Starting phenix.real_space_refine on Wed Nov 20 13:55:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ble_16108/11_2024/8ble_16108.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ble_16108/11_2024/8ble_16108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ble_16108/11_2024/8ble_16108.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ble_16108/11_2024/8ble_16108.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ble_16108/11_2024/8ble_16108.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ble_16108/11_2024/8ble_16108.cif" } resolution = 4.0 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= 0.004 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 76 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 29.22, per 1000 atoms: 0.54 Number of scatterers: 54474 At special positions: 0 Unit cell: (152.64, 152.64, 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: 13.04 Conformation dependent library (CDL) restraints added in 6.9 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: 280 helices and 103 sheets defined 59.6% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.79 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.540A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 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 169 removed outlier: 3.601A pdb=" N GLY A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) 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 355 Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.893A pdb=" N GLY A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 409 removed outlier: 3.536A pdb=" N GLU A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 433 through 448 removed outlier: 3.941A pdb=" N GLU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) 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: 3.799A 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: 3.560A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 88 through 108 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 169 removed outlier: 3.568A 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: 3.549A pdb=" N GLU B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 425 Processing helix chain 'B' and resid 433 through 448 removed outlier: 3.911A pdb=" N GLU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) 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: 3.768A pdb=" N THR B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.528A pdb=" N ARG C 13 " --> pdb=" O GLY C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.622A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 85 Processing helix chain 'C' and resid 88 through 108 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: 3.631A 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: 3.948A pdb=" N GLY C 375 " --> pdb=" O LYS C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 409 removed outlier: 3.531A 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: 3.934A 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: 3.890A 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 86 Processing helix chain 'D' and resid 88 through 109 Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 removed outlier: 3.607A 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: 3.907A pdb=" N GLY D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 409 removed outlier: 3.557A pdb=" N GLU D 409 " --> pdb=" O ALA D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 425 Processing helix chain 'D' and resid 433 through 448 removed outlier: 3.964A 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: 3.788A 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: 3.515A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 86 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: 3.513A 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: 3.881A pdb=" N GLY E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 409 removed outlier: 3.595A pdb=" N GLU E 409 " --> pdb=" O ALA E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 425 Processing helix chain 'E' and resid 433 through 448 removed outlier: 3.895A 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: 3.846A 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: 3.572A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 86 Processing helix chain 'F' and resid 88 through 108 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: 3.624A 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: 3.886A pdb=" N GLY F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 409 removed outlier: 3.535A pdb=" N GLU F 409 " --> pdb=" O ALA F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 425 Processing helix chain 'F' and resid 433 through 448 removed outlier: 3.932A 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: 3.917A pdb=" N THR F 516 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.506A pdb=" N ARG G 13 " --> pdb=" O GLY G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 60 removed outlier: 3.504A pdb=" N VAL G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A) 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 169 removed outlier: 3.553A 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: 3.898A 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 425 Processing helix chain 'G' and resid 433 through 448 removed outlier: 3.851A pdb=" N GLU G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 459 Processing helix chain 'G' and resid 461 through 472 Processing helix chain 'G' and resid 488 through 492 Processing helix chain 'G' and resid 497 through 516 removed outlier: 3.741A 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 60 Processing helix chain 'H' and resid 64 through 86 Processing helix chain 'H' and resid 88 through 109 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 removed outlier: 3.602A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) 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: 3.909A pdb=" N GLY H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 409 removed outlier: 3.545A pdb=" N GLU H 409 " --> pdb=" O ALA H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 425 Processing helix chain 'H' and resid 433 through 448 removed outlier: 3.942A 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: 3.731A 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 60 removed outlier: 3.533A pdb=" N VAL I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 85 Processing helix chain 'I' and resid 88 through 108 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 169 removed outlier: 3.559A 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: 3.893A pdb=" N GLY I 375 " --> pdb=" O LYS I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 409 removed outlier: 3.516A pdb=" N GLU I 409 " --> pdb=" O ALA I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 416 through 425 Processing helix chain 'I' and resid 433 through 448 removed outlier: 3.957A pdb=" N GLU I 448 " --> pdb=" O LEU I 444 " (cutoff:3.500A) 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: 3.525A 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: 3.501A pdb=" N VAL J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 86 Processing helix chain 'J' and resid 88 through 108 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: 3.653A 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: 3.934A pdb=" N GLY J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 409 removed outlier: 3.604A 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: 3.949A 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: 3.609A pdb=" N THR J 516 " --> pdb=" O GLY J 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 29 removed outlier: 3.561A pdb=" N ARG K 13 " --> pdb=" O GLY K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 60 Processing helix chain 'K' and resid 64 through 86 Processing helix chain 'K' and resid 88 through 108 Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 169 removed outlier: 3.604A 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: 3.918A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 409 removed outlier: 3.571A pdb=" N GLU K 409 " --> pdb=" O ALA K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 416 through 425 Processing helix chain 'K' and resid 433 through 448 removed outlier: 3.940A 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: 3.713A 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: 3.518A pdb=" N VAL L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 86 