Starting phenix.real_space_refine on Fri Jul 26 15:25:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/07_2024/6gve_0071.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/07_2024/6gve_0071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/07_2024/6gve_0071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/07_2024/6gve_0071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/07_2024/6gve_0071.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/07_2024/6gve_0071.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 16 5.49 5 S 180 5.16 5 C 20896 2.51 5 N 5880 2.21 5 O 6440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 12": "NH1" <-> "NH2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "E TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "E ARG 199": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 288": "NH1" <-> "NH2" Residue "F TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F ARG 288": "NH1" <-> "NH2" Residue "I TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 198": "NH1" <-> "NH2" Residue "I ARG 199": "NH1" <-> "NH2" Residue "I ARG 235": "NH1" <-> "NH2" Residue "I ARG 288": "NH1" <-> "NH2" Residue "K TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 198": "NH1" <-> "NH2" Residue "K ARG 199": "NH1" <-> "NH2" Residue "K ARG 235": "NH1" <-> "NH2" Residue "K ARG 288": "NH1" <-> "NH2" Residue "N TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 198": "NH1" <-> "NH2" Residue "N ARG 199": "NH1" <-> "NH2" Residue "N ARG 235": "NH1" <-> "NH2" Residue "N ARG 288": "NH1" <-> "NH2" Residue "O TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 198": "NH1" <-> "NH2" Residue "O ARG 199": "NH1" <-> "NH2" Residue "O ARG 235": "NH1" <-> "NH2" Residue "O ARG 288": "NH1" <-> "NH2" Residue "J ARG 27": "NH1" <-> "NH2" Residue "J ARG 145": "NH1" <-> "NH2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "G ARG 27": "NH1" <-> "NH2" Residue "G ARG 145": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Residue "L ARG 145": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "H ARG 12": "NH1" <-> "NH2" Residue "M ARG 12": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 33412 Number of models: 1 Model: "" Number of chains: 24 Chain: "P" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 590 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "D" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "A" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "E" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "F" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "I" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "K" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "N" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "O" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "J" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2533 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 302} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2533 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 302} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2533 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 302} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2533 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 302} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 590 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "H" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 590 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "M" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 590 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.70, per 1000 atoms: 0.56 Number of scatterers: 33412 At special positions: 0 Unit cell: (143.439, 114.123, 213.588, 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 180 16.00 P 16 15.00 O 6440 8.00 N 5880 7.00 C 20896 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 29 " distance=2.05 Simple disulfide: pdb=" SG CYS P 61 " - pdb=" SG CYS P 70 " distance=2.02 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 41 " distance=2.03 Simple disulfide: pdb=" SG CYS J 230 " - pdb=" SG CYS J 236 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 41 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 236 " distance=2.02 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 41 " distance=2.03 Simple disulfide: pdb=" SG CYS G 230 " - pdb=" SG CYS G 236 " distance=2.02 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 41 " distance=2.03 Simple disulfide: pdb=" SG CYS L 230 " - pdb=" SG CYS L 236 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 29 " distance=2.05 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 70 " distance=2.02 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 29 " distance=2.05 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 70 " distance=2.02 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 29 " distance=2.05 Simple disulfide: pdb=" SG CYS M 61 " - pdb=" SG CYS M 70 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.26 Conformation dependent library (CDL) restraints added in 6.4 seconds 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 46 sheets defined 37.5% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'P' and resid 2 through 22 removed outlier: 4.057A pdb=" N GLU P 9 " --> pdb=" O GLU P 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS P 19 " --> pdb=" O ALA P 15 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP P 20 " --> pdb=" O HIS P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 52 Processing helix chain 'P' and resid 56 through 64 removed outlier: 4.253A pdb=" N ASP P 62 " --> pdb=" O GLN P 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 23 Processing helix chain 'D' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN D 43 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 86 removed outlier: 3.656A pdb=" N ASN D 85 " --> pdb=" O ASN D 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU D 86 " --> pdb=" O PRO D 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 82 through 86' Processing helix chain 'D' and resid 105 through 115 removed outlier: 3.812A pdb=" N LYS D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 170 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 215 through 222 removed outlier: 4.174A pdb=" N GLY D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 226 Processing helix chain 'D' and resid 255 through 270 removed outlier: 3.617A pdb=" N VAL D 259 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 288 removed outlier: 3.747A pdb=" N ARG D 288 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 319 through 334 Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.655A pdb=" N ASN A 85 " --> pdb=" O ASN A 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A 86 " --> pdb=" O PRO A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 86' Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.811A pdb=" N LYS A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 170 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 215 through 222 removed outlier: 4.175A pdb=" N GLY A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 226 Processing helix chain 'A' and resid 255 through 270 removed outlier: 3.618A pdb=" N VAL A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 removed outlier: 3.749A pdb=" N ARG A 288 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'E' and resid 10 through 23 Processing helix chain 'E' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN E 43 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 86 removed outlier: 3.656A pdb=" N ASN E 85 " --> pdb=" O ASN E 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU E 86 " --> pdb=" O PRO E 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 82 through 86' Processing helix chain 'E' and resid 105 through 115 removed outlier: 3.811A pdb=" N LYS E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 170 Proline residue: E 161 - end of helix Processing helix chain 'E' and resid 196 through 200 Processing helix chain 'E' and resid 215 through 222 removed outlier: 4.174A pdb=" N GLY E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 226 Processing helix chain 'E' and resid 255 through 270 removed outlier: 3.618A pdb=" N VAL E 259 " --> pdb=" O ILE E 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN E 260 " --> pdb=" O ALA E 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 288 removed outlier: 3.748A pdb=" N ARG E 288 " --> pdb=" O SER E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 301 No H-bonds generated for 'chain 'E' and resid 299 through 301' Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'F' and resid 10 through 23 Processing helix chain 'F' and resid 39 through 48 removed outlier: 3.696A pdb=" N ASN F 43 " --> pdb=" O ASP F 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS F 45 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 86 removed outlier: 3.656A pdb=" N ASN F 85 " --> pdb=" O ASN F 82 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU F 86 " --> pdb=" O PRO F 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 82 through 86' Processing helix chain 'F' and resid 105 through 115 removed outlier: 3.812A pdb=" N LYS F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS F 112 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 170 Proline residue: F 161 - end of helix Processing helix chain 'F' and resid 196 through 200 Processing helix chain 'F' and resid 215 through 222 removed outlier: 4.174A pdb=" N GLY F 219 " --> pdb=" O ALA F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 226 Processing helix chain 'F' and resid 255 through 270 removed outlier: 3.617A pdb=" N VAL F 259 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN F 260 " --> pdb=" O ALA F 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 288 removed outlier: 3.749A pdb=" N ARG F 288 " --> pdb=" O SER F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'I' and resid 10 through 23 Processing helix chain 'I' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN I 43 " --> pdb=" O ASP I 39 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA I 44 " --> pdb=" O PRO I 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 86 removed outlier: 3.656A pdb=" N ASN I 85 " --> pdb=" O ASN I 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU I 86 " --> pdb=" O PRO I 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 82 through 86' Processing helix chain 'I' and resid 105 through 115 removed outlier: 3.812A pdb=" N LYS I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS I 112 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 170 Proline residue: I 161 - end of helix Processing helix chain 'I' and resid 196 through 200 Processing helix chain 'I' and resid 215 through 222 removed outlier: 4.175A pdb=" N GLY I 219 " --> pdb=" O ALA I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 226 Processing helix chain 'I' and resid 255 through 270 removed outlier: 3.617A pdb=" N VAL I 259 " --> pdb=" O ILE I 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN I 260 " --> pdb=" O ALA I 256 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU I 268 " --> pdb=" O LYS I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 288 removed outlier: 3.748A pdb=" N ARG I 288 " --> pdb=" O SER I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 299 through 301 No H-bonds generated for 'chain 'I' and resid 299 through 301' Processing helix chain 'I' and resid 319 through 334 Processing helix chain 'K' and resid 10 through 23 Processing helix chain 'K' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA K 44 " --> pdb=" O PRO K 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS K 45 " --> pdb=" O ARG K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 86 removed outlier: 3.656A pdb=" N ASN K 85 " --> pdb=" O ASN K 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU K 86 " --> pdb=" O PRO K 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 82 through 86' Processing helix chain 'K' and resid 105 through 115 removed outlier: 3.812A pdb=" N LYS K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS K 112 " --> pdb=" O GLY K 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU K 113 " --> pdb=" O ALA K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 170 Proline residue: K 161 - end of helix Processing helix chain 'K' and resid 196 through 200 Processing helix chain 'K' and resid 215 through 222 removed outlier: 4.175A pdb=" N GLY K 219 " --> pdb=" O ALA K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 226 Processing helix chain 'K' and resid 255 through 270 removed outlier: 3.617A pdb=" N VAL K 259 " --> pdb=" O ILE K 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN K 260 " --> pdb=" O ALA K 