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 VAL cc_start: 0.8515 (t) cc_final: 0.8252 (t) REVERT: A 114 MET cc_start: 0.7028 (tmm) cc_final: 0.6751 (tmm) REVERT: A 488 MET cc_start: 0.7949 (mmt) cc_final: 0.7351 (mmt) REVERT: A 517 THR cc_start: 0.9430 (m) cc_final: 0.9112 (p) REVERT: A 520 MET cc_start: 0.7871 (mtp) cc_final: 0.7522 (mtp) REVERT: B 114 MET cc_start: 0.7068 (tmm) cc_final: 0.6718 (tmm) REVERT: B 419 LEU cc_start: 0.9349 (mt) cc_final: 0.9097 (mp) REVERT: B 488 MET cc_start: 0.8401 (mmt) cc_final: 0.7907 (mmp) REVERT: B 520 MET cc_start: 0.7049 (mtp) cc_final: 0.6629 (mtp) REVERT: C 111 MET cc_start: 0.7629 (mmm) cc_final: 0.7324 (mmm) REVERT: C 114 MET cc_start: 0.7041 (tmm) cc_final: 0.6730 (tmm) REVERT: C 307 MET cc_start: 0.8709 (pmm) cc_final: 0.8383 (pmm) REVERT: E 307 MET cc_start: 0.8940 (pmm) cc_final: 0.8705 (pmm) REVERT: E 488 MET cc_start: 0.8136 (mmt) cc_final: 0.7598 (mmt) REVERT: F 111 MET cc_start: 0.7677 (mmm) cc_final: 0.7416 (mmm) REVERT: F 488 MET cc_start: 0.7776 (mmt) cc_final: 0.7004 (mmt) REVERT: F 519 CYS cc_start: 0.6182 (t) cc_final: 0.5956 (t) REVERT: G 22 VAL cc_start: 0.8915 (t) cc_final: 0.8428 (t) REVERT: G 111 MET cc_start: 0.7726 (mmm) cc_final: 0.7075 (mmm) REVERT: G 114 MET cc_start: 0.6703 (tmm) cc_final: 0.6442 (tmm) REVERT: G 288 MET cc_start: 0.9484 (ppp) cc_final: 0.9156 (ppp) REVERT: G 488 MET cc_start: 0.8475 (tpt) cc_final: 0.7817 (mmm) REVERT: H 22 VAL cc_start: 0.8522 (t) cc_final: 0.8230 (t) REVERT: H 111 MET cc_start: 0.7616 (mmm) cc_final: 0.7096 (mmm) REVERT: H 114 MET cc_start: 0.7092 (tmm) cc_final: 0.6591 (tmm) REVERT: H 488 MET cc_start: 0.7994 (mmp) cc_final: 0.7756 (mmt) REVERT: H 520 MET cc_start: 0.7110 (mtp) cc_final: 0.6905 (mtp) REVERT: I 114 MET cc_start: 0.7068 (tmm) cc_final: 0.6667 (tmm) REVERT: I 488 MET cc_start: 0.8740 (mmt) cc_final: 0.8147 (mmt) REVERT: J 203 TYR cc_start: 0.8495 (m-10) cc_final: 0.8293 (m-80) REVERT: J 307 MET cc_start: 0.8593 (pmm) cc_final: 0.8350 (pmm) REVERT: K 114 MET cc_start: 0.6866 (tmm) cc_final: 0.6562 (tmm) REVERT: L 114 MET cc_start: 0.6941 (tmm) cc_final: 0.6586 (tmm) REVERT: L 307 MET cc_start: 0.8426 (pmm) cc_final: 0.8034 (pmm) REVERT: M 22 VAL cc_start: 0.8767 (t) cc_final: 0.8344 (t) REVERT: M 111 MET cc_start: 0.7810 (mmm) cc_final: 0.7498 (mmm) REVERT: M 267 MET cc_start: 0.6433 (mmm) cc_final: 0.5894 (ptt) REVERT: N 111 MET cc_start: 0.7274 (mmm) cc_final: 0.7019 (mmm) REVERT: N 114 MET cc_start: 0.6821 (tmm) cc_final: 0.6483 (tmm) REVERT: N 288 MET cc_start: 0.9389 (ppp) cc_final: 0.9176 (ppp) REVERT: N 488 MET cc_start: 0.8454 (tpt) cc_final: 0.7810 (mmm) outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.4695 time to fit residues: 409.7911 Evaluate side-chains 403 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 5.