Processing helix chain 'L' and resid 88 through 108 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: 3.583A 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: 3.909A pdb=" N GLY L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 409 removed outlier: 3.555A 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: 3.971A 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: 3.824A 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 60 Processing helix chain 'M' and resid 64 through 86 Processing helix chain 'M' and resid 88 through 108 Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 removed outlier: 3.618A 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: 3.966A pdb=" N GLY M 375 " --> pdb=" O LYS M 371 " (cutoff:3.500A) Processing helix chain 'M' and resid 385 through 409 removed outlier: 3.540A pdb=" N GLU M 409 " --> pdb=" O ALA M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 425 Processing helix chain 'M' and resid 433 through 448 removed outlier: 3.934A 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: 3.852A pdb=" N THR M 516 " --> pdb=" O GLY M 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 29 Processing helix chain 'N' and resid 52 through 60 removed outlier: 3.541A pdb=" N VAL N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 86 Processing helix chain 'N' and resid 88 through 109 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 169 removed outlier: 3.552A 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: 3.952A pdb=" N GLY N 375 " --> pdb=" O LYS N 371 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 409 removed outlier: 3.526A pdb=" N GLU N 409 " --> pdb=" O ALA N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 425 Processing helix chain 'N' and resid 433 through 448 removed outlier: 3.865A pdb=" N GLU N 448 " --> pdb=" O LEU N 444 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 459 Processing helix chain 'N' and resid 461 through 472 Processing helix chain 'N' and resid 488 through 492 Processing helix chain 'N' and resid 497 through 516 removed outlier: 3.643A 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 7 removed outlier: 4.075A pdb=" N THR A 517 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL B 39 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 6.378A 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: 6.856A pdb=" N ASN A 37 " --> pdb=" O THR G 517 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N CYS G 519 " --> pdb=" O ASN A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.465A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.120A 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: 6.362A pdb=" N GLY A 335 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA A 320 " --> pdb=" O GLY A 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 216 removed outlier: 9.353A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.360A 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: 4.024A pdb=" N THR B 517 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL C 39 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS B 519 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.538A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.367A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 213 through 216 removed outlier: 9.341A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 7.378A 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 5 removed outlier: 4.026A pdb=" N THR C 517 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL D 39 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 6.331A 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: 6.529A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 7.151A 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: 6.353A pdb=" N GLY C 335 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA C 320 " --> pdb=" O GLY C 335 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 213 through 216 removed outlier: 9.340A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 7.365A 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: 4.074A pdb=" N THR D 517 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL E 39 " --> pdb=" O THR D 517 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N CYS D 519 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 174 through 179 removed outlier: 6.603A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 7.432A 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: 6.359A pdb=" N GLY D 335 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA D 320 " --> pdb=" O GLY D 335 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 213 through 216 removed outlier: 9.365A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 7.378A 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 5 removed outlier: 4.020A pdb=" N THR E 517 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL F 39 " --> pdb=" O THR E 517 " (cutoff:3.500A) removed outlier: 6.184A 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: 6.521A pdb=" N VAL E 174 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE E 379 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR E 176 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL E 381 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU E 178 " --> pdb=" O VAL E 381 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 193 through 195 removed outlier: 6.387A pdb=" N GLY E 335 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA E 320 " --> pdb=" O GLY E 335 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 213 through 216 removed outlier: 9.342A pdb=" N ILE E 301 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 7.359A 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 5 removed outlier: 3.595A pdb=" N ASP F 5 " --> pdb=" O THR F 522 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 174 through 179 removed outlier: 6.509A pdb=" N VAL F 174 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE F 379 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 7.157A 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: 6.368A pdb=" N GLY F 335 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA F 320 " --> pdb=" O GLY F 335 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 213 through 216 removed outlier: 9.362A pdb=" N ILE F 301 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 7.373A 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 'F' and resid 517 through 520 removed outlier: 3.989A pdb=" N THR F 517 " --> pdb=" O ASN G 37 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL G 39 " --> pdb=" O THR F 517 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N CYS F 519 " --> pdb=" O VAL G 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 174 through 179 removed outlier: 6.479A pdb=" N VAL G 174 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE G 379 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR G 176 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL G 381 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLU G 178 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 192 through 195 removed outlier: 6.370A pdb=" N GLY G 335 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA G 320 " --> pdb=" O GLY G 335 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 213 through 216 removed outlier: 9.330A pdb=" N ILE G 301 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU G 222 " --> pdb=" O ILE G 301 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 226 through 227 Processing sheet with id=AF4, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AF5, first strand: chain 'G' and resid 476 through 479 Processing sheet with id=AF6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AF7, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.925A pdb=" N ASN H 37 " --> pdb=" O THR N 517 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N CYS N 519 " --> pdb=" O ASN H 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 174 through 179 removed outlier: 6.426A pdb=" N VAL H 174 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE H 379 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR H 176 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL H 381 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLU H 178 " --> pdb=" O VAL H 381 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 192 through 195 removed outlier: 6.365A pdb=" N GLY H 335 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA H 320 " --> pdb=" O GLY