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 288 removed outlier: 3.748A pdb=" N ARG K 288 " --> pdb=" O SER K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 301 No H-bonds generated for 'chain 'K' and resid 299 through 301' Processing helix chain 'K' and resid 319 through 334 Processing helix chain 'N' and resid 10 through 23 Processing helix chain 'N' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN N 43 " --> pdb=" O ASP N 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA N 44 " --> pdb=" O PRO N 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 86 removed outlier: 3.655A pdb=" N ASN N 85 " --> pdb=" O ASN N 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU N 86 " --> pdb=" O PRO N 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 82 through 86' Processing helix chain 'N' and resid 105 through 115 removed outlier: 3.812A pdb=" N LYS N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS N 112 " --> pdb=" O GLY N 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 170 Proline residue: N 161 - end of helix Processing helix chain 'N' and resid 196 through 200 Processing helix chain 'N' and resid 215 through 222 removed outlier: 4.174A pdb=" N GLY N 219 " --> pdb=" O ALA N 215 " (cutoff:3.500A) Processing helix chain 'N' and resid 223 through 226 Processing helix chain 'N' and resid 255 through 270 removed outlier: 3.618A pdb=" N VAL N 259 " --> pdb=" O ILE N 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN N 260 " --> pdb=" O ALA N 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU N 268 " --> pdb=" O LYS N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 288 removed outlier: 3.748A pdb=" N ARG N 288 " --> pdb=" O SER N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 299 through 301 No H-bonds generated for 'chain 'N' and resid 299 through 301' Processing helix chain 'N' and resid 319 through 334 Processing helix chain 'O' and resid 10 through 23 Processing helix chain 'O' and resid 39 through 48 removed outlier: 3.695A pdb=" N ASN O 43 " --> pdb=" O ASP O 39 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA O 44 " --> pdb=" O PRO O 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS O 45 " --> pdb=" O ARG O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 86 removed outlier: 3.656A pdb=" N ASN O 85 " --> pdb=" O ASN O 82 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU O 86 " --> pdb=" O PRO O 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 82 through 86' Processing helix chain 'O' and resid 105 through 115 removed outlier: 3.812A pdb=" N LYS O 111 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS O 112 " --> pdb=" O GLY O 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 153 through 170 Proline residue: O 161 - end of helix Processing helix chain 'O' and resid 196 through 200 Processing helix chain 'O' and resid 215 through 222 removed outlier: 4.173A pdb=" N GLY O 219 " --> pdb=" O ALA O 215 " (cutoff:3.500A) Processing helix chain 'O' and resid 223 through 226 Processing helix chain 'O' and resid 255 through 270 removed outlier: 3.617A pdb=" N VAL O 259 " --> pdb=" O ILE O 255 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN O 260 " --> pdb=" O ALA O 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU O 268 " --> pdb=" O LYS O 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 288 removed outlier: 3.748A pdb=" N ARG O 288 " --> pdb=" O SER O 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 299 through 301 No H-bonds generated for 'chain 'O' and resid 299 through 301' Processing helix chain 'O' and resid 319 through 334 Processing helix chain 'J' and resid 22 through 32 removed outlier: 3.900A pdb=" N ARG J 26 " --> pdb=" O SER J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 67 through 80 removed outlier: 3.563A pdb=" N TYR J 72 " --> pdb=" O PHE J 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN J 80 " --> pdb=" O LYS J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 149 removed outlier: 3.519A pdb=" N LYS J 144 " --> pdb=" O ALA J 140 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU J 149 " --> pdb=" O ARG J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 172 removed outlier: 3.708A pdb=" N ASN J 162 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA J 163 " --> pdb=" O ALA J 159 " (cutoff:3.500A) Proline residue: J 166 - end of helix Processing helix chain 'J' and resid 173 through 176 Processing helix chain 'J' and resid 267 through 275 removed outlier: 3.824A pdb=" N ILE J 273 " --> pdb=" O GLU J 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU J 274 " --> pdb=" O LEU J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 294 Processing helix chain 'J' and resid 303 through 325 removed outlier: 3.852A pdb=" N LEU J 307 " --> pdb=" O ASN J 303 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL J 310 " --> pdb=" O GLY J 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 32 removed outlier: 3.899A pdb=" N ARG B 26 " --> pdb=" O SER B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 67 through 80 removed outlier: 3.563A pdb=" N TYR B 72 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 149 removed outlier: 3.519A pdb=" N LYS B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 172 removed outlier: 3.707A pdb=" N ASN B 162 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Proline residue: B 166 - end of helix Processing helix chain 'B' and resid 173 through 176 Processing helix chain 'B' and resid 267 through 275 removed outlier: 3.824A pdb=" N ILE B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 Processing helix chain 'B' and resid 303 through 325 removed outlier: 3.852A pdb=" N LEU B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 32 removed outlier: 3.900A pdb=" N ARG G 26 " --> pdb=" O SER G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 57 Processing helix chain 'G' and resid 67 through 80 removed outlier: 3.563A pdb=" N TYR G 72 " --> pdb=" O PHE G 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN G 80 " --> pdb=" O LYS G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 149 removed outlier: 3.519A pdb=" N LYS G 144 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU G 149 " --> pdb=" O ARG G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 172 removed outlier: 3.708A pdb=" N ASN G 162 " --> pdb=" O ILE G 158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) Proline residue: G 166 - end of helix Processing helix chain 'G' and resid 173 through 176 Processing helix chain 'G' and resid 267 through 275 removed outlier: 3.824A pdb=" N ILE G 273 " --> pdb=" O GLU G 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU G 274 " --> pdb=" O LEU G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 294 Processing helix chain 'G' and resid 303 through 325 removed outlier: 3.851A pdb=" N LEU G 307 " --> pdb=" O ASN G 303 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL G 310 " --> pdb=" O GLY G 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 32 removed outlier: 3.900A pdb=" N ARG L 26 " --> pdb=" O SER L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 57 Processing helix chain 'L' and resid 67 through 80 removed outlier: 3.563A pdb=" N TYR L 72 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS L 79 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN L 80 " --> pdb=" O LYS L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 149 removed outlier: 3.519A pdb=" N LYS L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU L 149 " --> pdb=" O ARG L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 156 through 172 removed outlier: 3.708A pdb=" N ASN L 162 " --> pdb=" O ILE L 158 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA L 163 " --> pdb=" O ALA L 159 " (cutoff:3.500A) Proline residue: L 166 - end of helix Processing helix chain 'L' and resid 173 through 176 Processing helix chain 'L' and resid 267 through 275 removed outlier: 3.824A pdb=" N ILE L 273 " --> pdb=" O GLU L 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU L 274 " --> pdb=" O LEU L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 294 Processing helix chain 'L' and resid 303 through 325 removed outlier: 3.852A pdb=" N LEU L 307 " --> pdb=" O ASN L 303 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL L 310 " --> pdb=" O GLY L 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 22 removed outlier: 4.057A pdb=" N GLU C 9 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP C 20 " --> pdb=" O HIS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 52 Processing helix chain 'C' and resid 56 through 64 removed outlier: 4.252A pdb=" N ASP C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 22 removed outlier: 4.057A pdb=" N GLU H 9 " --> pdb=" O GLU H 5 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP H 20 " --> pdb=" O HIS H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 52 Processing helix chain 'H' and resid 56 through 64 removed outlier: 4.253A pdb=" N ASP H 62 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 22 removed outlier: 4.057A pdb=" N GLU M 9 " --> pdb=" O GLU M 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS M 19 " --> pdb=" O ALA M 15 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP M 20 " --> pdb=" O HIS M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 52 Processing helix chain 'M' and resid 56 through 64 removed outlier: 4.253A pdb=" N ASP M 62 " --> pdb=" O GLN M 58 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 61 through 63 removed outlier: 9.538A pdb=" N GLU D 30 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS D 76 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL D 32 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL D 78 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 34 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL D 2 " --> pdb=" O GLU D 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL D 32 " --> pdb=" O VAL D 2 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL D 4 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE D 34 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE D 6 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 95 " --> pdb=" O ARG D 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL D 96 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR D 123 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU D 98 " --> pdb=" O THR D 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 49 through 50 Processing sheet with id=AA3, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.960A pdb=" N THR D 212 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY D 231 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN D 174 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER D 182 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL D 241 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL D 312 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.960A pdb=" N THR D 212 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY D 231 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN D 174 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER D 182 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL D 241 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 63 removed outlier: 9.539A pdb=" N GLU A 30 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS A 76 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 32 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL A 78 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 34 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL A 2 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 32 " --> pdb=" O VAL A 2 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 4 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE A 34 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 6 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 95 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL A 96 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR A 123 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU A 98 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 49 through 50 Processing sheet with id=AA7, first strand: chain 'A' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR A 212 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A 231 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 174 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 182 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A 241 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL A 312 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR A 212 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A 231 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 174 