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 638 optimal weight: 10.0000 chunk 672 optimal weight: 5.9990 chunk 613 optimal weight: 6.9990 chunk 653 optimal weight: 2.9990 chunk 393 optimal weight: 6.9990 chunk 284 optimal weight: 20.0000 chunk 513 optimal weight: 0.6980 chunk 200 optimal weight: 0.0170 chunk 590 optimal weight: 50.0000 chunk 618 optimal weight: 0.9990 chunk 651 optimal weight: 20.0000 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 ASN ** M 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 54894 Z= 0.220 Angle : 0.559 7.049 74214 Z= 0.304 Chirality : 0.042 0.159 9002 Planarity : 0.003 0.026 9632 Dihedral : 7.806 69.136 8218 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.10), residues: 7322 helix: 1.39 (0.08), residues: 4284 sheet: -0.16 (0.15), residues: 1050 loop : -0.69 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.012 0.001 PHE G 195 TYR 0.010 0.001 TYR H 476 ARG 0.005 0.000 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 510 time to evaluate : 4.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 VAL cc_start: 0.9327 (t) cc_final: 0.9126 (p) REVERT: A 114 MET cc_start: 0.6999 (tmm) cc_final: 0.6738 (tmm) REVERT: A 488 MET cc_start: 0.7944 (mmt) cc_final: 0.7413 (mmt) REVERT: A 517 THR cc_start: 0.9420 (m) cc_final: 0.9115 (p) REVERT: B 16 MET cc_start: 0.8346 (mtm) cc_final: 0.8060 (mtm) REVERT: B 114 MET cc_start: 0.6994 (tmm) cc_final: 0.6671 (tmm) REVERT: B 203 TYR cc_start: 0.8249 (m-80) cc_final: 0.8015 (m-80) REVERT: B 419 LEU cc_start: 0.9315 (mt) cc_final: 0.9079 (mp) REVERT: C 22 VAL cc_start: 0.8593 (t) cc_final: 0.8371 (t) REVERT: C 111 MET cc_start: 0.7653 (mmm) cc_final: 0.7275 (mmm) REVERT: C 114 MET cc_start: 0.6977 (tmm) cc_final: 0.6630 (tmm) REVERT: C 307 MET cc_start: 0.8672 (pmm) cc_final: 0.8338 (pmm) REVERT: D 22 VAL cc_start: 0.8774 (t) cc_final: 0.8534 (t) REVERT: D 203 TYR cc_start: 0.8231 (m-80) cc_final: 0.7906 (m-80) REVERT: E 307 MET cc_start: 0.8968 (pmm) cc_final: 0.8721 (pmm) REVERT: E 488 MET cc_start: 0.8105 (mmt) cc_final: 0.7654 (mmt) REVERT: F 488 MET cc_start: 0.7849 (mmt) cc_final: 0.7143 (mmt) REVERT: F 519 CYS cc_start: 0.6178 (t) cc_final: 0.5927 (t) REVERT: G 22 VAL cc_start: 0.8897 (t) cc_final: 0.8438 (t) REVERT: G 111 MET cc_start: 0.7700 (mmm) cc_final: 0.7062 (mmm) REVERT: G 288 MET cc_start: 0.9470 (ppp) cc_final: 0.9152 (ppp) REVERT: G 488 MET cc_start: 0.8429 (tpt) cc_final: 0.7732 (mmm) REVERT: H 61 GLU cc_start: 0.6794 (pt0) cc_final: 0.6545 (mt-10) REVERT: H 69 MET cc_start: 0.8772 (mtp) cc_final: 0.8536 (mtt) REVERT: H 111 MET cc_start: 0.7419 (mmm) cc_final: 0.6931 (mmm) REVERT: H 114 MET cc_start: 0.6822 (tmm) cc_final: 0.6398 (tmm) REVERT: H 288 MET cc_start: 0.9469 (ppp) cc_final: 0.9220 (ppp) REVERT: H 488 MET cc_start: 0.7976 (mmp) cc_final: 0.7769 (mmt) REVERT: H 520 MET cc_start: 0.7089 (mtp) cc_final: 0.6832 (mtp) REVERT: I 114 MET cc_start: 0.6993 (tmm) cc_final: 0.6605 (tmm) REVERT: I 488 MET cc_start: 0.8678 (mmt) cc_final: 0.8179 (mmt) REVERT: J 307 MET cc_start: 0.8594 (pmm) cc_final: 0.8341 (pmm) REVERT: K 114 MET cc_start: 0.6751 (tmm) cc_final: 0.6443 (tmm) REVERT: K 517 THR cc_start: 0.9631 (m) cc_final: 0.9187 (p) REVERT: L 114 MET cc_start: 0.6942 (tmm) cc_final: 0.6606 (tmm) REVERT: L 307 MET cc_start: 