H 335 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 213 through 216 removed outlier: 9.376A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 226 through 227 Processing sheet with id=AG3, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AG4, first strand: chain 'H' and resid 476 through 479 Processing sheet with id=AG5, first strand: chain 'H' and resid 517 through 520 removed outlier: 4.076A pdb=" N THR H 517 " --> pdb=" O ASN I 37 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL I 39 " --> pdb=" O THR H 517 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N CYS H 519 " --> pdb=" O VAL I 39 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AG7, first strand: chain 'I' and resid 174 through 179 removed outlier: 6.552A pdb=" N VAL I 174 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE I 379 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR I 176 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL I 381 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLU I 178 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 192 through 195 removed outlier: 6.371A pdb=" N GLY I 335 " --> pdb=" O ALA I 320 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA I 320 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 213 through 216 removed outlier: 9.343A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 226 through 227 Processing sheet with id=AH2, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AH3, first strand: chain 'I' and resid 476 through 479 Processing sheet with id=AH4, first strand: chain 'I' and resid 517 through 520 removed outlier: 4.044A pdb=" N THR I 517 " --> pdb=" O ASN J 37 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL J 39 " --> pdb=" O THR I 517 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS I 519 " --> pdb=" O VAL J 39 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 4 through 7 removed outlier: 4.085A pdb=" N THR J 517 " --> pdb=" O ASN K 37 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL K 39 " --> pdb=" O THR J 517 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS J 519 " --> pdb=" O VAL K 39 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 174 through 179 removed outlier: 6.524A pdb=" N VAL J 174 " --> pdb=" O ALA J 377 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE J 379 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR J 176 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL J 381 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU J 178 " --> pdb=" O VAL J 381 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 192 through 195 removed outlier: 6.357A pdb=" N GLY J 335 " --> pdb=" O ALA J 320 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA J 320 " --> pdb=" O GLY J 335 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 213 through 216 removed outlier: 9.368A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU J 222 " --> pdb=" O ILE J 301 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 226 through 227 Processing sheet with id=AI1, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AI2, first strand: chain 'J' and resid 476 through 479 Processing sheet with id=AI3, first strand: chain 'K' and resid 4 through 7 removed outlier: 4.071A pdb=" N THR K 517 " --> pdb=" O ASN L 37 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N VAL L 39 " --> pdb=" O THR K 517 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N CYS K 519 " --> pdb=" O VAL L 39 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 174 through 179 removed outlier: 6.491A pdb=" N VAL K 174 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE K 379 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR K 176 " --> pdb=" O ILE K 379 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL K 381 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLU K 178 " --> pdb=" O VAL K 381 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 192 through 195 removed outlier: 6.372A pdb=" N GLY K 335 " --> pdb=" O ALA K 320 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA K 320 " --> pdb=" O GLY K 335 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 213 through 216 removed outlier: 9.351A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 226 through 227 Processing sheet with id=AI8, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AI9, first strand: chain 'K' and resid 476 through 479 Processing sheet with id=AJ1, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.071A pdb=" N THR L 517 " --> pdb=" O ASN M 37 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL M 39 " --> pdb=" O THR L 517 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N CYS L 519 " --> pdb=" O VAL M 39 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 174 through 179 removed outlier: 6.508A pdb=" N VAL L 174 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ILE L 379 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR L 176 " --> pdb=" O ILE L 379 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N VAL L 381 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLU L 178 " --> pdb=" O VAL L 381 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'L' and resid 193 through 195 removed outlier: 6.377A pdb=" N GLY L 335 " --> pdb=" O ALA L 320 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA L 320 " --> pdb=" O GLY L 335 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'L' and resid 213 through 216 removed outlier: 9.361A pdb=" N ILE L 301 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU L 222 " --> pdb=" O ILE L 301 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'L' and resid 226 through 227 Processing sheet with id=AJ6, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AJ7, first strand: chain 'L' and resid 476 through 479 Processing sheet with id=AJ8, first strand: chain 'M' and resid 4 through 5 Processing sheet with id=AJ9, first strand: chain 'M' and resid 174 through 179 removed outlier: 6.550A pdb=" N VAL M 174 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE M 379 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL M 381 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLU M 178 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'M' and resid 192 through 195 removed outlier: 6.366A pdb=" N GLY M 335 " --> pdb=" O ALA M 320 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA M 320 " --> pdb=" O GLY M 335 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'M' and resid 213 through 216 removed outlier: 9.355A pdb=" N ILE M 301 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU M 222 " --> pdb=" O ILE M 301 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'M' and resid 226 through 227 Processing sheet with id=AK4, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AK5, first strand: chain 'M' and resid 476 through 479 Processing sheet with id=AK6, first strand: chain 'M' and resid 517 through 520 removed outlier: 4.053A pdb=" N THR M 517 " --> pdb=" O ASN N 37 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL N 39 " --> pdb=" O THR M 517 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS M 519 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'N' and resid 4 through 5 Processing sheet with id=AK8, first strand: chain 'N' and resid 174 through 179 removed outlier: 6.466A pdb=" N VAL N 174 " --> pdb=" O ALA N 377 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE N 379 " --> pdb=" O VAL N 174 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR N 176 " --> pdb=" O ILE N 379 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL N 381 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU N 178 " --> pdb=" O VAL N 381 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'N' and resid 193 through 195 removed outlier: 6.367A pdb=" N GLY N 335 " --> pdb=" O ALA N 320 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA N 320 " --> pdb=" O GLY N 335 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'N' and resid 213 through 216 removed outlier: 9.359A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'N' and resid 226 through 227 Processing sheet with id=AL3, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AL4, first strand: chain 'N' and resid 476 through 479 3801 hydrogen bonds defined for protein. 