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 182 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL A 241 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 61 through 63 removed outlier: 9.539A pdb=" N GLU E 30 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS E 76 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL E 32 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL E 78 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE E 34 " --> pdb=" O VAL E 78 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL E 2 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL E 32 " --> pdb=" O VAL E 2 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL E 4 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE E 34 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE E 6 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 95 " --> pdb=" O ARG E 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL E 96 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR E 123 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU E 98 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 49 through 50 Processing sheet with id=AB2, first strand: chain 'E' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR E 212 " --> pdb=" O GLY E 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY E 231 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN E 174 " --> pdb=" O GLN E 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER E 182 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL E 241 " --> pdb=" O SER E 182 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL E 312 " --> pdb=" O ASP E 297 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR E 212 " --> pdb=" O GLY E 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY E 231 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN E 174 " --> pdb=" O GLN E 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER E 182 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL E 241 " --> pdb=" O SER E 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 61 through 63 removed outlier: 9.539A pdb=" N GLU F 30 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS F 76 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL F 32 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL F 78 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE F 34 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL F 2 " --> pdb=" O GLU F 30 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL F 32 " --> pdb=" O VAL F 2 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL F 4 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE F 34 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE F 6 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU F 95 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL F 96 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR F 123 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU F 98 " --> pdb=" O THR F 123 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 49 through 50 Processing sheet with id=AB6, first strand: chain 'F' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR F 212 " --> pdb=" O GLY F 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY F 231 " --> pdb=" O THR F 212 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 174 " --> pdb=" O GLN F 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER F 182 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL F 241 " --> pdb=" O SER F 182 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL F 312 " --> pdb=" O ASP F 297 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR F 212 " --> pdb=" O GLY F 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY F 231 " --> pdb=" O THR F 212 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 174 " --> pdb=" O GLN F 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER F 182 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL F 241 " --> pdb=" O SER F 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 61 through 63 removed outlier: 9.539A pdb=" N GLU I 30 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS I 76 " --> pdb=" O GLU I 30 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL I 32 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL I 78 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE I 34 " --> pdb=" O VAL I 78 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL I 2 " --> pdb=" O GLU I 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL I 32 " --> pdb=" O VAL I 2 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL I 4 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE I 34 " --> pdb=" O VAL I 4 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE I 6 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU I 95 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL I 96 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR I 123 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU I 98 " --> pdb=" O THR I 123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 49 through 50 Processing sheet with id=AC1, first strand: chain 'I' and resid 208 through 212 removed outlier: 3.958A pdb=" N THR I 212 " --> pdb=" O GLY I 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY I 231 " --> pdb=" O THR I 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN I 174 " --> pdb=" O GLN I 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER I 182 " --> pdb=" O VAL I 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL I 241 " --> pdb=" O SER I 182 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL I 312 " --> pdb=" O ASP I 297 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 208 through 212 removed outlier: 3.958A pdb=" N THR I 212 " --> pdb=" O GLY I 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY I 231 " --> pdb=" O THR I 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN I 174 " --> pdb=" O GLN I 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER I 182 " --> pdb=" O VAL I 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL I 241 " --> pdb=" O SER I 182 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 61 through 63 removed outlier: 9.538A pdb=" N GLU K 30 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS K 76 " --> pdb=" O GLU K 30 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL K 32 " --> pdb=" O LYS K 76 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL K 78 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE K 34 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL K 2 " --> pdb=" O GLU K 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL K 32 " --> pdb=" O VAL K 2 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL K 4 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE K 34 " --> pdb=" O VAL K 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE K 6 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU K 95 " --> pdb=" O ARG K 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL K 96 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR K 123 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU K 98 " --> pdb=" O THR K 123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 49 through 50 Processing sheet with id=AC5, first strand: chain 'K' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR K 212 " --> pdb=" O GLY K 231 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY K 231 " --> pdb=" O THR K 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN K 174 " --> pdb=" O GLN K 249 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER K 182 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL K 241 " --> pdb=" O SER K 182 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL K 312 " --> pdb=" O ASP K 297 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR K 212 " --> pdb=" O GLY K 231 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY K 231 " --> pdb=" O THR K 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN K 174 " --> pdb=" O GLN K 249 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER K 182 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL K 241 " --> pdb=" O SER K 182 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 61 through 63 removed outlier: 9.539A pdb=" N GLU N 30 " --> pdb=" O ALA N 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS N 76 " --> pdb=" O GLU N 30 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL N 32 " --> pdb=" O LYS N 76 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL N 78 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE N 34 " --> pdb=" O VAL N 78 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL N 2 " --> pdb=" O GLU N 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL N 32 " --> pdb=" O VAL N 2 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL N 4 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE N 34 " --> pdb=" O VAL N 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE N 6 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU N 95 " --> pdb=" O ARG N 3 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL N 96 " --> pdb=" O LEU N 121 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR N 123 " --> pdb=" O VAL N 96 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLU N 98 " --> pdb=" O THR N 123 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 49 through 50 Processing sheet with id=AC9, first strand: chain 'N' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR N 212 " --> pdb=" O GLY N 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY N 231 " --> pdb=" O THR N 212 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN N 174 " --> pdb=" O GLN N 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER N 182 " --> pdb=" O VAL N 241 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL N 241 " --> pdb=" O SER N 182 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL N 312 " --> pdb=" O ASP N 297 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR N 212 " --> pdb=" O GLY N 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY N 231 " --> pdb=" O THR N 212 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN N 174 " --> pdb=" O GLN N 249 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N SER N 182 " --> pdb=" O VAL N 241 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL N 241 " --> pdb=" O SER N 182 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 61 through 63 removed outlier: 9.539A pdb=" N GLU O 30 " --> pdb=" O ALA O 74 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N LYS O 76 " --> pdb=" O GLU O 30 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL O 32 " --> pdb=" O LYS O 76 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL O 78 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE O 34 " --> pdb=" O VAL O 78 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N VAL O 2 " --> pdb=" O GLU O 30 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL O 32 " --> pdb=" O VAL O 2 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL O 4 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE O 34 " --> pdb=" O VAL O 4 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE O 6 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU O 95 " --> pdb=" O ARG O 3 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL O 96 " --> pdb=" O LEU O 121 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR O 123 " --> pdb=" O VAL O 96 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N GLU O 98 " --> pdb=" O THR O 123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 49 through 50 Processing sheet with id=AD4, first strand: chain 'O' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR O 212 " --> pdb=" O GLY O 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY O 231 " --> pdb=" O THR O 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN O 174 " --> pdb=" O GLN O 249 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER O 182 " --> pdb=" O VAL O 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL O 241 " --> pdb=" O SER O 182 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N VAL O 312 " --> pdb=" O ASP O 297 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR O 212 " --> pdb=" O GLY O 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY O 231 " --> pdb=" O THR O 212 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN O 174 " --> pdb=" O GLN O 249 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER O 182 " --> pdb=" O VAL O 241 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL O 241 " --> pdb=" O SER O 182 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 37 through 38 removed outlier: 3.531A pdb=" N VAL J 181 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU J 258 " --> pdb=" O MET J 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN J 206 " --> pdb=" O