0.8461 (pmm) cc_final: 0.8073 (pmm) REVERT: M 22 VAL cc_start: 0.8739 (t) cc_final: 0.8311 (t) REVERT: M 111 MET cc_start: 0.7696 (mmm) cc_final: 0.7413 (mmm) REVERT: M 267 MET cc_start: 0.6298 (mmm) cc_final: 0.5762 (ptt) REVERT: M 514 MET cc_start: 0.8525 (ttt) cc_final: 0.8267 (ttm) REVERT: M 520 MET cc_start: 0.7578 (mtp) cc_final: 0.7216 (mtp) REVERT: N 111 MET cc_start: 0.7247 (mmm) cc_final: 0.6946 (mmm) REVERT: N 114 MET cc_start: 0.6800 (tmm) cc_final: 0.6469 (tmm) REVERT: N 488 MET cc_start: 0.8440 (tpt) cc_final: 0.7723 (mmm) outliers start: 0 outliers final: 0 residues processed: 510 average time/residue: 0.4579 time to fit residues: 415.2718 Evaluate side-chains 415 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 4.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 4.9990 chunk 691 optimal weight: 10.0000 chunk 422 optimal weight: 0.6980 chunk 328 optimal weight: 2.9990 chunk 480 optimal weight: 0.9980 chunk 725 optimal weight: 0.3980 chunk 667 optimal weight: 2.9990 chunk 577 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 446 optimal weight: 8.9990 chunk 354 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 326 ASN ** F 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 54894 Z= 0.175 Angle : 0.545 8.587 74214 Z= 0.294 Chirality : 0.041 0.169 9002 Planarity : 0.003 0.025 9632 Dihedral : 7.545 68.135 8218 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.10), residues: 7322 helix: 1.50 (0.08), residues: 4270 sheet: -0.10 (0.15), residues: 1050 loop : -0.75 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 401 PHE 0.013 0.001 PHE G 195 TYR 0.009 0.001 TYR H 476 ARG 0.006 0.000 ARG G 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14644 Ramachandran restraints generated. 7322 Oldfield, 0 Emsley, 7322 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 4.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 VAL cc_start: 0.9349 (t) cc_final: 0.9142 (p) REVERT: A 114 MET cc_start: 0.6933 (tmm) cc_final: 0.6704 (tmm) REVERT: A 488 MET cc_start: 0.7907 (mmt) cc_final: 0.7417 (mmt) REVERT: A 517 THR cc_start: 0.9416 (m) cc_final: 0.9123 (p) REVERT: A 520 MET cc_start: 0.7851 (mtp) cc_final: 0.7557 (mtp) REVERT: B 114 MET cc_start: 0.6883 (tmm) cc_final: 0.6550 (tmm) REVERT: B 419 LEU cc_start: 0.9305 (mt) cc_final: 0.9096 (mp) REVERT: C 22 VAL cc_start: 0.8539 (t) cc_final: 0.8304 (t) REVERT: C 69 MET cc_start: 0.8558 (mtt) cc_final: 0.8336 (mtp) REVERT: C 114 MET cc_start: 0.6952 (tmm) cc_final: 0.6654 (tmm) REVERT: C 307 MET cc_start: 0.8676 (pmm) cc_final: 0.8330 (pmm) REVERT: D 29 VAL cc_start: 0.9192 (t) cc_final: 0.8985 (t) REVERT: D 69 MET cc_start: 0.8614 (mtp) cc_final: 0.8344 (mtp) REVERT: D 203 TYR cc_start: 0.8247 (m-80) cc_final: 0.7978 (m-80) REVERT: E 307 MET cc_start: 0.8970 (pmm) cc_final: 0.8759 (pmm) REVERT: E 488 MET cc_start: 0.8027 (mmt) cc_final: 0.7616 (mmt) REVERT: G 22 VAL cc_start: 0.8859 (t) cc_final: 0.8377 (t) REVERT: G 61 GLU cc_start: 0.7389 (pp20) cc_final: 0.6830 (pp20) REVERT: G 111 MET cc_start: 0.7502 (mmm) cc_final: 