10956 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: 32.29 Time building geometry restraints manager: 15.13 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: 18652 1.34 - 1.46: 9056 1.46 - 1.58: 26654 1.58 - 1.70: 14 1.70 - 1.83: 518 Bond restraints: 54894 Sorted by residual: bond pdb=" CB MET C 16 " pdb=" CG MET C 16 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.40e+00 bond pdb=" SD MET L 69 " pdb=" CE MET L 69 " ideal model delta sigma weight residual 1.791 1.735 0.056 2.50e-02 1.60e+03 5.06e+00 bond pdb=" CB MET E 69 " pdb=" CG MET E 69 " ideal model delta sigma weight residual 1.520 1.457 0.063 3.00e-02 1.11e+03 4.45e+00 bond pdb=" CB ASP K 41 " pdb=" CG ASP K 41 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.41e+00 bond pdb=" CB VAL F 39 " pdb=" CG1 VAL F 39 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.26e+00 ... (remaining 54889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 72813 2.61 - 5.22: 1159 5.22 - 7.83: 201 7.83 - 10.44: 25 10.44 - 13.05: 16 Bond angle restraints: 74214 Sorted by residual: angle pdb=" CA MET M 514 " pdb=" CB MET M 514 " pdb=" CG MET M 514 " ideal model delta sigma weight residual 114.10 126.60 -12.50 2.00e+00 2.50e-01 3.91e+01 angle pdb=" CA MET E 514 " pdb=" CB MET E 514 " pdb=" CG MET E 514 " ideal model delta sigma weight residual 114.10 126.13 -12.03 2.00e+00 2.50e-01 3.62e+01 angle pdb=" CA MET A 514 " pdb=" CB MET A 514 " pdb=" CG MET A 514 " ideal model delta sigma weight residual 114.10 125.08 -10.98 2.00e+00 2.50e-01 3.01e+01 angle pdb=" N GLU B 164 " pdb=" CA GLU B 164 " pdb=" CB GLU B 164 " ideal model delta sigma weight residual 110.16 117.28 -7.12 1.48e+00 4.57e-01 2.31e+01 angle pdb=" N GLU L 164 " pdb=" CA GLU L 164 " pdb=" CB GLU L 164 " ideal model delta sigma weight residual 110.16 117.07 -6.91 1.48e+00 4.57e-01 2.18e+01 ... (remaining 74209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 30934 16.73 - 33.45: 2565 33.45 - 50.18: 609 50.18 - 66.90: 170 66.90 - 83.63: 22 Dihedral angle restraints: 34300 sinusoidal: 13566 harmonic: 20734 Sorted by residual: dihedral pdb=" CA ASP H 41 " pdb=" C ASP H 41 " pdb=" N LYS H 42 " pdb=" CA LYS H 42 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ASP I 41 " pdb=" C ASP I 41 " pdb=" N LYS I 42 " pdb=" CA LYS I 42 " ideal model delta harmonic sigma weight residual 180.00 153.92 26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASP M 41 " pdb=" C ASP M 41 " pdb=" N LYS M 42 " pdb=" CA LYS M 42 " ideal model delta harmonic sigma weight residual 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 34297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 6384 0.047 - 0.095: 1889 0.095 - 0.142: 647 0.142 - 0.190: 62 0.190 - 0.237: 20 Chirality restraints: 9002 Sorted by residual: chirality pdb=" CB VAL H 521 " pdb=" CA VAL H 521 " pdb=" CG1 VAL H 521 " pdb=" CG2 VAL H 521 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB VAL K 521 " pdb=" CA VAL K 521 " pdb=" CG1 VAL K 521 " pdb=" CG2 VAL K 521 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB VAL G 521 " pdb=" CA VAL G 521 " pdb=" CG1 VAL G 521 " pdb=" CG2 VAL G 521 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 8999 not shown) Planarity restraints: 9632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP K 41 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" CG ASP K 41 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP K 41 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP K 41 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 41 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" CG ASP B 41 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP B 41 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 41 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 41 " -0.011 2.00e-02 2.50e+03 2.33e-02 5.42e+00 pdb=" CG ASP H 41 " 0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP H 41 " -0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP H 41 " -0.014 2.00e-02 2.50e+03 ... (remaining 9629 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 8056 2.76 - 3.29: 56604 3.29 - 3.83: 96636 3.83 - 4.36: 111264 4.36 - 4.90: 188354 Nonbonded interactions: 460914 Sorted by model distance: nonbonded pdb=" OH TYR K 360 " pdb=" OE1 GLN L 184 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR E 360 " pdb=" OE1 GLN F 184 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR L 360 " pdb=" OE1 GLN M 184 " model vdw 2.235 3.040 nonbonded pdb=" OH TYR H 360 " pdb=" OE1 GLN I 184 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP E 495 " pdb=" O2' ATP E 601 " model vdw 2.299 3.040 ... (remaining 460909 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: 3.290 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: 0.050 Extract box with map and model: 1.980 Check model and map are aligned: 0.370 Set scattering table: 0.440 Process input model: 123.380 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.400 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 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 : 0.005 0.076 54894 Z= 0.339 Angle : 0.845 13.052 74214 Z= 0.466 Chirality : 0.051 0.237 9002 Planarity : 0.005 0.037 9632 Dihedral : 13.611 83.629 21000 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -0.61 (0.09), residues: 7322 helix: 0.01 (0.07), residues: 4046 sheet: -0.63 (0.16), residues: 1064 loop : -0.78 (0.12), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS M 401 PHE 0.025 0.002 PHE G 8 TYR 0.039 0.002 TYR D 360 ARG 0.004 0.001 ARG J 362 *********************** 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 416 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 6.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8314 (mtp) cc_final: 0.8045 (ttm) REVERT: A 288 MET cc_start: 0.9233 (ppp) cc_final: 0.9021 (ppp) REVERT: B 16 MET cc_start: 0.8215 (ttm) cc_final: 0.7329 (ttp) REVERT: B 233 MET cc_start: 0.8534 (mmp) cc_final: 0.8308 (mmp) REVERT: C 69 MET cc_start: 0.8364 (mtt) cc_final: 0.7962 (mtt) REVERT: C 114 MET cc_start: 0.8319 (mmm) cc_final: 0.8085 (mmm) REVERT: D 233 MET cc_start: 0.8519 (mmp) cc_final: 0.8222 (mmp) REVERT: D 267 MET cc_start: 0.3479 (ttt) cc_final: 0.3268 (ttm) REVERT: E 233 MET cc_start: 0.8401 (mmp) cc_final: 0.7432 (tpp) REVERT: G 114 MET cc_start: 0.8367 (mmm) cc_final: 0.8042 (mmm) REVERT: G 233 MET cc_start: 0.8524 (mmp) cc_final: 0.8160 (mmm) REVERT: H 233 MET cc_start: 0.8656 (mmp) cc_final: 0.8401 (mmp) REVERT: I 506 TYR cc_start: 0.7620 (m-80) cc_final: 0.7398 (m-80) REVERT: J 29 VAL cc_start: 0.8987 (t) cc_final: 0.8599 (m) REVERT: J 69 MET cc_start: 0.8175 (mtp) cc_final: 0.7900 (ttm) REVERT: K 267 MET cc_start: 0.2657 (ttp) cc_final: 0.2429 (ttm) REVERT: K 520 MET cc_start: 0.8334 (mtt) cc_final: 0.8085 (mtt) REVERT: N 16 MET cc_start: 0.8375 (ttp) cc_final: 0.8090 (ttp) REVERT: N 233 MET cc_start: 0.8743 (mmp) cc_final: 0.8518 (mmm) REVERT: N 506 TYR cc_start: 0.7628 (m-80) cc_final: 0.7359 (m-80) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.6032 time to fit residues: 438.0156 Evaluate side-chains 348 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 6.340 ------------------------------------------------------------------------------- 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: 0.0370 chunk 551 optimal weight: 20.0000 chunk 306 optimal weight: 0.8980 chunk 188 optimal weight: 30.0000 chunk 372 optimal weight: 3.9990 chunk 294 optimal weight: 6.9990 chunk 570 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 424 optimal weight: 2.9990 chunk 661 optimal weight: 30.0000 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN C 37 ASN E 37 ASN L 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 54894 Z= 0.251 Angle : 0.581 12.490 74214 Z= 0.314 Chirality : 0.043 0.146 9002 Planarity : 0.003 0.026 9632 Dihedral : 8.467 66.560 8218 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.65 % Allowed : 5.75 % Favored : 93.60 % 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: -0.04 (0.09), residues: 7322 helix: 0.69 (0.08), residues: 4172 sheet: -0.46 (0.16), residues: 1008 loop : -1.03 (0.11), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS J 401 PHE 0.021 0.002 PHE F 195 TYR 0.025 0.001 TYR I 360 ARG 0.005 0.000 ARG C 285 *********************** 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 396 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 359 time to evaluate : 6.327 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: A 16 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7677 (ttt) REVERT: A 166 MET cc_start: 0.9185 (mmm) cc_final: 0.8979 (mmm) REVERT: A 288 MET cc_start: 0.9215 (ppp) cc_final: 0.8984 (ppp) REVERT: B 16 MET cc_start: 0.8388 (ttm) cc_final: 0.8099 (ttm) REVERT: B 233 MET cc_start: 0.8578 (mmp) cc_final: 