SER J 256 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 84 through 89 removed outlier: 6.528A pdb=" N ILE J 84 " --> pdb=" O LYS J 101 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS J 101 " --> pdb=" O ILE J 84 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS J 86 " --> pdb=" O PRO J 99 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE J 88 " --> pdb=" O ASP J 97 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 217 through 218 Processing sheet with id=AD9, first strand: chain 'J' and resid 223 through 231 Processing sheet with id=AE1, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.532A pdb=" N VAL B 181 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 258 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 206 " --> pdb=" O SER B 256 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.528A pdb=" N ILE B 84 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS B 101 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS B 86 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 88 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 217 through 218 Processing sheet with id=AE4, first strand: chain 'B' and resid 223 through 231 Processing sheet with id=AE5, first strand: chain 'G' and resid 37 through 38 removed outlier: 3.532A pdb=" N VAL G 181 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU G 258 " --> pdb=" O MET G 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN G 206 " --> pdb=" O SER G 256 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 84 through 89 removed outlier: 6.527A pdb=" N ILE G 84 " --> pdb=" O LYS G 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS G 101 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS G 86 " --> pdb=" O PRO G 99 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE G 88 " --> pdb=" O ASP G 97 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 217 through 218 Processing sheet with id=AE8, first strand: chain 'L' and resid 37 through 38 removed outlier: 3.532A pdb=" N VAL L 181 " --> pdb=" O SER L 128 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 258 " --> pdb=" O MET L 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN L 206 " --> pdb=" O SER L 256 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 84 through 89 removed outlier: 6.528A pdb=" N ILE L 84 " --> pdb=" O LYS L 101 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS L 101 " --> pdb=" O ILE L 84 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS L 86 " --> pdb=" O PRO L 99 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE L 88 " --> pdb=" O ASP L 97 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 217 through 218 1612 hydrogen bonds defined for protein. 4500 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: 15.76 Time building geometry restraints manager: 14.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10572 1.33 - 1.45: 5793 1.45 - 1.57: 17411 1.57 - 1.69: 32 1.69 - 1.81: 288 Bond restraints: 34096 Sorted by residual: bond pdb=" O3 NAD K1001 " pdb=" PA NAD K1001 " ideal model delta sigma weight residual 1.653 1.593 0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" O3 NAD N1001 " pdb=" PA NAD N1001 " ideal model delta sigma weight residual 1.653 1.594 0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" O3 NAD I1001 " pdb=" PA NAD I1001 " ideal model delta sigma weight residual 1.653 1.594 0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" O3 NAD A1001 " pdb=" PA NAD A1001 " ideal model delta sigma weight residual 1.653 1.594 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" O3 NAD D1001 " pdb=" PA NAD D1001 " ideal model delta sigma weight residual 1.653 1.594 0.059 2.00e-02 2.50e+03 8.81e+00 ... (remaining 34091 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.31: 744 105.31 - 112.53: 18087 112.53 - 119.75: 11906 119.75 - 126.96: 15166 126.96 - 134.18: 425 Bond angle restraints: 46328 Sorted by residual: angle pdb=" C TYR J 154 " pdb=" N GLU J 155 " pdb=" CA GLU J 155 " ideal model delta sigma weight residual 121.54 132.05 -10.51 1.91e+00 2.74e-01 3.03e+01 angle pdb=" C TYR G 154 " pdb=" N GLU G 155 " pdb=" CA GLU G 155 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.02e+01 angle pdb=" C TYR B 154 " pdb=" N GLU B 155 " pdb=" CA GLU B 155 " ideal model delta sigma weight residual 121.54 132.00 -10.46 1.91e+00 2.74e-01 3.00e+01 angle pdb=" C TYR L 154 " pdb=" N GLU L 155 " pdb=" CA GLU L 155 " ideal model delta sigma weight residual 121.54 131.99 -10.45 1.91e+00 2.74e-01 2.99e+01 angle pdb=" C LEU L 218 " pdb=" N PHE L 219 " pdb=" CA PHE L 219 " ideal model delta sigma weight residual 121.54 129.55 -8.01 1.91e+00 2.74e-01 1.76e+01 ... (remaining 46323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 19389 15.12 - 30.24: 1095 30.24 - 45.35: 200 45.35 - 60.47: 52 60.47 - 75.59: 16 Dihedral angle restraints: 20752 sinusoidal: 8428 harmonic: 12324 Sorted by residual: dihedral pdb=" CB CYS H 19 " pdb=" SG CYS H 19 " pdb=" SG CYS H 29 " pdb=" CB CYS H 29 " ideal model delta sinusoidal sigma weight residual 93.00 19.46 73.54 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS P 19 " pdb=" SG CYS P 19 " pdb=" SG CYS P 29 " pdb=" CB CYS P 29 " ideal model delta sinusoidal sigma weight residual 93.00 19.46 73.54 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS C 19 " pdb=" SG CYS C 19 " pdb=" SG CYS C 29 " pdb=" CB CYS C 29 " ideal model delta sinusoidal sigma weight residual 93.00 19.46 73.54 1 1.00e+01 1.00e-02 6.88e+01 ... (remaining 20749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4093 0.073 - 0.146: 988 0.146 - 0.218: 99 0.218 - 0.291: 28 0.291 - 0.364: 12 Chirality restraints: 5220 Sorted by residual: chirality pdb=" CB ILE K 148 " pdb=" CA ILE K 148 " pdb=" CG1 ILE K 148 " pdb=" CG2 ILE K 148 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE F 148 " pdb=" CA ILE F 148 " pdb=" CG1 ILE F 148 " pdb=" CG2 ILE F 148 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE N 148 " pdb=" CA ILE N 148 " pdb=" CG1 ILE N 148 " pdb=" CG2 ILE N 148 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 5217 not shown) Planarity restraints: 5980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD E1001 " -0.013 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" C2N NAD E1001 " 0.049 2.00e-02 2.50e+03 pdb=" C3N NAD E1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD E1001 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD E1001 " -0.003 2.00e-02 2.50e+03 pdb=" C6N NAD E1001 " -0.027 2.00e-02 2.50e+03 pdb=" C7N NAD E1001 " -0.039 2.00e-02 2.50e+03 pdb=" N1N NAD E1001 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A1001 " -0.013 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" C2N NAD A1001 " 0.049 2.00e-02 2.50e+03 pdb=" C3N NAD A1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD A1001 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD A1001 " -0.003 2.00e-02 2.50e+03 pdb=" C6N NAD A1001 " -0.027 2.00e-02 2.50e+03 pdb=" C7N NAD A1001 " -0.039 2.00e-02 2.50e+03 pdb=" N1N NAD A1001 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD K1001 " -0.013 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" C2N NAD K1001 " 0.049 2.00e-02 2.50e+03 pdb=" C3N NAD K1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD K1001 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD K1001 " -0.003 2.00e-02 2.50e+03 pdb=" C6N NAD K1001 " -0.027 2.00e-02 2.50e+03 pdb=" C7N NAD K1001 " -0.039 2.00e-02 2.50e+03 pdb=" N1N NAD K1001 " 0.003 2.00e-02 2.50e+03 ... (remaining 5977 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1179 2.69 - 3.24: 32023 3.24 - 3.79: 56109 3.79 - 4.35: 69876 4.35 - 4.90: 116320 Nonbonded interactions: 275507 Sorted by model distance: nonbonded pdb=" OH TYR C 73 " pdb=" O1A NAD E1001 " model vdw 2.133 2.440 nonbonded pdb=" OG1 THR J 226 " pdb=" OG1 THR G 226 " model vdw 2.252 2.440 nonbonded pdb=" OH TYR M 73 " pdb=" O1A NAD N1001 " model vdw 2.263 2.440 nonbonded pdb=" NH1 ARG E 81 " pdb=" OD2 ASP C 66 " model vdw 2.264 2.520 nonbonded pdb=" OG1 THR B 226 " pdb=" OG1 THR L 226 " model vdw 2.270 2.440 ... (remaining 275502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' selection = chain 'P' } 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: 5.230 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: 0.040 Extract box with map and model: 1.470 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 96.660 Find NCS groups from input model: 3.620 Set up NCS constraints: 0.280 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: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.010 0.067 34096 Z= 0.633 Angle : 0.986 10.513 46328 Z= 0.530 Chirality : 0.064 0.364 5220 Planarity : 0.008 0.077 5980 Dihedral : 10.439 75.588 12784 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.10), residues: 4240 helix: -2.67 (0.10), residues: 1412 sheet: -2.27 (0.15), residues: 896 loop : -2.26 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP J 227 HIS 0.011 0.003 HIS B 295 PHE 0.022 0.003 PHE D 9 TYR 0.027 0.003 TYR D 315 ARG 0.009 0.002 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1006 time to evaluate : 4.024 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 46 GLN cc_start: 0.8488 (tp40) cc_final: 0.8199 (tp-100) REVERT: P 55 THR cc_start: 0.6559 (p) cc_final: 0.6336 (p) REVERT: D 133 TYR cc_start: 0.7991 (m-80) cc_final: 0.7737 (m-80) REVERT: D 173 GLN cc_start: 0.8513 (mt0) cc_final: 0.8058 (mp10) REVERT: D 174 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7837 (mt0) REVERT: D 177 MET cc_start: 0.8419 (ppp) cc_final: 0.8106 (ttp) REVERT: D 179 THR cc_start: 0.8018 (t) cc_final: 0.7752 (t) REVERT: D 238 THR cc_start: 0.9143 (p) cc_final: 0.8715 (t) REVERT: D 249 GLN cc_start: 0.7833 (tt0) cc_final: 0.7269 (tt0) REVERT: D 261 GLN cc_start: 0.8956 (tp40) cc_final: 0.8735 (tp40) REVERT: D 286 ASP cc_start: 0.8199 (m-30) cc_final: 0.7469 (m-30) REVERT: D 295 ILE cc_start: 0.9289 (mp) cc_final: 0.8840 (mm) REVERT: A 85 ASN cc_start: 0.9007 (m-40) cc_final: 0.8713 (m110) REVERT: A 147 ASP cc_start: 0.8429 (p0) cc_final: 0.8102 (p0) REVERT: A 176 MET cc_start: 0.8644 (mmt) cc_final: 0.8307 (mmt) REVERT: A 177 MET cc_start: 0.9024 (ppp) cc_final: 0.8705 (ppp) REVERT: A 225 LEU cc_start: 0.9202 (mt) cc_final: 0.8982 (tp) REVERT: A 271 MET cc_start: 0.7575 (mmt) cc_final: 0.7209 (mmp) REVERT: A 302 MET cc_start: 0.7533 (ptp) cc_final: 0.6180 (ptp) REVERT: A 323 GLN cc_start: 0.9434 (mm-40) cc_final: 0.8925 (mt0) REVERT: A 331 HIS cc_start: 0.8489 (t70) cc_final: 0.8188 (t-90) REVERT: E 133 TYR cc_start: 0.8229 (m-80) cc_final: 0.8021 (m-80) REVERT: E 173 GLN cc_start: 0.8704 (mt0) cc_final: 0.8371 (mp10) REVERT: E 179 THR cc_start: 0.7981 (t) cc_final: 0.7757 (t) REVERT: E 182 SER cc_start: 0.9270 (p) cc_final: 0.8970 (t) REVERT: E 188 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7626 (mmm-85) REVERT: E 238 THR cc_start: 0.9060 (p) cc_final: 0.8586 (t) REVERT: E 249 GLN cc_start: 0.7698 (tt0) cc_final: 0.7433 (tt0) REVERT: E 286 ASP cc_start: 0.8372 (m-30) cc_final: 0.7948 (m-30) REVERT: F 17 MET cc_start: 0.8857 (tpt) cc_final: 0.8587 (tpt) REVERT: F 20 TRP cc_start: 0.8703 (t60) cc_final: 0.7961 (t60) REVERT: F 67 CYS cc_start: 0.8517 (m) cc_final: 0.7953 (p) REVERT: F 69 TYR cc_start: 0.8545 (m-80) cc_final: 0.8323 (m-80) REVERT: F 129 ASN cc_start: 0.8249 (m-40) cc_final: 0.7753 (p0) REVERT: F 176 MET cc_start: 0.8886 (mmt) cc_final: 0.7736 (mmt) REVERT: F 177 MET cc_start: 0.9187 (ppp) cc_final: 0.8706 (ppp) REVERT: F 284 SER cc_start: 0.8633 (p) cc_final: 0.8368 (p) REVERT: F 302 MET cc_start: 0.7437 (ptp) cc_final: 0.6977 (ptp) REVERT: F 323 GLN cc_start: 0.9307 (mm-40) cc_final: 0.8544 (mt0) REVERT: F 327 ASP cc_start: 0.8893 (m-30) cc_final: 0.8372 (m-30) REVERT: I 86 LEU cc_start: 0.9155 (mt) cc_final: 0.8817 (mt) REVERT: I 133 TYR cc_start: 0.7996 (m-80) cc_final: 0.7486 (m-80) REVERT: I 173 GLN cc_start: 0.8427 (mt0) cc_final: 0.8034 (mp10) REVERT: I 176 MET cc_start: 0.8516 (mmt) cc_final: 0.8248 (mmt) REVERT: I 238 THR cc_start: 0.8844 (p) cc_final: 0.8446 (t) REVERT: I 249 GLN cc_start: 0.7821 (tt0) cc_final: 0.7204 (tt0) REVERT: K 17 MET cc_start: 0.8794 (tpt) cc_final: 0.8426 (tpt) REVERT: K 20 TRP cc_start: 0.8616 (t60) cc_final: 0.7993 (t60) REVERT: K 93 ILE cc_start: 0.8808 (mm) cc_final: 0.8442 (tp) REVERT: K 129 ASN cc_start: 0.8556 (m-40) cc_final: 0.8184 (m-40) REVERT: K 183 TYR cc_start: 0.8956 (p90) cc_final: 0.8471 (p90) REVERT: K 246 PHE cc_start: 0.9048 (t80) cc_final: 0.8684 (t80) REVERT: K 258 GLN cc_start: 0.8960 (tt0) cc_final: 0.8646 (mt0) REVERT: K 302 MET cc_start: 0.7478 (ptp) cc_final: 0.6220 (ptp) REVERT: K 323 GLN cc_start: 0.9273 (mm-40) cc_final: 0.8518 (mt0) REVERT: K 327 ASP cc_start: 0.8789 (m-30) cc_final: 0.8491 (m-30) REVERT: N 43 ASN cc_start: 0.8107 (p0) cc_final: 0.7893 (p0) REVERT: N 55 ILE cc_start: 0.8793 (mt) cc_final: 0.8557 (mt) REVERT: N 142 TYR cc_start: 0.7480 (p90) cc_final: 0.7124 (p90) REVERT: N 179 THR cc_start: 0.7923 (t) cc_final: 0.7707 (t) REVERT: N 238 THR cc_start: 0.9098 (p) cc_final: 0.8687 (t) REVERT: N 286 ASP cc_start: 0.8260 (m-30) cc_final: 0.7844 (m-30) REVERT: N 295 ILE cc_start: 0.9275 (mp) cc_final: 0.8824 (mm) REVERT: O 21 LEU cc_start: 0.9317 (mt) cc_final: 0.8960 (mt) REVERT: O 93 ILE cc_start: 0.8925 (mm) cc_final: 0.8652 (tp) REVERT: O 129 ASN cc_start: 0.8204 (m-40) cc_final: 0.7643 (p0) REVERT: O 159 LEU cc_start: 0.8964 (tp) cc_final: 0.8648 (tp) REVERT: O 176 MET cc_start: 0.8664 (mmt) cc_final: 0.7654 (mmt) REVERT: O 249 GLN cc_start: 0.8640 (tt0) cc_final: 0.8340 (tm-30) REVERT: O 258 GLN cc_start: 0.8777 (tt0) cc_final: 0.8503 (mt0) REVERT: O 323 GLN cc_start: 0.9350 (mm-40) cc_final: 0.8464 (mt0) REVERT: O 327 ASP cc_start: 0.8975 (m-30) cc_final: 0.8548 (m-30) REVERT: O 331 HIS cc_start: 0.8510 (t70) cc_final: 0.8025 (t-90) REVERT: J 309 GLN cc_start: 0.9077 (mt0) cc_final: 0.8681 (mp10) REVERT: B 46 HIS cc_start: 0.7146 (m170) cc_final: 0.6639 (m170) REVERT: B 66 ASN cc_start: 0.7613 (m-40) cc_final: 0.7309 (m-40) REVERT: B 233 LYS cc_start: 0.8918 (mtpp) cc_final: 0.8703 (mmtp) REVERT: B 308 PHE cc_start: 0.9021 (m-10) cc_final: 0.8745 (m-10) REVERT: B 309 GLN cc_start: 0.8896 (mt0) cc_final: 0.8461 (mt0) REVERT: G 46 HIS cc_start: 0.7543 (m170) cc_final: 0.7162 (m170) REVERT: G 66 ASN cc_start: 0.7588 (m-40) cc_final: 0.7159 (m-40) REVERT: G 106 HIS cc_start: 0.7077 (m-70) cc_final: 0.6844 (m170) REVERT: G 116 LEU cc_start: 0.9050 (tp) cc_final: 0.8720 (tp) REVERT: G 127 PHE cc_start: 0.8252 (t80) cc_final: 0.7880 (t80) REVERT: G 309 GLN cc_start: 0.9029 (mt0) cc_final: 0.8708 (mt0) REVERT: L 106 HIS cc_start: 0.7392 (m-70) cc_final: 0.7101 (m170) REVERT: L 116 LEU cc_start: 0.8943 (tp) cc_final: 0.8633 (tp) REVERT: L 204 MET cc_start: 0.7705 (ptm) cc_final: 0.7473 (ptm) REVERT: L 308 PHE cc_start: 0.9096 (m-10) cc_final: 0.8753 (m-10) REVERT: L 309 GLN cc_start: 0.8927 (mt0) cc_final: 0.8296 (mp10) REVERT: C 28 GLN cc_start: 0.8841 (mp-120) cc_final: 0.8617 (mp10) REVERT: C 63 ASP cc_start: 0.6752 (p0) cc_final: 0.6539 (p0) REVERT: H 1 MET cc_start: 0.5974 (ttm) cc_final: 0.5669 (tpp) REVERT: H 28 GLN cc_start: 0.8450 (mp-120) cc_final: 0.8043 (mt0) REVERT: M 28 GLN cc_start: 0.8317 (mp-120) cc_final: 0.7735 (tm-30) REVERT: M 46 GLN cc_start: 0.8524 (tp40) cc_final: 0.8250 (tp40) outliers start: 4 outliers final: 4 residues processed: 1010 average time/residue: 0.4506 time to fit residues: 724.0117 Evaluate side-chains 577 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 573 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain L residue 182 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 351 optimal weight: 6.9990 chunk 315 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 212 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 326 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 198 optimal weight: 0.8980 chunk 242 optimal weight: 2.9990 chunk 377 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS P 64 ASN D 15 ASN D 173 GLN D 181 HIS A 15 ASN A 45 HIS A 173 GLN A 181 HIS A 187 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 ASN E 45 HIS E 173 GLN E 181 HIS F 15 ASN F 45 HIS F 181 HIS F 323 GLN I 15 ASN I 173 GLN I 181 HIS I 240 ASN K 15 ASN K 45 HIS K 173 GLN K 181 HIS K 187 GLN K 323 GLN N 15 ASN N 173 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 181 HIS N 331 HIS O 15 ASN O 45 HIS O 173 GLN O 181 HIS O 290 HIS O 323 GLN O 331 HIS J 90 ASN J 114 HIS ** J 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN G 90 ASN G 184 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 ASN L 114 HIS L 184 GLN L 279 ASN C 10 GLN C 64 ASN H 64 ASN M 45 HIS M 64 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34096 Z= 0.183 Angle : 0.609 8.673 46328 Z= 0.321 Chirality : 0.047 0.196 5220 Planarity : 0.005 0.056 5980 Dihedral : 7.304 59.443 5084 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.71 % Allowed : 11.00 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.11), residues: 4240 helix: -1.03 (0.13), residues: 1444 sheet: -1.85 (0.16), residues: 848 loop : -1.75 (0.12), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 20 HIS 0.012 0.001 HIS J 46 PHE 0.022 0.002 PHE J 127 TYR 0.020 0.002 TYR F 49 ARG 0.007 0.001 ARG F 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 738 time to evaluate : 4.184 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: P 1 MET cc_start: 0.5789 (ttm) cc_final: 0.5463 (tpp) REVERT: P 12 ARG cc_start: 0.7648 (ttt180) cc_final: 0.7440 (ttt180) REVERT: P 28 GLN cc_start: 0.8866 (mp10) cc_final: 0.8600 (mp10) REVERT: P 54 LYS cc_start: 0.7651 (pmmt) cc_final: 0.6930 (tptp) REVERT: P 63 ASP cc_start: 0.6893 (p0) cc_final: 0.6689 (p0) REVERT: D 52 MET cc_start: 0.7833 (tpp) cc_final: 0.7179 (tpt) REVERT: D 173 GLN cc_start: 0.8413 (mt0) cc_final: 0.8094 (mp10) REVERT: D 176 MET cc_start: 0.8505 (mmm) cc_final: 0.8083 (mmm) REVERT: D 240 ASN cc_start: 0.7714 (t0) cc_final: 0.7459 (t0) REVERT: D 249 GLN cc_start: 0.7925 (tt0) cc_final: 0.7048 (tt0) REVERT: D 295 ILE cc_start: 0.9174 (mp) cc_final: 0.8723 (mt) REVERT: D 323 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8105 (mm-40) REVERT: A 67 CYS cc_start: 0.8441 (m) cc_final: 0.7829 (t) REVERT: A 85 ASN cc_start: 0.8898 (m-40) cc_final: 0.8676 (m110) REVERT: A 93 ILE cc_start: 0.8812 (mm) cc_final: 0.8245 (tp) REVERT: A 147 ASP cc_start: 0.8606 (p0) cc_final: 0.8174 (p0) REVERT: A 173 GLN cc_start: 0.8723 (mt0) cc_final: 0.8390 (mm-40) REVERT: A 176 MET cc_start: 0.8248 (mmt) cc_final: 0.7494 (mmt) REVERT: A 268 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8242 (pp20) REVERT: A 302 MET cc_start: 0.7276 (ptp) cc_final: 0.6540 (ptp) REVERT: A 323 GLN cc_start: 0.9383 (mm-40) cc_final: 0.9181 (mm-40) REVERT: A 327 ASP cc_start: 0.8959 (m-30) cc_final: 0.8613 (m-30) REVERT: E 173 GLN cc_start: 0.8685 (mt0) cc_final: 0.8376 (mp10) REVERT: E 177 MET cc_start: 0.7981 (ttp) cc_final: 0.7751 (ttp) REVERT: E 182 SER cc_start: 0.9200 (p) cc_final: 0.8744 (t) REVERT: E 188 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.7517 (mmm-85) REVERT: E 196 ASP cc_start: 0.8607 (t0) cc_final: 0.8219 (t0) REVERT: E 205 MET cc_start: 0.8294 (mtp) cc_final: 0.7941 (mtp) REVERT: E 238 THR cc_start: 0.8749 (p) cc_final: 0.8413 (t) REVERT: E 249 GLN cc_start: 0.7741 (tt0) cc_final: 0.7466 (tt0) REVERT: E 295 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8377 (mm) REVERT: E 323 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8154 (mm-40) REVERT: F 1 MET cc_start: 0.7940 (pmm) cc_final: 0.7673 (pmm) REVERT: F 16 PHE cc_start: 0.9268 (t80) cc_final: 0.8979 (t80) REVERT: F 20 TRP cc_start: 0.8430 (t60) cc_final: 0.7882 (t60) REVERT: F 40 PRO cc_start: 0.9027 (Cg_exo) cc_final: 0.8758 (Cg_endo) REVERT: F 49 TYR cc_start: 0.9047 (m-80) cc_final: 0.8729 (m-10) REVERT: F 52 MET cc_start: 0.8000 (mmm) cc_final: 0.7685 (mmm) REVERT: F 65 ASP cc_start: 0.8620 (p0) cc_final: 0.7365 (t0) REVERT: F 67 CYS cc_start: 0.8405 (m) cc_final: 0.7843 (p) REVERT: F 176 MET cc_start: 0.8606 (mmt) cc_final: 0.8271 (mmt) REVERT: F 284 SER cc_start: 0.8795 (p) cc_final: 0.8441 (p) REVERT: F 302 MET cc_start: 0.7330 (ptp) cc_final: 0.5949 (ptp) REVERT: F 323 GLN cc_start: 0.9228 (mm110) cc_final: 0.8863 (mm-40) REVERT: F 327 ASP cc_start: 0.8724 (m-30) cc_final: 0.8275 (m-30) REVERT: I 173 GLN cc_start: 0.8508 (mt0) cc_final: 0.7847 (mp10) REVERT: I 249 GLN cc_start: 0.7875 (tt0) cc_final: 0.6571 (tt0) REVERT: I 295 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8507 (mm) REVERT: I 314 TRP cc_start: 0.9338 (m100) cc_final: 0.8547 (m100) REVERT: K 20 TRP cc_start: 0.8429 (t60) cc_final: 0.7889 (t60) REVERT: K 49 TYR cc_start: 0.8841 (m-80) cc_final: 0.8358 (m-10) REVERT: K 93 ILE cc_start: 0.8775 (mm) cc_final: 0.8408 (tp) REVERT: K 173 GLN cc_start: 0.8567 (mt0) cc_final: 0.8343 (mm-40) REVERT: K 176 MET cc_start: 0.8270 (mmt) cc_final: 0.7537 (mmt) REVERT: K 177 MET cc_start: 0.8937 (ppp) cc_final: 0.8723 (tmm) REVERT: K 183 TYR cc_start: 0.8998 (p90) cc_final: 0.8469 (p90) REVERT: K 258 GLN cc_start: 0.8879 (tt0) cc_final: 0.8598 (mt0) REVERT: K 284 SER cc_start: 0.8934 (p) cc_final: 0.8633 (m) REVERT: K 302 MET cc_start: 0.7126 (ptp) cc_final: 0.5934 (ptp) REVERT: K 323 GLN cc_start: 0.9174 (mm110) cc_final: 0.8626 (mt0) REVERT: K 327 ASP cc_start: 0.8718 (m-30) cc_final: 0.8508 (m-30) REVERT: N 55 ILE cc_start: 0.8852 (mt) cc_final: 0.8623 (mt) REVERT: N 142 TYR cc_start: 0.7269 (p90) cc_final: 0.6794 (p90) REVERT: N 176 MET cc_start: 0.8441 (mmm) cc_final: 0.8168 (mmm) REVERT: N 196 ASP cc_start: 0.8593 (t0) cc_final: 0.8162 (t0) REVERT: N 228 LYS cc_start: 0.8553 (mttt) cc_final: 0.8205 (mtmm) REVERT: N 240 ASN cc_start: 0.8119 (t0) cc_final: 0.7561 (t0) REVERT: N 249 GLN cc_start: 0.7989 (tt0) cc_final: 0.7769 (tt0) REVERT: N 295 ILE cc_start: 0.9108 (mp) cc_final: 0.8504 (mt) REVERT: N 323 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8271 (mm-40) REVERT: O 17 MET cc_start: 0.8686 (tpt) cc_final: 0.8463 (tpt) REVERT: O 20 TRP cc_start: 0.8392 (t60) cc_final: 0.7504 (t60) REVERT: O 93 ILE cc_start: 0.8904 (mm) cc_final: 0.8660 (tp) REVERT: O 129 ASN cc_start: 0.8033 (m-40) cc_final: 0.7814 (p0) REVERT: O 159 LEU cc_start: 0.8900 (tp) cc_final: 0.8586 (tp) REVERT: O 176 MET cc_start: 0.8034 (mmt) cc_final: 0.7113 (mmt) REVERT: O 249 GLN cc_start: 0.8542 (tt0) cc_final: 0.8054 (tm-30) REVERT: O 286 ASP cc_start: 0.8290 (m-30) cc_final: 0.7980 (m-30) REVERT: O 323 GLN cc_start: 0.9177 (mm110) cc_final: 0.8847 (mt0) REVERT: O 327 ASP cc_start: 0.9075 (m-30) cc_final: 0.8709 (m-30) REVERT: J 46 HIS cc_start: 0.7534 (m170) cc_final: 0.7099 (m170) REVERT: J 156 ASP cc_start: 0.7935 (t0) cc_final: 0.7306 (t70) REVERT: B 71 MET cc_start: 0.8747 (ptp) cc_final: 0.8483 (ptp) REVERT: B 116 LEU cc_start: 0.8949 (tp) cc_final: 0.8633 (tt) REVERT: B 180 ASP cc_start: 0.7455 (m-30) cc_final: 0.7059 (m-30) REVERT: B 270 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9190 (tt) REVERT: B 279 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8124 (t0) REVERT: G 127 PHE cc_start: 0.8236 (t80) cc_final: 0.7599 (t80) REVERT: L 180 ASP cc_start: 0.7680 (m-30) cc_final: 0.7367 (m-30) REVERT: L 308 PHE cc_start: 0.9006 (m-10) cc_final: 0.8642 (m-10) REVERT: L 309 GLN cc_start: 0.8800 (mt0) cc_final: 0.8166 (mp10) REVERT: C 28 GLN cc_start: 0.8805 (mp-120) cc_final: 0.8545 (mp10) REVERT: C 54 LYS cc_start: 0.6965 (pmmt) cc_final: 0.6463 (tptp) REVERT: C 63 ASP cc_start: 0.6910 (p0) cc_final: 0.6632 (p0) REVERT: H 28 GLN cc_start: 0.8417 (mp-120) cc_final: 0.7964 (mt0) REVERT: M 12 ARG cc_start: 0.7508 (ttt180) cc_final: 0.7290 (ttt180) REVERT: M 28 GLN cc_start: 0.8200 (mp-120) cc_final: 0.7712 (tm-30) REVERT: M 42 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8173 (mm-30) outliers start: 96 outliers final: 66 residues processed: 795 average time/residue: 0.4039 time to fit residues: 536.0354 Evaluate side-chains 630 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 560 time to evaluate : 3.