0.6959 (mmm) REVERT: G 288 MET cc_start: 0.9446 (ppp) cc_final: 0.9135 (ppp) REVERT: G 488 MET cc_start: 0.8376 (tpt) cc_final: 0.7748 (mmm) REVERT: H 22 VAL cc_start: 0.8448 (t) cc_final: 0.8195 (t) REVERT: H 61 GLU cc_start: 0.6915 (pt0) cc_final: 0.6534 (mt-10) REVERT: H 69 MET cc_start: 0.8691 (mtp) cc_final: 0.8400 (mtt) REVERT: H 111 MET cc_start: 0.7289 (mmm) cc_final: 0.6792 (mmm) REVERT: H 114 MET cc_start: 0.6794 (tmm) cc_final: 0.6406 (tmm) REVERT: H 288 MET cc_start: 0.9457 (ppp) cc_final: 0.9196 (ppp) REVERT: H 520 MET cc_start: 0.6994 (mtp) cc_final: 0.6390 (mtp) REVERT: I 22 VAL cc_start: 0.8817 (t) cc_final: 0.8564 (t) REVERT: I 114 MET cc_start: 0.6902 (tmm) cc_final: 0.6533 (tmm) REVERT: I 488 MET cc_start: 0.8616 (mmt) cc_final: 0.8178 (mmt) REVERT: J 307 MET cc_start: 0.8583 (pmm) cc_final: 0.8344 (pmm) REVERT: K 114 MET cc_start: 0.6651 (tmm) cc_final: 0.6400 (tmm) REVERT: K 203 TYR cc_start: 0.8162 (m-80) cc_final: 0.7930 (m-80) REVERT: K 517 THR cc_start: 0.9608 (m) cc_final: 0.9186 (p) REVERT: L 307 MET cc_start: 0.8439 (pmm) cc_final: 0.8043 (pmm) REVERT: M 22 VAL cc_start: 0.8668 (t) cc_final: 0.8245 (t) REVERT: M 69 MET cc_start: 0.8552 (mtp) cc_final: 0.8065 (mtt) REVERT: M 111 MET cc_start: 0.7601 (mmm) cc_final: 0.7330 (mmm) REVERT: M 267 MET cc_start: 0.6251 (mmm) cc_final: 0.5679 (ptm) REVERT: M 517 THR cc_start: 0.9408 (m) cc_final: 0.8989 (p) REVERT: M 520 MET cc_start: 0.7521 (mtp) cc_final: 0.7301 (mtp) REVERT: N 111 MET cc_start: 0.7148 (mmm) cc_final: 0.6460 (mmt) REVERT: N 114 MET cc_start: 0.6767 (tmm) cc_final: 0.6456 (tmm) REVERT: N 488 MET cc_start: 0.8384 (tpt) cc_final: 0.7672 (mmm) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.4608 time to fit residues: 445.4441 Evaluate side-chains 431 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 4.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 0.6980 chunk 615 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 532 optimal weight: 0.6980 chunk 85 optimal weight: 30.0000 chunk 160 optimal weight: 0.5980 chunk 578 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 593 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.088321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.056846 restraints weight = 232948.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058811 restraints weight = 140987.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059757 restraints weight = 92782.059| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 54894 Z= 0.160 Angle : 0.536 7.379 74214 Z= 0.289 Chirality : 0.041 0.161 9002 Planarity : 0.003 0.026 9632 Dihedral : 7.287 67.612 8218 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.10), residues: 7322 helix: 1.56 (0.08), residues: 4256 sheet: 0.10 (0.17), residues: 910 loop : -0.58 (0.12), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 401 PHE 0.013 0.001 PHE G 195 TYR 0.008 0.001 TYR E 476 ARG 0.003 0.000 ARG M 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8570.96 seconds wall clock time: 153 minutes 36.22 seconds (9216.22 seconds total)