0.8318 (mmp) REVERT: C 69 MET cc_start: 0.8449 (mtt) cc_final: 0.8084 (mtt) REVERT: C 114 MET cc_start: 0.8344 (mmm) cc_final: 0.7994 (mmm) REVERT: D 166 MET cc_start: 0.9322 (mmm) cc_final: 0.9106 (mmm) REVERT: D 233 MET cc_start: 0.8579 (mmp) cc_final: 0.8299 (mmp) REVERT: D 520 MET cc_start: 0.8533 (mtt) cc_final: 0.8279 (mtt) REVERT: E 233 MET cc_start: 0.8442 (mmp) cc_final: 0.7440 (tpp) REVERT: E 288 MET cc_start: 0.9033 (ppp) cc_final: 0.8769 (ppp) REVERT: F 288 MET cc_start: 0.9170 (ppp) cc_final: 0.8921 (ppp) REVERT: G 233 MET cc_start: 0.8606 (mmp) cc_final: 0.8332 (mmm) REVERT: H 233 MET cc_start: 0.8666 (mmp) cc_final: 0.8436 (mmp) REVERT: H 288 MET cc_start: 0.8999 (ppp) cc_final: 0.8696 (ppp) REVERT: J 288 MET cc_start: 0.9042 (ppp) cc_final: 0.8774 (ppp) REVERT: K 233 MET cc_start: 0.8603 (mmm) cc_final: 0.8393 (mmp) REVERT: K 267 MET cc_start: 0.2847 (ttp) cc_final: 0.2558 (ttm) REVERT: K 520 MET cc_start: 0.8265 (mtt) cc_final: 0.7992 (mtt) REVERT: L 233 MET cc_start: 0.8420 (mmm) cc_final: 0.8193 (mmp) REVERT: L 288 MET cc_start: 0.9086 (ppp) cc_final: 0.8831 (ppp) REVERT: M 233 MET cc_start: 0.8656 (mmm) cc_final: 0.8441 (mmp) REVERT: N 233 MET cc_start: 0.8812 (mmp) cc_final: 0.8555 (mmm) outliers start: 37 outliers final: 15 residues processed: 375 average time/residue: 0.6142 time to fit residues: 405.3062 Evaluate side-chains 358 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 342 time to evaluate : 6.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain I residue 363 GLU Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 363 GLU Chi-restraints excluded: chain K residue 193 MET Chi-restraints excluded: chain L residue 193 MET Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 69 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 367 optimal weight: 0.9980 chunk 205 optimal weight: 0.0020 chunk 550 optimal weight: 9.9990 chunk 450 optimal weight: 7.9990 chunk 182 optimal weight: 7.9990 chunk 662 optimal weight: 10.0000 chunk 715 optimal weight: 7.9990 chunk 589 optimal weight: 6.9990 chunk 656 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 531 optimal weight: 5.9990 overall best weight: 4.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 54894 Z= 0.378 Angle : 0.607 10.207 74214 Z= 0.327 Chirality : 0.044 0.161 9002 Planarity : 0.003 0.035 9632 Dihedral : 8.194 66.084 8218 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.10 % Allowed : 8.19 % Favored : 90.72 % 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: 0.05 (0.09), residues: 7322 helix: 0.74 (0.08), residues: 4214 sheet: -0.52 (0.16), residues: 1008 loop : -0.95 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 401 PHE 0.016 0.002 PHE F 8 TYR 0.022 0.002 TYR I 360 ARG 0.006 0.000 ARG L 395 *********************** 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 398 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 336 time to evaluate : 6.095 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7967 (ttt) REVERT: A 166 MET cc_start: 0.9222 (mmm) cc_final: 0.9020 (mmm) REVERT: B 16 MET cc_start: 0.8442 (ttm) cc_final: 0.8076 (ttm) REVERT: B 233 MET cc_start: 0.8617 (mmp) cc_final: 0.8348 (mmp) REVERT: C 69 MET cc_start: 0.8493 (mtt) cc_final: 0.8210 (mtt) REVERT: D 166 MET cc_start: 0.9310 (mmm) cc_final: 0.9100 (mmm) REVERT: D 233 MET cc_start: 0.8683 (mmp) cc_final: 0.8396 (mmp) REVERT: E 16 MET cc_start: 0.8187 (ttt) cc_final: 0.7563 (ttt) REVERT: E 233 MET cc_start: 0.8518 (mmp) cc_final: 0.7689 (tpp) REVERT: E 288 MET cc_start: 0.9027 (ppp) cc_final: 0.8806 (ppp) REVERT: G 233 MET cc_start: 0.8659 (mmp) cc_final: 0.8025 (tpp) REVERT: H 233 MET cc_start: 0.8795 (mmp) cc_final: 0.8530 (mmp) REVERT: H 288 MET cc_start: 0.9018 (ppp) cc_final: 0.8773 (ppp) REVERT: I 16 MET cc_start: 0.8449 (ttm) cc_final: 0.8239 (ttm) REVERT: I 83 ASP cc_start: 0.8303 (t0) cc_final: 0.7974 (t70) REVERT: I 166 MET cc_start: 0.9365 (mmm) cc_final: 0.9040 (mmm) REVERT: I 233 MET cc_start: 0.8510 (mmp) cc_final: 0.8270 (mmm) REVERT: J 16 MET cc_start: 0.8640 (ttm) cc_final: 0.7738 (ttt) REVERT: J 114 MET cc_start: 0.8366 (mmm) cc_final: 0.8087 (mmm) REVERT: J 233 MET cc_start: 0.8540 (mmp) cc_final: 0.8300 (mmp) REVERT: J 288 MET cc_start: 0.9049 (ppp) cc_final: 0.8826 (ppp) REVERT: K 267 MET cc_start: 0.2831 (ttp) cc_final: 0.2578 (ttm) REVERT: L 8 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7437 (p90) REVERT: L 233 MET cc_start: 0.8562 (mmm) cc_final: 0.8340 (mmp) REVERT: L 288 MET cc_start: 0.9105 (ppp) cc_final: 0.8874 (ppp) REVERT: M 41 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: M 288 MET cc_start: 0.9209 (ppp) cc_final: 0.8950 (ppp) REVERT: N 233 MET cc_start: 0.8853 (mmp) cc_final: 0.8581 (mmp) REVERT: N 514 MET cc_start: 0.7975 (ttm) cc_final: 0.7753 (ttm) outliers start: 62 outliers final: 33 residues processed: 386 average time/residue: 0.6228 time to fit residues: 421.6771 Evaluate side-chains 366 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 330 time to evaluate : 6.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 363 GLU Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 8 PHE Chi-restraints excluded: chain M residue 6 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 164 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 654 optimal weight: 2.9990 chunk 497 optimal weight: 20.0000 chunk 343 optimal weight: 40.0000 chunk 73 optimal weight: 0.7980 chunk 316 optimal weight: 2.9990 chunk 444 optimal weight: 5.9990 chunk 664 optimal weight: 2.9990 chunk 703 optimal weight: 20.0000 chunk 347 optimal weight: 8.9990 chunk 629 optimal weight: 2.9990 chunk 189 optimal weight: 0.2980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 54894 Z= 0.221 Angle : 0.541 10.014 74214 Z= 0.289 Chirality : 0.041 0.144 9002 Planarity : 0.003 0.024 9632 Dihedral : 7.792 65.500 8218 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.06 % Allowed : 9.60 % Favored : 89.34 % 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: 0.34 (0.09), residues: 7322 helix: 1.00 (0.08), residues: 4242 sheet: -0.49 (0.16), residues: 1008 loop : -0.86 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 401 PHE 0.013 0.001 PHE L 195 TYR 0.019 0.001 TYR I 360 ARG 0.003 0.000 ARG F 395 *********************** 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 411 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 351 time to evaluate : 6.239 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.8612 (mmm) cc_final: 0.8221 (mmp) REVERT: A 288 MET cc_start: 0.9259 (ppp) cc_final: 0.9049 (ppp) REVERT: B 233 MET cc_start: 0.8620 (mmp) cc_final: 0.8349 (mmp) REVERT: B 288 MET cc_start: 0.9147 (ppp) cc_final: 0.8892 (ppp) REVERT: C 69 MET cc_start: 0.8504 (mtt) cc_final: 0.8081 (mtt) REVERT: C 288 MET cc_start: 0.9196 (ppp) cc_final: 0.8853 (ppp) REVERT: D 233 MET cc_start: 0.8698 (mmp) cc_final: 0.8406 (mmp) REVERT: E 69 MET cc_start: 0.8509 (mtt) cc_final: 0.8094 (mmt) REVERT: E 233 MET cc_start: 0.8535 (mmp) cc_final: 0.7686 (tpp) REVERT: E 288 MET cc_start: 0.9075 (ppp) cc_final: 0.8825 (ppp) REVERT: F 41 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7260 (m-30) REVERT: F 288 MET cc_start: 0.9149 (ppp) cc_final: 0.8884 (ppp) REVERT: G 233 MET cc_start: 0.8671 (mmp) cc_final: 0.8019 (tpp) REVERT: G 288 MET cc_start: 0.9261 (ppp) cc_final: 0.9014 (ppp) REVERT: H 233 MET cc_start: 0.8836 (mmp) cc_final: 0.8547 (mmp) REVERT: H 288 MET cc_start: 0.9027 (ppp) cc_final: 0.8764 (ppp) REVERT: I 16 MET cc_start: 0.8450 (ttm) cc_final: 0.8248 (ttm) REVERT: I 166 MET cc_start: 0.9286 (mmm) cc_final: 0.9000 (mmm) REVERT: I 233 MET cc_start: 0.8558 (mmp) cc_final: 0.8295 (mmp) REVERT: I 288 MET cc_start: 0.9306 (ppp) cc_final: 0.8965 (ppp) REVERT: J 114 MET cc_start: 0.8339 (mmm) cc_final: 0.8058 (mmm) REVERT: J 233 MET cc_start: 0.8556 (mmp) cc_final: 0.8334 (mmp) REVERT: J 288 MET cc_start: 0.9025 (ppp) cc_final: 0.8789 (ppp) REVERT: K 520 MET cc_start: 0.8544 (mtt) cc_final: 0.8331 (mtt) REVERT: L 288 MET cc_start: 0.9138 (ppp) cc_final: 0.8900 (ppp) REVERT: M 41 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7581 (m-30) REVERT: N 233 MET cc_start: 0.8864 (mmp) cc_final: 0.8587 (mmp) REVERT: N 288 MET cc_start: 0.9175 (ppp) cc_final: 0.8904 (ppp) outliers start: 60 outliers final: 40 residues processed: 392 average time/residue: 0.6150 time to fit residues: 424.4837 Evaluate side-chains 376 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 334 time to evaluate : 6.