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 245 ASP Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 279 ASN Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 8 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 209 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 314 optimal weight: 0.8980 chunk 257 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 378 optimal weight: 5.9990 chunk 408 optimal weight: 5.9990 chunk 337 optimal weight: 0.9990 chunk 375 optimal weight: 10.0000 chunk 129 optimal weight: 3.9990 chunk 303 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 ASN K 7 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN O 249 GLN ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN ** J 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 309 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN G 309 GLN L 106 HIS L 184 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 279 ASN L 295 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34096 Z= 0.209 Angle : 0.590 12.967 46328 Z= 0.306 Chirality : 0.046 0.202 5220 Planarity : 0.004 0.055 5980 Dihedral : 6.861 58.991 5084 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.03 % Allowed : 13.15 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4240 helix: -0.26 (0.13), residues: 1440 sheet: -1.54 (0.16), residues: 880 loop : -1.37 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP P 33 HIS 0.021 0.001 HIS O 290 PHE 0.020 0.001 PHE K 246 TYR 0.017 0.002 TYR L 217 ARG 0.005 0.000 ARG F 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 614 time to evaluate : 3.959 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: P 12 ARG cc_start: 0.7557 (ttt180) cc_final: 0.7314 (ttt180) REVERT: P 28 GLN cc_start: 0.8869 (mp10) cc_final: 0.8619 (mp10) REVERT: P 54 LYS cc_start: 0.7806 (pmmt) cc_final: 0.7197 (tptp) REVERT: P 63 ASP cc_start: 0.6939 (p0) cc_final: 0.6582 (p0) REVERT: D 142 TYR cc_start: 0.7552 (p90) cc_final: 0.7253 (p90) REVERT: D 177 MET cc_start: 0.7328 (tmm) cc_final: 0.6863 (tmm) REVERT: D 284 SER cc_start: 0.8671 (p) cc_final: 0.8233 (m) REVERT: D 295 ILE cc_start: 0.9180 (mp) cc_final: 0.8674 (mm) REVERT: D 323 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8107 (mm-40) REVERT: A 20 TRP cc_start: 0.8417 (t60) cc_final: 0.7637 (t60) REVERT: A 67 CYS cc_start: 0.8382 (m) cc_final: 0.7802 (t) REVERT: A 85 ASN cc_start: 0.8921 (m-40) cc_final: 0.8679 (m110) REVERT: A 147 ASP cc_start: 0.8726 (p0) cc_final: 0.8314 (p0) REVERT: A 173 GLN cc_start: 0.8559 (mt0) cc_final: 0.8211 (mp10) REVERT: A 176 MET cc_start: 0.8528 (mmt) cc_final: 0.7649 (mmt) REVERT: A 268 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8258 (pp20) REVERT: A 284 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8412 (m) REVERT: A 302 MET cc_start: 0.7449 (ptp) cc_final: 0.5948 (ptp) REVERT: A 323 GLN cc_start: 0.9368 (mm-40) cc_final: 0.9126 (mm-40) REVERT: A 327 ASP cc_start: 0.8969 (m-30) cc_final: 0.8581 (m-30) REVERT: E 182 SER cc_start: 0.9352 (p) cc_final: 0.8889 (t) REVERT: E 196 ASP cc_start: 0.8657 (t0) cc_final: 0.8251 (t0) REVERT: E 205 MET cc_start: 0.8519 (mtp) cc_final: 0.8312 (mtp) REVERT: E 238 THR cc_start: 0.8827 (p) cc_final: 0.8483 (t) REVERT: E 295 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8875 (mm) REVERT: E 323 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8126 (mm-40) REVERT: F 20 TRP cc_start: 0.8467 (t60) cc_final: 0.7757 (t60) REVERT: F 40 PRO cc_start: 0.9019 (Cg_exo) cc_final: 0.8725 (Cg_endo) REVERT: F 52 MET cc_start: 0.8174 (mmm) cc_final: 0.7945 (mmm) REVERT: F 65 ASP cc_start: 0.8597 (p0) cc_final: 0.7466 (t0) REVERT: F 176 MET cc_start: 0.8615 (mmt) cc_final: 0.7417 (mmt) REVERT: F 284 SER cc_start: 0.8823 (p) cc_final: 0.8471 (m) REVERT: F 302 MET cc_start: 0.7201 (ptp) cc_final: 0.5700 (ptp) REVERT: F 323 GLN cc_start: 0.9280 (mm110) cc_final: 0.8867 (mm-40) REVERT: F 327 ASP cc_start: 0.8738 (m-30) cc_final: 0.8371 (m-30) REVERT: I 142 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6857 (p90) REVERT: I 177 MET cc_start: 0.8141 (ttp) cc_final: 0.7551 (tmm) REVERT: I 295 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8371 (mm) REVERT: I 302 MET cc_start: 0.8000 (ptp) cc_final: 0.7743 (ptp) REVERT: K 20 TRP cc_start: 0.8406 (t60) cc_final: 0.7964 (t60) REVERT: K 49 TYR cc_start: 0.8841 (m-80) cc_final: 0.8509 (m-10) REVERT: K 93 ILE cc_start: 0.8777 (mm) cc_final: 0.8549 (tp) REVERT: K 147 ASP cc_start: 0.8590 (p0) cc_final: 0.8341 (p0) REVERT: K 173 GLN cc_start: 0.8475 (mt0) cc_final: 0.8168 (mp10) REVERT: K 176 MET cc_start: 0.8287 (mmt) cc_final: 0.7376 (mmt) REVERT: K 177 MET cc_start: 0.9010 (ppp) cc_final: 0.8783 (tmm) REVERT: K 284 SER cc_start: 0.8948 (p) cc_final: 0.8600 (m) REVERT: K 302 MET cc_start: 0.7188 (ptp) cc_final: 0.5747 (ptp) REVERT: K 323 GLN cc_start: 0.9312 (mm110) cc_final: 0.8636 (mt0) REVERT: N 133 TYR cc_start: 0.8063 (m-80) cc_final: 0.7837 (m-80) REVERT: N 196 ASP cc_start: 0.8617 (t0) cc_final: 0.8227 (t0) REVERT: N 228 LYS cc_start: 0.8543 (mttt) cc_final: 0.8169 (mtmm) REVERT: N 240 ASN cc_start: 0.8138 (t0) cc_final: 0.7786 (t0) REVERT: N 295 ILE cc_start: 0.9167 (mp) cc_final: 0.8595 (mm) REVERT: N 297 ASP cc_start: 0.9082 (OUTLIER) cc_final: 0.8567 (m-30) REVERT: N 323 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8244 (mm-40) REVERT: O 17 MET cc_start: 0.8898 (tpt) cc_final: 0.8636 (tpt) REVERT: O 20 TRP cc_start: 0.8405 (t60) cc_final: 0.7422 (t60) REVERT: O 65 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.7762 (t0) REVERT: O 93 ILE cc_start: 0.8889 (mm) cc_final: 0.8662 (tp) REVERT: O 159 LEU cc_start: 0.8890 (tp) cc_final: 0.8566 (tp) REVERT: O 176 MET cc_start: 0.8271 (mmt) cc_final: 0.7368 (mmt) REVERT: O 249 GLN cc_start: 0.8606 (tt0) cc_final: 0.8228 (tm-30) REVERT: O 284 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8613 (m) REVERT: O 323 GLN cc_start: 0.9279 (mm110) cc_final: 0.8990 (mm-40) REVERT: O 327 ASP cc_start: 0.9014 (m-30) cc_final: 0.8732 (m-30) REVERT: J 241 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8349 (tp) REVERT: B 46 HIS cc_start: 0.7433 (m170) cc_final: 0.7041 (m170) REVERT: B 66 ASN cc_start: 0.7663 (m-40) cc_final: 0.6731 (m-40) REVERT: B 67 ASN cc_start: 0.8791 (m110) cc_final: 0.8231 (p0) REVERT: B 180 ASP cc_start: 0.7529 (m-30) cc_final: 0.7142 (m-30) REVERT: B 279 ASN cc_start: 0.8423 (OUTLIER) cc_final: 0.8130 (t0) REVERT: G 46 HIS cc_start: 0.7792 (m-70) cc_final: 0.7472 (m-70) REVERT: G 127 PHE cc_start: 0.8194 (t80) cc_final: 0.7579 (t80) REVERT: L 180 ASP cc_start: 0.7902 (m-30) cc_final: 0.7476 (m-30) REVERT: L 279 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8104 (t0) REVERT: L 309 GLN cc_start: 0.8835 (mt0) cc_final: 0.8196 (mp10) REVERT: C 28 GLN cc_start: 0.8867 (mp-120) cc_final: 0.8533 (mp10) REVERT: C 36 LEU cc_start: 0.9291 (tp) cc_final: 0.8950 (tt) REVERT: C 54 LYS cc_start: 0.7629 (pmmt) cc_final: 0.6647 (tptp) REVERT: C 63 ASP cc_start: 0.7100 (p0) cc_final: 0.6793 (p0) REVERT: H 28 GLN cc_start: 0.8512 (mp-120) cc_final: 0.8035 (mt0) REVERT: M 28 GLN cc_start: 0.8285 (mp-120) cc_final: 0.7775 (tm-30) REVERT: M 42 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8235 (mm-30) outliers start: 143 outliers final: 91 residues processed: 708 average time/residue: 0.4193 time to fit residues: 495.2039 Evaluate side-chains 633 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 532 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 297 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 279 ASN Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain H residue 8 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 373 optimal weight: 30.0000 chunk 284 optimal weight: 1.9990 chunk 196 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 379 optimal weight: 8.9990 chunk 402 optimal weight: 2.9990 chunk 198 optimal weight: 4.9990 chunk 359 optimal weight: 0.9980 chunk 108 optimal weight: 0.3980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS P 59 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 HIS K 323 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN O 249 GLN O 290 HIS ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 GLN J 206 GLN J 279 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN G 184 GLN ** G 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN L 106 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 279 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34096 Z= 0.242 Angle : 0.605 9.262 46328 Z= 0.311 Chirality : 0.046 0.215 5220 Planarity : 0.004 0.054 5980 Dihedral : 6.795 59.296 5084 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 4.63 % Allowed : 14.70 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 4240 helix: 0.10 (0.14), residues: 1468 sheet: -1.18 (0.16), residues: 872 loop : -1.21 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 20 HIS 0.006 0.001 HIS J 46 PHE 0.024 0.002 PHE J 127 TYR 0.017 0.002 TYR A 49 ARG 0.004 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 551 time to evaluate : 4.048 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: P 54 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7224 (tptp) REVERT: P 63 ASP cc_start: 0.6881 (p0) cc_final: 0.6520 (p0) REVERT: D 102 VAL cc_start: 0.8137 (t) cc_final: 0.7879 (p) REVERT: D 177 MET cc_start: 0.7277 (tmm) cc_final: 0.6765 (tmm) REVERT: D 271 MET cc_start: 0.8405 (mmt) cc_final: 0.8179 (mmm) REVERT: D 284 SER cc_start: 0.8759 (p) cc_final: 0.8348 (m) REVERT: D 295 ILE cc_start: 0.9158 (mp) cc_final: 0.8632 (mm) REVERT: D 323 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8087 (mm-40) REVERT: A 1 MET cc_start: 0.7649 (pmm) cc_final: 0.7249 (ptp) REVERT: A 67 CYS cc_start: 0.8386 (m) cc_final: 0.7434 (p) REVERT: A 85 ASN cc_start: 0.8906 (m-40) cc_final: 0.8701 (m110) REVERT: A 147 ASP cc_start: 0.8779 (p0) cc_final: 0.8396 (p0) REVERT: A 173 GLN cc_start: 0.8393 (mt0) cc_final: 0.7961 (mp10) REVERT: A 176 MET cc_start: 0.8582 (mmt) cc_final: 0.7602 (mmt) REVERT: A 268 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8277 (pp20) REVERT: A 302 MET cc_start: 0.7470 (ptp) cc_final: 0.6038 (ptp) REVERT: A 323 GLN cc_start: 0.9355 (mm-40) cc_final: 0.8554 (tt0) REVERT: A 327 ASP cc_start: 0.9018 (m-30) cc_final: 0.8623 (m-30) REVERT: E 177 MET cc_start: 0.8020 (ttp) cc_final: 0.7776 (ttp) REVERT: E 182 SER cc_start: 0.9401 (p) cc_final: 0.8901 (t) REVERT: E 196 ASP cc_start: 0.8729 (t0) cc_final: 0.8352 (t0) REVERT: E 238 THR cc_start: 0.8892 (p) cc_final: 0.8495 (t) REVERT: E 240 ASN cc_start: 0.7869 (t0) cc_final: 0.7633 (t0) REVERT: E 323 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8116 (mm-40) REVERT: F 1 MET cc_start: 0.7934 (pmm) cc_final: 0.7282 (pmm) REVERT: F 20 TRP cc_start: 0.8534 (t60) cc_final: 0.7875 (t60) REVERT: F 65 ASP cc_start: 0.8580 (p0) cc_final: 0.7595 (t0) REVERT: F 176 MET cc_start: 0.8688 (mmt) cc_final: 0.7273 (mmt) REVERT: F 284 SER cc_start: 0.8889 (p) cc_final: 0.8562 (m) REVERT: F 302 MET cc_start: 0.7240 (ptp) cc_final: 0.5697 (ptp) REVERT: F 323 GLN cc_start: 0.9246 (mm110) cc_final: 0.8897 (mm-40) REVERT: F 327 ASP cc_start: 0.8749 (m-30) cc_final: 0.8405 (m-30) REVERT: I 142 TYR cc_start: 0.7498 (OUTLIER) cc_final: 0.6818 (p90) REVERT: I 177 MET cc_start: 0.8139 (ttp) cc_final: 0.7477 (tmm) REVERT: I 246 PHE cc_start: 0.8354 (t80) cc_final: 0.8070 (t80) REVERT: I 295 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8441 (mm) REVERT: K 20 TRP cc_start: 0.8355 (t60) cc_final: 0.7972 (t60) REVERT: K 93 ILE cc_start: 0.8835 (mm) cc_final: 0.8582 (tp) REVERT: K 147 ASP cc_start: 0.8703 (p0) cc_final: 0.8493 (p0) REVERT: K 173 GLN cc_start: 0.8398 (mt0) cc_final: 0.8097 (mp10) REVERT: K 176 MET cc_start: 0.8075 (mmt) cc_final: 0.7590 (mmt) REVERT: K 177 MET cc_start: 0.9058 (ppp) cc_final: 0.8806 (tmm) REVERT: K 284 SER cc_start: 0.8957 (p) cc_final: 0.8582 (m) REVERT: K 302 MET cc_start: 0.7225 (ptp) cc_final: 0.5912 (ptp) REVERT: K 323 GLN cc_start: 0.9228 (mm-40) cc_final: 0.8770 (mt0) REVERT: N 228 LYS cc_start: 0.8500 (mttt) cc_final: 0.8126 (mtmm) REVERT: N 240 ASN cc_start: 0.8036 (t0) cc_final: 0.7779 (t0) REVERT: N 295 ILE cc_start: 0.9135 (mp) cc_final: 0.8587 (mm) REVERT: N 297 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8554 (m-30) REVERT: N 323 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8287 (mm-40) REVERT: O 17 MET cc_start: 0.8850 (tpt) cc_final: 0.8541 (tpt) REVERT: O 20 TRP cc_start: 0.8433 (t60) cc_final: 0.7480 (t60) REVERT: O 65 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.7790 (t0) REVERT: O 93 ILE cc_start: 0.8816 (mm) cc_final: 0.8593 (tp) REVERT: O 176 MET cc_start: 0.8229 (mmt) cc_final: 0.7287 (mmt) REVERT: O 249 GLN cc_start: 0.8692 (tt0) cc_final: 0.8147 (tm-30) REVERT: O 284 SER cc_start: 0.9068 (OUTLIER) cc_final: 0.8529 (m) REVERT: O 323 GLN cc_start: 0.9314 (mm110) cc_final: 0.8988 (mm-40) REVERT: O 327 ASP cc_start: 0.8988 (m-30) cc_final: 0.8601 (m-30) REVERT: J 46 HIS cc_start: 0.7318 (m90) cc_final: 0.7057 (m90) REVERT: J 84 ILE cc_start: 0.8078 (tp) cc_final: 0.7862 (tp) REVERT: J 241 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8372 (tp) REVERT: B 46 HIS cc_start: 0.7315 (m170) cc_final: 0.6315 (m170) REVERT: B 66 ASN cc_start: 0.7790 (m-40) cc_final: 0.6723 (m-40) REVERT: B 67 ASN cc_start: 0.8899 (m110) cc_final: 0.8204 (p0) REVERT: B 279 ASN cc_start: 0.8439 (OUTLIER) cc_final: 0.8065 (t0) REVERT: G 46 HIS cc_start: 0.7952 (m-70) cc_final: 0.7598 (m-70) REVERT: G 127 PHE cc_start: 0.8228 (t80) cc_final: 0.7694 (t80) REVERT: G 131 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9175 (mp) REVERT: L 180 ASP cc_start: 0.8075 (m-30) cc_final: 0.7667 (m-30) REVERT: L 279 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8188 (t0) REVERT: L 309 GLN cc_start: 0.8908 (mt0) cc_final: 0.8183 (mp10) REVERT: C 28 GLN cc_start: 0.8835 (mp-120) cc_final: 0.8586 (mp10) REVERT: C 36 LEU cc_start: 0.9267 (tp) cc_final: 0.8942 (tt) REVERT: C 63 ASP cc_start: 0.7097 (p0) cc_final: 0.6835 (p0) REVERT: H 28 GLN cc_start: 0.8552 (mp-120) cc_final: 0.7970 (mt0) REVERT: M 42 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8213 (mm-30) outliers start: 164 outliers final: 113 residues processed: 656 average time/residue: 0.4015 time to fit residues: 444.9249 Evaluate side-chains 623 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 500 time to evaluate : 4.