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 521 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 164 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 586 optimal weight: 7.9990 chunk 399 optimal weight: 40.0000 chunk 10 optimal weight: 0.9990 chunk 523 optimal weight: 3.9990 chunk 290 optimal weight: 7.9990 chunk 600 optimal weight: 5.9990 chunk 486 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 359 optimal weight: 8.9990 chunk 631 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 54894 Z= 0.268 Angle : 0.555 12.839 74214 Z= 0.296 Chirality : 0.042 0.156 9002 Planarity : 0.003 0.027 9632 Dihedral : 7.588 64.440 8218 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.54 % Allowed : 10.54 % Favored : 87.92 % 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: 0.41 (0.09), residues: 7322 helix: 1.09 (0.08), residues: 4242 sheet: -0.55 (0.15), residues: 1148 loop : -0.87 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.016 0.002 PHE J 195 TYR 0.019 0.001 TYR M 360 ARG 0.004 0.000 ARG F 395 *********************** 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 434 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 347 time to evaluate : 6.186 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: 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: B 233 MET cc_start: 0.8678 (mmp) cc_final: 0.8394 (mmp) REVERT: C 69 MET cc_start: 0.8557 (mtt) cc_final: 0.8326 (mtt) REVERT: C 233 MET cc_start: 0.8485 (mmm) cc_final: 0.8281 (mmp) REVERT: D 233 MET cc_start: 0.8728 (mmp) cc_final: 0.8407 (mmp) REVERT: E 233 MET cc_start: 0.8552 (mmp) cc_final: 0.7992 (tpp) REVERT: E 288 MET cc_start: 0.9090 (ppp) cc_final: 0.8843 (ppp) REVERT: F 41 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7915 (m-30) REVERT: G 233 MET cc_start: 0.8708 (mmp) cc_final: 0.8066 (tpp) REVERT: H 41 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: H 233 MET cc_start: 0.8853 (mmp) cc_final: 0.8551 (mmp) REVERT: H 288 MET cc_start: 0.9036 (ppp) cc_final: 0.8773 (ppp) REVERT: I 166 MET cc_start: 0.9277 (mmm) cc_final: 0.9044 (mmm) REVERT: J 233 MET cc_start: 0.8645 (mmp) cc_final: 0.8414 (mmp) REVERT: L 233 MET cc_start: 0.8554 (mmp) cc_final: 0.8234 (mmp) REVERT: M 41 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7690 (m-30) REVERT: M 233 MET cc_start: 0.8689 (mmm) cc_final: 0.8470 (mmp) REVERT: M 288 MET cc_start: 0.9166 (ppp) cc_final: 0.8880 (ppp) REVERT: N 8 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7193 (p90) REVERT: N 111 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7439 (mtm) REVERT: N 233 MET cc_start: 0.8886 (mmp) cc_final: 0.8592 (mmp) outliers start: 87 outliers final: 49 residues processed: 418 average time/residue: 0.5990 time to fit residues: 440.3187 Evaluate side-chains 388 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 334 time to evaluate : 6.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 164 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 236 optimal weight: 7.9990 chunk 633 optimal weight: 1.9990 chunk 139 optimal weight: 30.0000 chunk 413 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 704 optimal weight: 7.9990 chunk 584 optimal weight: 0.9990 chunk 326 optimal weight: 9.9990 chunk 58 optimal weight: 0.6980 chunk 232 optimal weight: 7.9990 chunk 369 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 54894 Z= 0.223 Angle : 0.552 15.166 74214 Z= 0.291 Chirality : 0.041 0.160 9002 Planarity : 0.003 0.023 9632 Dihedral : 7.362 65.350 8218 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.68 % Allowed : 11.46 % Favored : 86.86 % 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: 0.53 (0.09), residues: 7322 helix: 1.20 (0.08), residues: 4242 sheet: -0.52 (0.15), residues: 1148 loop : -0.84 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 401 PHE 0.029 0.001 PHE M 195 TYR 0.027 0.001 TYR M 360 ARG 0.003 0.000 ARG K 395 *********************** 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 452 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 357 time to evaluate : 6.224 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: 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 8 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7151 (p90) REVERT: A 69 MET cc_start: 0.8475 (mtp) cc_final: 0.8202 (ttm) REVERT: A 233 MET cc_start: 0.8570 (mmm) cc_final: 0.8114 (mmp) REVERT: A 288 MET cc_start: 0.9165 (ppp) cc_final: 0.8822 (ppp) REVERT: B 233 MET cc_start: 0.8692 (mmp) cc_final: 0.8394 (mmp) REVERT: B 288 MET cc_start: 0.9143 (ppp) cc_final: 0.8747 (ppp) REVERT: C 233 MET cc_start: 0.8522 (mmm) cc_final: 0.8321 (mmp) REVERT: D 233 MET cc_start: 0.8758 (mmp) cc_final: 0.8412 (mmp) REVERT: D 288 MET cc_start: 0.9195 (ppp) cc_final: 0.8885 (ppp) REVERT: E 233 MET cc_start: 0.8583 (mmp) cc_final: 0.8030 (tpp) REVERT: E 288 MET cc_start: 0.9105 (ppp) cc_final: 0.8855 (ppp) REVERT: F 288 MET cc_start: 0.9104 (ppp) cc_final: 0.8818 (ppp) REVERT: G 233 MET cc_start: 0.8726 (mmp) cc_final: 0.8098 (tpp) REVERT: G 288 MET cc_start: 0.9259 (ppp) cc_final: 0.9032 (ppp) REVERT: G 506 TYR cc_start: 0.7667 (m-80) cc_final: 0.7197 (m-80) REVERT: H 41 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: H 233 MET cc_start: 0.8896 (mmp) cc_final: 0.8574 (mmp) REVERT: H 288 MET cc_start: 0.9055 (ppp) cc_final: 0.8778 (ppp) REVERT: I 69 MET cc_start: 0.8599 (ttt) cc_final: 0.8388 (mtt) REVERT: I 166 MET cc_start: 0.9264 (mmm) cc_final: 0.9037 (mmm) REVERT: I 288 MET cc_start: 0.9287 (ppp) cc_final: 0.8961 (ppp) REVERT: J 8 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7061 (p90) REVERT: J 233 MET cc_start: 0.8661 (mmp) cc_final: 0.8449 (mmp) REVERT: J 307 MET cc_start: 0.7862 (pmm) cc_final: 0.7659 (pmm) REVERT: K 233 MET cc_start: 0.8504 (mmp) cc_final: 0.8297 (mmp) REVERT: L 233 MET cc_start: 0.8565 (mmp) cc_final: 0.8280 (mmp) REVERT: L 288 MET cc_start: 0.9178 (ppp) cc_final: 0.8856 (ppp) REVERT: M 41 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: M 233 MET cc_start: 0.8735 (mmm) cc_final: 0.8534 (mmm) REVERT: M 288 MET cc_start: 0.9229 (ppp) cc_final: 0.8957 (ppp) REVERT: N 8 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7167 (p90) REVERT: N 233 MET cc_start: 0.8901 (mmp) cc_final: 0.8606 (mmp) REVERT: N 288 MET cc_start: 0.9186 (ppp) cc_final: 0.8917 (ppp) outliers start: 95 outliers final: 68 residues processed: 424 average time/residue: 0.5909 time to fit residues: 442.0881 Evaluate side-chains 412 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 339 time to evaluate : 6.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 8 PHE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 521 VAL Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 69 MET Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 267 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 679 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 chunk 514 optimal weight: 0.7980 chunk 398 optimal weight: 20.0000 chunk 592 optimal weight: 9.9990 chunk 393 optimal weight: 9.9990 chunk 701 optimal weight: 10.0000 chunk 439 optimal weight: 8.9990 chunk 427 optimal weight: 4.9990 chunk 323 optimal weight: 4.9990 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 467 ASN ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 54894 Z= 0.351 Angle : 0.612 14.496 74214 Z= 0.324 Chirality : 0.043 0.193 9002 Planarity : 0.003 0.039 9632 Dihedral : 7.429 64.278 8218 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.94 % Allowed : 12.13 % Favored : 85.93 % 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: 0.48 (0.09), residues: 7322 helix: 1.06 (0.08), residues: 4256 sheet: -0.44 (0.14), residues: 1190 loop : -0.66 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS I 401 PHE 0.024 0.002 PHE M 195 TYR 0.018 0.002 TYR M 360 ARG 0.005 0.000 ARG C 395 *********************** 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 443 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 333 time to evaluate : 5.944 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: 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 8 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.7140 (p90) REVERT: A 233 MET cc_start: 0.8691 (mmm) cc_final: 0.8263 (mmp) REVERT: A 288 MET cc_start: 0.9212 (ppp) cc_final: 0.8844 (ppp) REVERT: B 8 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7153 (p90) REVERT: B 233 MET cc_start: 0.8822 (mmp) cc_final: 0.8466 (mmp) REVERT: B 288 MET cc_start: 0.9150 (ppp) cc_final: 0.8919 (ppp) REVERT: C 288 MET cc_start: 0.9157 (ppp) cc_final: 0.8901 (ppp) REVERT: D 233 MET cc_start: 0.8781 (mmp) cc_final: 0.8428 (mmp) REVERT: D 288 MET cc_start: 0.9225 (ppp) cc_final: 0.8965 (ppp) REVERT: E 233 MET cc_start: 0.8601 (mmp) cc_final: 0.8072 (tpp) REVERT: E 288 MET cc_start: 0.9102 (ppp) cc_final: 0.8868 (ppp) REVERT: G 233 MET cc_start: 0.8756 (mmp) cc_final: 0.7979 (tpp) REVERT: H 41 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: H 233 MET cc_start: 0.8911 (mmp) cc_final: 0.8587 (mmp) REVERT: I 8 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7505 (p90) REVERT: I 69 MET cc_start: 0.8690 (ttt) cc_final: 0.8473 (mtt) REVERT: I 166 MET cc_start: 0.9232 (mmm) cc_final: 0.8992 (mmm) REVERT: I 288 MET cc_start: 0.9296 (ppp) cc_final: 0.8971 (ppp) REVERT: I 389 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.6710 (mmt) REVERT: J 8 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7134 (p90) REVERT: J 233 MET cc_start: 0.8652 (mmp) cc_final: 0.8451 (mmp) REVERT: L 233 MET cc_start: 0.8595 (mmp) cc_final: 0.8339 (mmp) REVERT: M 307 MET cc_start: 0.7523 (pmm) cc_final: 0.7254 (pmm) REVERT: N 8 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7169 (p90) REVERT: N 111 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.7541 (mtm) REVERT: N 233 MET cc_start: 0.8929 (mmp) cc_final: 0.8627 (mmp) REVERT: N 288 MET cc_start: 0.9202 (ppp) cc_final: 0.8980 (ppp) outliers start: 110 outliers final: 77 residues processed: 419 average time/residue: 0.5899 time to fit residues: 436.4873 Evaluate side-chains 409 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 324 time to evaluate : 6.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 8 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 8 PHE Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 8 PHE Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 111 MET Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 56 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain M residue 6 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 107 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 213 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 434 optimal weight: 3.9990 chunk 280 optimal weight: 0.0000 chunk 419 optimal weight: 0.9990 chunk 211 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 135 optimal weight: 0.0980 chunk 446 optimal weight: 10.0000 chunk 478 optimal weight: 1.9990 chunk 346 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 551 optimal weight: 40.0000 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 366 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 54894 Z= 0.156 Angle : 0.553 15.298 74214 Z= 0.288 Chirality : 0.041 0.148 9002 Planarity : 0.003 0.023 9632 Dihedral : 7.060 68.554 8218 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.49 % Allowed : 13.19 % Favored : 85.33 % 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: 0.74 (0.10), residues: 7322 helix: 1.32 (0.08), residues: 4242 sheet: -0.27 (0.14), residues: 1190 loop : -0.75 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS N 401 PHE 0.024 0.001 PHE M 195 TYR 0.016 0.001 TYR A 360 ARG 0.003 0.000 ARG A 13 *********************** 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 456 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 372 time to evaluate : 6.445 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: 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: B 233 MET cc_start: 0.8794 (mmp) cc_final: 0.8441 (mmp) REVERT: B 288 MET cc_start: 0.9183 (ppp) cc_final: 0.8835 (ppp) REVERT: C 100 ILE cc_start: 0.8822 (tp) cc_final: 0.8407 (tt) REVERT: C 288 MET cc_start: 0.9249 (ppp) cc_final: 0.8913 (ppp) REVERT: C 491 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8058 (mtm) REVERT: D 233 MET cc_start: 0.8765 (mmp) cc_final: 0.8415 (mmp) REVERT: E 114 MET cc_start: 0.8398 (mmm) cc_final: 0.8153 (mmm) REVERT: E 233 MET cc_start: 0.8621 (mmp) cc_final: 0.8088 (tpp) REVERT: E 288 MET cc_start: 0.9109 (ppp) cc_final: 0.8876 (ppp) REVERT: F 73 MET cc_start: 0.7811 (mtp) cc_final: 0.7352 (mtp) REVERT: G 233 MET cc_start: 0.8749 (mmp) cc_final: 0.7909 (tpp) REVERT: G 288 MET cc_start: 0.9256 (ppp) cc_final: 0.9049 (ppp) REVERT: G 506 TYR cc_start: 0.7601 (m-80) cc_final: 0.7167 (m-80) REVERT: H 69 MET cc_start: 0.8559 (ttt) cc_final: 0.8272 (mtp) REVERT: H 233 MET cc_start: 0.8916 (mmp) cc_final: 0.8588 (mmp) REVERT: H 288 MET cc_start: 0.9067 (ppp) cc_final: 0.8671 (ppp) REVERT: I 69 MET cc_start: 0.8540 (ttt) cc_final: 0.8276 (mtt) REVERT: I 288 MET cc_start: 0.9322 (ppp) cc_final: 0.9010 (ppp) REVERT: I 389 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6711 (mmt) REVERT: J 8 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6966 (p90) REVERT: J 233 MET cc_start: 0.8675 (mmp) cc_final: 0.8425 (mmp) REVERT: J 307 MET cc_start: 0.7745 (pmm) cc_final: 0.7517 (pmm) REVERT: L 114 MET cc_start: 0.8497 (mmm) cc_final: 0.8080 (mmm) REVERT: L 233 MET cc_start: 0.8546 (mmp) cc_final: 0.8306 (mmp) REVERT: L 288 MET cc_start: 0.9153 (ppp) cc_final: 0.8863 (ppp) REVERT: L 307 MET cc_start: 0.7528 (pmm) cc_final: 0.6891 (pmm) REVERT: M 233 MET cc_start: 0.8559 (mmm) cc_final: 0.8312 (mmp) REVERT: M 288 MET cc_start: 0.9138 (ppp) cc_final: 0.8837 (ppp) REVERT: M 307 MET cc_start: 0.7620 (pmm) cc_final: 0.7371 (pmm) REVERT: N 8 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7142 (p90) REVERT: N 111 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7681 (mtt) REVERT: N 114 MET cc_start: 0.8479 (mmm) cc_final: 0.8163 (mmm) REVERT: N 233 MET cc_start: 0.8903 (mmp) cc_final: 0.8613 (mmp) outliers start: 84 outliers final: 56 residues processed: 425 average time/residue: 0.6037 time to fit residues: 451.7828 Evaluate side-chains 410 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 349 time to evaluate : 6.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 329 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 40 LEU Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 8 PHE Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain K residue 267 MET Chi-restraints excluded: chain L residue 111 MET Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain M residue 267 MET Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 213 VAL 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: 7.9990 chunk 613 optimal weight: 0.6980 chunk 653 optimal weight: 30.0000 chunk 393 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 513 optimal weight: 6.9990 chunk 200 optimal weight: 0.4980 chunk 590 optimal weight: 7.9990 chunk 618 optimal weight: 3.9990 chunk 651 optimal weight: 8.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 : 0.005 0.058 54894 Z= 0.328 Angle : 0.626 15.102 74214 Z= 0.326 Chirality : 0.043 0.172 9002 Planarity : 0.003 0.036 9632 Dihedral : 7.144 65.612 8218 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.66 % Allowed : 13.60 % Favored : 84.74 % 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: 0.56 (0.10), residues: 7322 helix: 1.20 (0.08), residues: 4228 sheet: -0.53 (0.15), residues: 1148 loop : -0.70 (0.13), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 401 PHE 0.029 0.002 PHE M 195 TYR 0.017 0.001 TYR C 360 ARG 0.004 0.000 ARG C 395 *********************** 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 429 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 335 time to evaluate : 6.521 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: 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 233 MET cc_start: 0.8574 (mmm) cc_final: 0.8275 (mmp) REVERT: A 520 MET cc_start: 0.8206 (mtt) cc_final: 0.7945 (mtp) REVERT: B 233 MET cc_start: 0.8833 (mmp) cc_final: 0.8479 (mmp) REVERT: B 288 MET cc_start: 0.9215 (ppp) cc_final: 0.8998 (ppp) REVERT: C 288 MET cc_start: 0.9229 (ppp) cc_final: 0.9002 (ppp) REVERT: D 233 MET cc_start: 0.8807 (mmp) cc_final: 0.8467 (mmp) REVERT: D 288 MET cc_start: 0.9209 (ppp) cc_final: 0.8932 (ppp) REVERT: E 233 MET cc_start: 0.8645 (mmp) cc_final: 0.8141 (tpp) REVERT: F 233 MET cc_start: 0.8244 (mmp) cc_final: 0.7838 (mmm) REVERT: G 233 MET cc_start: 0.8774 (mmp) cc_final: 0.7988 (tpp) REVERT: G 288 MET cc_start: 0.9245 (ppp) cc_final: 0.9041 (ppp) REVERT: G 506 TYR cc_start: 0.7747 (m-80) cc_final: 0.7249 (m-80) REVERT: H 41 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: H 69 MET cc_start: 0.8649 (ttt) cc_final: 0.8376 (mtt) REVERT: H 233 MET cc_start: 0.8897 (mmp) cc_final: 0.8567 (mmp) REVERT: H 288 MET cc_start: 0.9054 (ppp) cc_final: 0.8712 (ppp) REVERT: I 69 MET cc_start: 0.8692 (ttt) cc_final: 0.8441 (mtt) REVERT: I 389 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.6789 (mmt) REVERT: J 8 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7160 (p90) REVERT: J 233 MET cc_start: 0.8737 (mmp) cc_final: 0.8476 (mmp) REVERT: J 307 MET cc_start: 0.7844 (pmm) cc_final: 0.7616 (pmm) REVERT: K 233 MET cc_start: 0.8554 (mmm) cc_final: 0.8332 (mmp) REVERT: K 307 MET cc_start: 0.7461 (pmm) cc_final: 0.7199 (pmm) REVERT: L 233 MET cc_start: 0.8544 (mmp) cc_final: 0.8289 (mmp) REVERT: L 288 MET cc_start: 0.9137 (ppp) cc_final: 0.8865 (ppp) REVERT: L 307 MET cc_start: 0.7608 (pmm) cc_final: 0.6926 (pmm) REVERT: M 233 MET cc_start: 0.8553 (mmm) cc_final: 0.8297 (mmp) REVERT: M 288 MET cc_start: 0.9142 (ppp) cc_final: 0.8856 (ppp) REVERT: M 307 MET cc_start: 0.7663 (pmm) cc_final: 0.7372 (pmm) REVERT: N 8 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7275 (p90) REVERT: N 111 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7787 (mtt) REVERT: N 233 MET cc_start: 0.8948 (mmp) cc_final: 0.8647 (mmp) REVERT: N 288 MET cc_start: 0.9159 (ppp) cc_final: 0.8903 (ppp) outliers start: 94 outliers final: 67 residues processed: 406 average time/residue: 0.6113 time to fit residues: 438.8515 Evaluate side-chains 399 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 327 time to evaluate : 6.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain H residue 417 VAL Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 8 PHE Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 39 VAL Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 429 optimal weight: 5.9990 chunk 691 optimal weight: 0.0870 chunk 422 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 chunk 480 optimal weight: 1.9990 chunk 725 optimal weight: 1.9990 chunk 667 optimal weight: 3.9990 chunk 577 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 446 optimal weight: 0.0970 chunk 354 optimal weight: 1.9990 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54894 Z= 0.172 Angle : 0.584 13.729 74214 Z= 0.300 Chirality : 0.041 0.143 9002 Planarity : 0.003 0.024 9632 Dihedral : 6.924 68.460 8218 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.27 % Allowed : 14.23 % Favored : 84.49 % 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: 0.73 (0.10), residues: 7322 helix: 1.35 (0.08), residues: 4242 sheet: -0.46 (0.15), residues: 1148 loop : -0.69 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS N 401 PHE 0.031 0.002 PHE E 195 TYR 0.019 0.001 TYR C 360 ARG 0.003 0.000 ARG A 285 ********************** 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 434 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 362 time to evaluate : 6.184 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: 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 233 MET cc_start: 0.8607 (mmm) cc_final: 0.8320 (mmp) REVERT: A 288 MET cc_start: 0.9178 (ppp) cc_final: 0.8735 (ppp) REVERT: B 233 MET cc_start: 0.8822 (mmp) cc_final: 0.8471 (mmp) REVERT: B 288 MET cc_start: 0.9192 (ppp) cc_final: 0.8971 (ppp) REVERT: B 514 MET cc_start: 0.8083 (tpt) cc_final: 0.7869 (tpt) REVERT: C 288 MET cc_start: 0.9209 (ppp) cc_final: 0.8988 (ppp) REVERT: C 307 MET cc_start: 0.7338 (pmm) cc_final: 0.7113 (pmm) REVERT: C 447 MET cc_start: 0.7997 (mtm) cc_final: 0.7638 (mtm) REVERT: D 233 MET cc_start: 0.8795 (mmp) cc_final: 0.8441 (mmp) REVERT: D 288 MET cc_start: 0.9215 (ppp) cc_final: 0.8939 (ppp) REVERT: E 114 MET cc_start: 0.8398 (mmm) cc_final: 0.8069 (mmm) REVERT: E 233 MET cc_start: 0.8630 (mmp) cc_final: 0.8110 (tpp) REVERT: E 288 MET cc_start: 0.9078 (ppp) cc_final: 0.8703 (ppp) REVERT: F 114 MET cc_start: 0.8260 (mmm) cc_final: 0.7938 (mmm) REVERT: F 233 MET cc_start: 0.8121 (mmp) cc_final: 0.7841 (mmp) REVERT: G 233 MET cc_start: 0.8750 (mmp) cc_final: 0.7929 (tpp) REVERT: G 288 MET cc_start: 0.9261 (ppp) cc_final: 0.9038 (ppp) REVERT: H 41 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7647 (m-30) REVERT: H 69 MET cc_start: 0.8558 (ttt) cc_final: 0.8326 (mtp) REVERT: H 233 MET cc_start: 0.8941 (mmp) cc_final: 0.8617 (mmp) REVERT: H 288 MET cc_start: 0.9081 (ppp) cc_final: 0.8759 (ppp) REVERT: I 69 MET cc_start: 0.8572 (ttt) cc_final: 0.8325 (mtt) REVERT: I 114 MET cc_start: 0.8347 (mmm) cc_final: 0.7943 (mmm) REVERT: I 288 MET cc_start: 0.9316 (ppp) cc_final: 0.8966 (ppp) REVERT: I 389 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.6806 (mmt) REVERT: J 233 MET cc_start: 0.8731 (mmp) cc_final: 0.8473 (mmp) REVERT: J 307 MET cc_start: 0.7857 (pmm) cc_final: 0.7625 (pmm) REVERT: K 233 MET cc_start: 0.8563 (mmm) cc_final: 0.8328 (mmp) REVERT: K 307 MET cc_start: 0.7501 (pmm) cc_final: 0.7288 (pmm) REVERT: L 114 MET cc_start: 0.8489 (mmm) cc_final: 0.8078 (mmm) REVERT: L 233 MET cc_start: 0.8533 (mmp) cc_final: 0.8273 (mmp) REVERT: L 288 MET cc_start: 0.9161 (ppp) cc_final: 0.8859 (ppp) REVERT: L 307 MET cc_start: 0.7635 (pmm) cc_final: 0.6989 (pmm) REVERT: M 114 MET cc_start: 0.8243 (mmm) cc_final: 0.7951 (mmm) REVERT: M 233 MET cc_start: 0.8570 (mmm) cc_final: 0.8311 (mmp) REVERT: M 288 MET cc_start: 0.9134 (ppp) cc_final: 0.8852 (ppp) REVERT: M 307 MET cc_start: 0.7658 (pmm) cc_final: 0.7371 (pmm) REVERT: N 8 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7140 (p90) REVERT: N 111 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7712 (mtt) REVERT: N 114 MET cc_start: 0.8572 (mmm) cc_final: 0.8252 (mmm) REVERT: N 233 MET cc_start: 0.8914 (mmp) cc_final: 0.8616 (mmp) REVERT: N 288 MET cc_start: 0.9162 (ppp) cc_final: 0.8909 (ppp) REVERT: N 307 MET cc_start: 0.7406 (pmm) cc_final: 0.6866 (pmm) outliers start: 72 outliers final: 59 residues processed: 414 average time/residue: 0.6319 time to fit residues: 460.2480 Evaluate side-chains 412 residues out of total 5670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 349 time to evaluate : 6.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 363 GLU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 111 MET Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 267 MET Chi-restraints excluded: chain G residue 164 GLU Chi-restraints excluded: chain G residue 213 VAL Chi-restraints excluded: chain G residue 363 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 164 GLU Chi-restraints excluded: chain H residue 213 VAL Chi-restraints excluded: chain I residue 164 GLU Chi-restraints excluded: chain I residue 213 VAL Chi-restraints excluded: chain I residue 267 MET Chi-restraints excluded: chain I residue 389 MET Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain J residue 213 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 213 VAL Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 164 GLU Chi-restraints excluded: chain L residue 213 VAL Chi-restraints excluded: chain L residue 329 THR Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 213 VAL Chi-restraints excluded: chain N residue 8 PHE Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain N residue 111 MET Chi-restraints excluded: chain N residue 164 GLU Chi-restraints excluded: chain N residue 213 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 728 random chunks: chunk 458 optimal weight: 4.9990 chunk 615 optimal weight: 8.9990 chunk 176 optimal weight: 0.7980 chunk 532 optimal weight: 1.9990 chunk 85 optimal weight: 40.0000 chunk 160 optimal weight: 4.9990 chunk 578 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 593 optimal weight: 6.9990 chunk 73 optimal weight: 50.0000 chunk 106 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.107782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.077327 restraints weight = 164808.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.074102 restraints weight = 135687.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.074681 restraints weight = 107630.190| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 54894 Z= 0.244 Angle : 0.609 15.047 74214 Z= 0.313 Chirality : 0.042 0.212 9002 Planarity : 0.003 0.042 9632 Dihedral : 6.837 66.752 8218 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.38 % Allowed : 14.29 % Favored : 84.34 % 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: 0.73 (0.10), residues: 7322 helix: 1.34 (0.08), residues: 4242 sheet: -0.46 (0.15), residues: 1148 loop : -0.67 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 401 PHE 0.032 0.002 PHE E 195 TYR 0.019 0.001 TYR C 360 ARG 0.005 0.000 ARG N 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9333.39 seconds wall clock time: 323 minutes 37.57 seconds (19417.57 seconds total)