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 245 ASP Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 297 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 292 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 279 ASN Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain H residue 8 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 7.9990 chunk 228 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 343 optimal weight: 0.8980 chunk 277 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 205 optimal weight: 10.0000 chunk 360 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS P 59 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 249 GLN O 187 GLN O 290 HIS ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN J 279 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN G 279 ASN L 106 HIS L 279 ASN C 28 GLN H 28 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34096 Z= 0.171 Angle : 0.578 13.302 46328 Z= 0.295 Chirality : 0.046 0.260 5220 Planarity : 0.004 0.052 5980 Dihedral : 6.499 58.247 5084 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.18 % Allowed : 16.03 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.87 (0.13), residues: 4240 helix: 0.34 (0.14), residues: 1452 sheet: -0.93 (0.16), residues: 880 loop : -1.02 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 20 HIS 0.013 0.001 HIS B 284 PHE 0.023 0.001 PHE F 16 TYR 0.019 0.001 TYR D 142 ARG 0.004 0.000 ARG M 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 580 time to evaluate : 3.938 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: P 54 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7219 (tptp) REVERT: P 63 ASP cc_start: 0.7037 (p0) cc_final: 0.6615 (p0) REVERT: D 102 VAL cc_start: 0.8139 (t) cc_final: 0.7893 (p) REVERT: D 177 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6914 (tmm) REVERT: D 271 MET cc_start: 0.8304 (mmt) cc_final: 0.8061 (mmm) REVERT: D 295 ILE cc_start: 0.9118 (mp) cc_final: 0.8540 (mt) REVERT: D 297 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8656 (m-30) REVERT: D 323 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8023 (mm-40) REVERT: A 1 MET cc_start: 0.7702 (pmm) cc_final: 0.7308 (ptp) REVERT: A 65 ASP cc_start: 0.8754 (p0) cc_final: 0.7766 (t0) REVERT: A 67 CYS cc_start: 0.8350 (m) cc_final: 0.7747 (t) REVERT: A 147 ASP cc_start: 0.8790 (p0) cc_final: 0.8441 (p0) REVERT: A 173 GLN cc_start: 0.8444 (mt0) cc_final: 0.8033 (mp10) REVERT: A 176 MET cc_start: 0.8447 (mmt) cc_final: 0.7510 (mmt) REVERT: A 268 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8258 (pp20) REVERT: A 284 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8377 (m) REVERT: A 302 MET cc_start: 0.7547 (ptp) cc_final: 0.6115 (ptp) REVERT: A 323 GLN cc_start: 0.9319 (mm-40) cc_final: 0.8517 (tt0) REVERT: A 327 ASP cc_start: 0.9030 (m-30) cc_final: 0.8635 (m-30) REVERT: E 142 TYR cc_start: 0.7581 (p90) cc_final: 0.7287 (p90) REVERT: E 182 SER cc_start: 0.9311 (p) cc_final: 0.8915 (t) REVERT: E 196 ASP cc_start: 0.8686 (t0) cc_final: 0.8302 (t0) REVERT: E 238 THR cc_start: 0.8810 (p) cc_final: 0.8486 (t) REVERT: E 246 PHE cc_start: 0.8273 (t80) cc_final: 0.7882 (t80) REVERT: E 323 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8122 (mm-40) REVERT: E 332 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7968 (mmt) REVERT: F 1 MET cc_start: 0.7917 (pmm) cc_final: 0.7313 (pmm) REVERT: F 20 TRP cc_start: 0.8469 (t60) cc_final: 0.7908 (t60) REVERT: F 65 ASP cc_start: 0.8507 (p0) cc_final: 0.7650 (t0) REVERT: F 176 MET cc_start: 0.8605 (mmt) cc_final: 0.7541 (mmt) REVERT: F 271 MET cc_start: 0.7744 (mmm) cc_final: 0.7529 (mmp) REVERT: F 284 SER cc_start: 0.8845 (p) cc_final: 0.8568 (p) REVERT: F 302 MET cc_start: 0.7276 (ptp) cc_final: 0.5850 (ptp) REVERT: F 323 GLN cc_start: 0.9176 (mm110) cc_final: 0.8773 (mm-40) REVERT: F 327 ASP cc_start: 0.8726 (m-30) cc_final: 0.8389 (m-30) REVERT: I 142 TYR cc_start: 0.7491 (OUTLIER) cc_final: 0.6556 (p90) REVERT: I 295 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8417 (mm) REVERT: I 314 TRP cc_start: 0.9377 (m100) cc_final: 0.8597 (m100) REVERT: K 17 MET cc_start: 0.9033 (tpt) cc_final: 0.8566 (tpt) REVERT: K 20 TRP cc_start: 0.8347 (t60) cc_final: 0.8037 (t60) REVERT: K 65 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.7582 (t0) REVERT: K 93 ILE cc_start: 0.8805 (mm) cc_final: 0.8562 (tp) REVERT: K 147 ASP cc_start: 0.8761 (p0) cc_final: 0.8546 (p0) REVERT: K 173 GLN cc_start: 0.8316 (mt0) cc_final: 0.8036 (mp10) REVERT: K 176 MET cc_start: 0.8178 (mmt) cc_final: 0.7753 (mmt) REVERT: K 177 MET cc_start: 0.9046 (ppp) cc_final: 0.8786 (tmm) REVERT: K 284 SER cc_start: 0.8941 (p) cc_final: 0.8619 (m) REVERT: K 302 MET cc_start: 0.7388 (ptp) cc_final: 0.6069 (ptp) REVERT: K 323 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8633 (mt0) REVERT: N 205 MET cc_start: 0.8828 (mtp) cc_final: 0.8499 (mtp) REVERT: N 228 LYS cc_start: 0.8488 (mttt) cc_final: 0.8143 (mtmm) REVERT: N 240 ASN cc_start: 0.7984 (t0) cc_final: 0.7779 (t0) REVERT: N 295 ILE cc_start: 0.9128 (mp) cc_final: 0.8620 (mt) REVERT: N 297 ASP cc_start: 0.9088 (OUTLIER) cc_final: 0.8627 (m-30) REVERT: N 323 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8230 (mm-40) REVERT: O 17 MET cc_start: 0.8874 (tpt) cc_final: 0.8563 (tpt) REVERT: O 20 TRP cc_start: 0.8435 (t60) cc_final: 0.7465 (t60) REVERT: O 26 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.7791 (t0) REVERT: O 65 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.7788 (t0) REVERT: O 93 ILE cc_start: 0.8749 (mm) cc_final: 0.8523 (tp) REVERT: O 176 MET cc_start: 0.8171 (mmt) cc_final: 0.7216 (mmt) REVERT: O 249 GLN cc_start: 0.8674 (tt0) cc_final: 0.8176 (tm-30) REVERT: O 284 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8605 (m) REVERT: O 323 GLN cc_start: 0.9202 (mm110) cc_final: 0.8541 (mt0) REVERT: O 327 ASP cc_start: 0.8998 (m-30) cc_final: 0.8591 (m-30) REVERT: J 46 HIS cc_start: 0.7278 (m90) cc_final: 0.7045 (m170) REVERT: J 84 ILE cc_start: 0.7970 (tp) cc_final: 0.7755 (tp) REVERT: J 131 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8955 (mp) REVERT: J 241 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8223 (tp) REVERT: B 46 HIS cc_start: 0.7224 (m170) cc_final: 0.6329 (m170) REVERT: B 66 ASN cc_start: 0.7693 (m-40) cc_final: 0.6790 (m110) REVERT: B 279 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8129 (t0) REVERT: G 46 HIS cc_start: 0.7991 (m-70) cc_final: 0.7658 (m-70) REVERT: G 110 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8085 (tp) REVERT: G 127 PHE cc_start: 0.8164 (t80) cc_final: 0.7545 (t80) REVERT: G 131 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9181 (mp) REVERT: G 206 GLN cc_start: 0.8378 (pt0) cc_final: 0.8163 (pt0) REVERT: G 279 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8178 (t0) REVERT: L 124 LEU cc_start: 0.8729 (tp) cc_final: 0.8411 (tt) REVERT: L 180 ASP cc_start: 0.8012 (m-30) cc_final: 0.7598 (m-30) REVERT: L 241 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8339 (tp) REVERT: L 279 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8237 (t0) REVERT: C 28 GLN cc_start: 0.8902 (mp10) cc_final: 0.8493 (mp10) REVERT: C 36 LEU cc_start: 0.9185 (tp) cc_final: 0.8828 (tt) REVERT: C 63 ASP cc_start: 0.7026 (p0) cc_final: 0.6782 (p0) REVERT: H 1 MET cc_start: 0.7471 (tpp) cc_final: 0.7242 (tmm) REVERT: H 63 ASP cc_start: 0.6482 (p0) cc_final: 0.6223 (p0) REVERT: M 28 GLN cc_start: 0.8254 (mp-120) cc_final: 0.7765 (tm-30) REVERT: M 47 ARG cc_start: 0.8260 (mmm160) cc_final: 0.7844 (tpt-90) outliers start: 148 outliers final: 101 residues processed: 668 average time/residue: 0.3989 time to fit residues: 447.0380 Evaluate side-chains 649 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 528 time to evaluate : 5.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 297 ASP Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 332 MET Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 297 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 292 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 279 ASN Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain H residue 8 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 7.9990 chunk 362 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 chunk 99 optimal weight: 0.0970 chunk 402 optimal weight: 8.9990 chunk 334 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN E 249 GLN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 HIS N 45 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN J 279 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN G 46 HIS L 106 HIS L 279 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34096 Z= 0.185 Angle : 0.579 12.780 46328 Z= 0.296 Chirality : 0.046 0.315 5220 Planarity : 0.004 0.051 5980 Dihedral : 6.386 57.921 5084 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.77 % Allowed : 16.28 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.66 (0.13), residues: 4240 helix: 0.43 (0.14), residues: 1460 sheet: -0.76 (0.17), residues: 880 loop : -0.87 (0.14), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 20 HIS 0.011 0.001 HIS O 290 PHE 0.023 0.001 PHE O 246 TYR 0.018 0.001 TYR J 217 ARG 0.003 0.000 ARG C 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 554 time to evaluate : 3.959 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: P 54 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7175 (tptp) REVERT: P 63 ASP cc_start: 0.7004 (p0) cc_final: 0.6655 (p0) REVERT: D 102 VAL cc_start: 0.8174 (t) cc_final: 0.7924 (p) REVERT: D 177 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6846 (tmm) REVERT: D 228 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7711 (mtmm) REVERT: D 271 MET cc_start: 0.8336 (mmt) cc_final: 0.8089 (mmm) REVERT: D 295 ILE cc_start: 0.9119 (mp) cc_final: 0.8536 (mt) REVERT: D 323 GLN cc_start: 0.8519 (mm-40) cc_final: 0.7978 (mm-40) REVERT: A 1 MET cc_start: 0.7708 (pmm) cc_final: 0.7499 (ptp) REVERT: A 65 ASP cc_start: 0.8760 (p0) cc_final: 0.7900 (t0) REVERT: A 147 ASP cc_start: 0.8833 (p0) cc_final: 0.8490 (p0) REVERT: A 173 GLN cc_start: 0.8540 (mt0) cc_final: 0.8224 (mp10) REVERT: A 176 MET cc_start: 0.8517 (mmt) cc_final: 0.7567 (mmt) REVERT: A 268 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8270 (pp20) REVERT: A 284 SER cc_start: 0.8768 (OUTLIER) cc_final: 0.8315 (m) REVERT: A 302 MET cc_start: 0.7562 (ptp) cc_final: 0.6178 (ptp) REVERT: A 323 GLN cc_start: 0.9302 (mm-40) cc_final: 0.8547 (tt0) REVERT: A 327 ASP cc_start: 0.9033 (m-30) cc_final: 0.8642 (m-30) REVERT: E 196 ASP cc_start: 0.8701 (t0) cc_final: 0.8302 (t0) REVERT: E 240 ASN cc_start: 0.7881 (t0) cc_final: 0.7302 (t0) REVERT: E 246 PHE cc_start: 0.8319 (t80) cc_final: 0.7897 (t80) REVERT: E 295 ILE cc_start: 0.8654 (mm) cc_final: 0.8112 (mm) REVERT: E 297 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8484 (m-30) REVERT: E 323 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8067 (mm-40) REVERT: F 1 MET cc_start: 0.7912 (pmm) cc_final: 0.7330 (pmm) REVERT: F 20 TRP cc_start: 0.8422 (t60) cc_final: 0.7961 (t60) REVERT: F 65 ASP cc_start: 0.8517 (p0) cc_final: 0.7774 (t0) REVERT: F 176 MET cc_start: 0.8659 (mmt) cc_final: 0.7458 (mmt) REVERT: F 284 SER cc_start: 0.8875 (p) cc_final: 0.8583 (p) REVERT: F 302 MET cc_start: 0.7283 (ptp) cc_final: 0.5873 (ptp) REVERT: F 323 GLN cc_start: 0.9161 (mm110) cc_final: 0.8743 (mm-40) REVERT: F 327 ASP cc_start: 0.8707 (m-30) cc_final: 0.8378 (m-30) REVERT: I 142 TYR cc_start: 0.7443 (OUTLIER) cc_final: 0.6359 (p90) REVERT: I 295 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8396 (mm) REVERT: I 314 TRP cc_start: 0.9372 (m100) cc_final: 0.8613 (m100) REVERT: K 20 TRP cc_start: 0.8390 (t60) cc_final: 0.8115 (t60) REVERT: K 21 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9272 (mp) REVERT: K 65 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.7668 (t0) REVERT: K 93 ILE cc_start: 0.8812 (mm) cc_final: 0.8568 (tp) REVERT: K 177 MET cc_start: 0.9046 (ppp) cc_final: 0.8759 (tmm) REVERT: K 284 SER cc_start: 0.8887 (p) cc_final: 0.8525 (m) REVERT: K 302 MET cc_start: 0.7400 (ptp) cc_final: 0.6011 (ptp) REVERT: K 323 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8776 (mt0) REVERT: N 228 LYS cc_start: 0.8420 (mttt) cc_final: 0.8117 (mtmm) REVERT: N 240 ASN cc_start: 0.7957 (t0) cc_final: 0.7698 (t0) REVERT: N 295 ILE cc_start: 0.9127 (mp) cc_final: 0.8581 (mm) REVERT: N 297 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8645 (m-30) REVERT: N 302 MET cc_start: 0.8037 (ptp) cc_final: 0.7815 (ptp) REVERT: N 323 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8240 (mm-40) REVERT: O 17 MET cc_start: 0.8836 (tpt) cc_final: 0.8505 (tpt) REVERT: O 20 TRP cc_start: 0.8490 (t60) cc_final: 0.7503 (t60) REVERT: O 26 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.7804 (t0) REVERT: O 65 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.7996 (t0) REVERT: O 93 ILE cc_start: 0.8783 (mm) cc_final: 0.8532 (tp) REVERT: O 147 ASP cc_start: 0.8356 (p0) cc_final: 0.8148 (p0) REVERT: O 176 MET cc_start: 0.8144 (mmt) cc_final: 0.7217 (mmt) REVERT: O 249 GLN cc_start: 0.8676 (tt0) cc_final: 0.8209 (tm-30) REVERT: O 284 SER cc_start: 0.9007 (OUTLIER) cc_final: 0.8672 (m) REVERT: O 302 MET cc_start: 0.7444 (ptp) cc_final: 0.6749 (ptp) REVERT: O 323 GLN cc_start: 0.9188 (mm110) cc_final: 0.8582 (mt0) REVERT: O 327 ASP cc_start: 0.9000 (m-30) cc_final: 0.8591 (m-30) REVERT: J 46 HIS cc_start: 0.7300 (m90) cc_final: 0.6978 (m170) REVERT: J 84 ILE cc_start: 0.7984 (tp) cc_final: 0.7761 (tp) REVERT: J 131 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8977 (mp) REVERT: J 241 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8230 (tp) REVERT: J 279 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8322 (t0) REVERT: B 46 HIS cc_start: 0.7181 (m170) cc_final: 0.6461 (m170) REVERT: B 66 ASN cc_start: 0.7708 (m-40) cc_final: 0.6822 (m110) REVERT: B 279 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8184 (t0) REVERT: G 46 HIS cc_start: 0.7678 (m170) cc_final: 0.7314 (m170) REVERT: G 127 PHE cc_start: 0.8192 (t80) cc_final: 0.7624 (t80) REVERT: G 131 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9193 (mp) REVERT: G 279 ASN cc_start: 0.8728 (t0) cc_final: 0.8256 (t0) REVERT: L 69 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7217 (t70) REVERT: L 78 LEU cc_start: 0.8701 (mm) cc_final: 0.8462 (mm) REVERT: L 124 LEU cc_start: 0.8702 (tp) cc_final: 0.8394 (tt) REVERT: L 180 ASP cc_start: 0.8035 (m-30) cc_final: 0.7653 (m-30) REVERT: L 241 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8246 (tp) REVERT: C 28 GLN cc_start: 0.8816 (mp10) cc_final: 0.8428 (mp10) REVERT: C 63 ASP cc_start: 0.7056 (p0) cc_final: 0.6838 (p0) REVERT: H 63 ASP cc_start: 0.6631 (p0) cc_final: 0.6388 (p0) REVERT: M 28 GLN cc_start: 0.8224 (mp-120) cc_final: 0.7692 (tm-30) REVERT: M 47 ARG cc_start: 0.8286 (mmm160) cc_final: 0.7885 (tpt-90) outliers start: 169 outliers final: 113 residues processed: 662 average time/residue: 0.4003 time to fit residues: 444.8989 Evaluate side-chains 647 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 514 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 43 ASN Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 245 ASP Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 297 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain H residue 54 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 388 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 338 optimal weight: 0.0000 chunk 224 optimal weight: 7.9990 chunk 400 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 185 optimal weight: 10.0000 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 59 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 HIS ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN O 290 HIS O 323 GLN ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 284 HIS G 206 GLN L 106 HIS M 10 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34096 Z= 0.186 Angle : 0.601 14.038 46328 Z= 0.303 Chirality : 0.046 0.306 5220 Planarity : 0.004 0.071 5980 Dihedral : 6.351 58.026 5084 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.88 % Allowed : 16.56 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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 (0.13), residues: 4240 helix: 0.47 (0.14), residues: 1468 sheet: -0.63 (0.17), residues: 888 loop : -0.81 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 20 HIS 0.009 0.001 HIS B 284 PHE 0.021 0.001 PHE B 127 TYR 0.021 0.001 TYR J 130 ARG 0.004 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 546 time to evaluate : 4.154 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: P 12 ARG cc_start: 0.7847 (ttt180) cc_final: 0.7617 (ttt180) REVERT: P 54 LYS cc_start: 0.7788 (pmmt) cc_final: 0.7176 (tptp) REVERT: P 63 ASP cc_start: 0.6981 (p0) cc_final: 0.6709 (p0) REVERT: D 102 VAL cc_start: 0.8192 (t) cc_final: 0.7943 (p) REVERT: D 177 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6825 (tmm) REVERT: D 228 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7673 (mtmm) REVERT: D 271 MET cc_start: 0.8343 (mmt) cc_final: 0.8096 (mmm) REVERT: D 295 ILE cc_start: 0.9099 (mp) cc_final: 0.8594 (mt) REVERT: D 323 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8006 (mm-40) REVERT: A 55 ILE cc_start: 0.9317 (mt) cc_final: 0.9112 (mm) REVERT: A 65 ASP cc_start: 0.8675 (p0) cc_final: 0.7885 (t0) REVERT: A 147 ASP cc_start: 0.8883 (p0) cc_final: 0.8535 (p0) REVERT: A 173 GLN cc_start: 0.8542 (mt0) cc_final: 0.8225 (mp10) REVERT: A 176 MET cc_start: 0.8525 (mmt) cc_final: 0.7612 (mmp) REVERT: A 268 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8263 (pp20) REVERT: A 284 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8325 (m) REVERT: A 302 MET cc_start: 0.7555 (ptp) cc_final: 0.6198 (ptp) REVERT: A 323 GLN cc_start: 0.9305 (mm-40) cc_final: 0.8543 (mt0) REVERT: A 327 ASP cc_start: 0.9028 (m-30) cc_final: 0.8586 (m-30) REVERT: E 182 SER cc_start: 0.9145 (p) cc_final: 0.8874 (t) REVERT: E 196 ASP cc_start: 0.8691 (t0) cc_final: 0.8310 (t0) REVERT: E 246 PHE cc_start: 0.8344 (t80) cc_final: 0.7909 (t80) REVERT: E 295 ILE cc_start: 0.8692 (mm) cc_final: 0.8130 (mm) REVERT: E 297 ASP cc_start: 0.8834 (OUTLIER) cc_final: 0.8480 (m-30) REVERT: F 1 MET cc_start: 0.7989 (pmm) cc_final: 0.7430 (pmm) REVERT: F 17 MET cc_start: 0.9289 (tpt) cc_final: 0.9014 (tpt) REVERT: F 20 TRP cc_start: 0.8439 (t60) cc_final: 0.7958 (t60) REVERT: F 65 ASP cc_start: 0.8526 (p0) cc_final: 0.7822 (t0) REVERT: F 176 MET cc_start: 0.8643 (mmt) cc_final: 0.7320 (mmt) REVERT: F 284 SER cc_start: 0.8843 (p) cc_final: 0.8549 (p) REVERT: F 302 MET cc_start: 0.7341 (ptp) cc_final: 0.6626 (ptp) REVERT: F 323 GLN cc_start: 0.9164 (mm110) cc_final: 0.8781 (mm-40) REVERT: F 327 ASP cc_start: 0.8715 (m-30) cc_final: 0.8394 (m-30) REVERT: I 142 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6435 (p90) REVERT: I 249 GLN cc_start: 0.7301 (tp40) cc_final: 0.7033 (tp-100) REVERT: I 295 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8373 (mm) REVERT: I 314 TRP cc_start: 0.9347 (m100) cc_final: 0.8638 (m100) REVERT: K 21 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9267 (mp) REVERT: K 65 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.7653 (t0) REVERT: K 93 ILE cc_start: 0.8859 (mm) cc_final: 0.8585 (tp) REVERT: K 176 MET cc_start: 0.8470 (mmt) cc_final: 0.7684 (mmt) REVERT: K 177 MET cc_start: 0.9017 (ppp) cc_final: 0.8740 (tmm) REVERT: K 284 SER cc_start: 0.8922 (p) cc_final: 0.8575 (m) REVERT: K 302 MET cc_start: 0.7397 (ptp) cc_final: 0.6009 (ptp) REVERT: K 323 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8784 (mt0) REVERT: N 228 LYS cc_start: 0.8459 (mttt) cc_final: 0.8098 (mtmm) REVERT: N 240 ASN cc_start: 0.7966 (t0) cc_final: 0.7691 (t0) REVERT: N 295 ILE cc_start: 0.9117 (mp) cc_final: 0.8497 (mt) REVERT: N 297 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8612 (m-30) REVERT: N 323 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8244 (mm-40) REVERT: O 17 MET cc_start: 0.8834 (tpt) cc_final: 0.8487 (tpt) REVERT: O 20 TRP cc_start: 0.8485 (t60) cc_final: 0.7491 (t60) REVERT: O 26 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.7824 (t0) REVERT: O 65 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.7985 (t0) REVERT: O 93 ILE cc_start: 0.8784 (mm) cc_final: 0.8541 (tp) REVERT: O 176 MET cc_start: 0.8136 (mmt) cc_final: 0.7180 (mmt) REVERT: O 261 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8504 (pp30) REVERT: O 284 SER cc_start: 0.9058 (OUTLIER) cc_final: 0.8655 (m) REVERT: O 323 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8620 (mt0) REVERT: O 327 ASP cc_start: 0.9008 (m-30) cc_final: 0.8597 (m-30) REVERT: J 46 HIS cc_start: 0.7299 (m90) cc_final: 0.6954 (m170) REVERT: J 84 ILE cc_start: 0.7964 (tp) cc_final: 0.7726 (tp) REVERT: J 241 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8230 (tp) REVERT: J 279 ASN cc_start: 0.8662 (m-40) cc_final: 0.8353 (t0) REVERT: B 46 HIS cc_start: 0.7126 (m170) cc_final: 0.6442 (m170) REVERT: B 66 ASN cc_start: 0.7678 (m-40) cc_final: 0.6870 (m110) REVERT: B 131 LEU cc_start: 0.9339 (tt) cc_final: 0.9048 (mm) REVERT: B 241 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8257 (tp) REVERT: G 46 HIS cc_start: 0.7587 (m170) cc_final: 0.7194 (m170) REVERT: G 67 ASN cc_start: 0.8176 (p0) cc_final: 0.7973 (p0) REVERT: G 69 ASP cc_start: 0.7828 (m-30) cc_final: 0.7158 (t70) REVERT: G 127 PHE cc_start: 0.8185 (t80) cc_final: 0.7628 (t80) REVERT: G 241 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8210 (tp) REVERT: G 279 ASN cc_start: 0.8725 (t0) cc_final: 0.8261 (t0) REVERT: L 69 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7217 (t70) REVERT: L 78 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8530 (mm) REVERT: L 110 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8238 (tt) REVERT: L 124 LEU cc_start: 0.8686 (tp) cc_final: 0.8384 (tt) REVERT: L 180 ASP cc_start: 0.8024 (m-30) cc_final: 0.7585 (m-30) REVERT: L 241 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8254 (tp) REVERT: C 28 GLN cc_start: 0.8812 (mp10) cc_final: 0.8422 (mp10) REVERT: C 63 ASP cc_start: 0.6999 (p0) cc_final: 0.6787 (p0) REVERT: H 54 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7246 (tptp) REVERT: H 63 ASP cc_start: 0.6379 (p0) cc_final: 0.6120 (p0) REVERT: M 47 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7887 (tpt-90) outliers start: 173 outliers final: 133 residues processed: 656 average time/residue: 0.3994 time to fit residues: 442.0622 Evaluate side-chains 668 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 515 time to evaluate : 4.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 7 GLN Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 142 TYR Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 275 ILE Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 55 ILE Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 245 ASP Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 297 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 54 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 254 optimal weight: 4.9990 chunk 273 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 315 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 HIS ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** E 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 260 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 HIS N 112 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN M 28 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34096 Z= 0.188 Angle : 0.604 14.728 46328 Z= 0.305 Chirality : 0.046 0.318 5220 Planarity : 0.004 0.049 5980 Dihedral : 6.317 58.356 5084 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.94 % Allowed : 16.93 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.44 (0.13), residues: 4240 helix: 0.55 (0.14), residues: 1468 sheet: -0.53 (0.17), residues: 888 loop : -0.74 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP K 20 HIS 0.009 0.001 HIS O 290 PHE 0.025 0.001 PHE G 68 TYR 0.018 0.001 TYR A 49 ARG 0.005 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 555 time to evaluate : 3.941 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: P 12 ARG cc_start: 0.7947 (ttt180) cc_final: 0.7609 (ttt180) REVERT: P 54 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7207 (tptp) REVERT: P 63 ASP cc_start: 0.7165 (p0) cc_final: 0.6838 (p0) REVERT: P 69 GLU cc_start: 0.7084 (mp0) cc_final: 0.6652 (mp0) REVERT: D 51 SER cc_start: 0.8428 (t) cc_final: 0.8196 (p) REVERT: D 102 VAL cc_start: 0.8197 (t) cc_final: 0.7953 (p) REVERT: D 173 GLN cc_start: 0.8616 (mt0) cc_final: 0.7836 (mp10) REVERT: D 177 MET cc_start: 0.7119 (OUTLIER) cc_final: 0.6795 (tmm) REVERT: D 249 GLN cc_start: 0.7370 (tp40) cc_final: 0.6907 (tp-100) REVERT: D 271 MET cc_start: 0.8359 (mmt) cc_final: 0.8101 (mmm) REVERT: D 295 ILE cc_start: 0.9096 (mp) cc_final: 0.8624 (mt) REVERT: D 323 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8003 (mm-40) REVERT: A 65 ASP cc_start: 0.8669 (p0) cc_final: 0.7909 (t0) REVERT: A 147 ASP cc_start: 0.8909 (p0) cc_final: 0.8525 (p0) REVERT: A 173 GLN cc_start: 0.8509 (mt0) cc_final: 0.8208 (mp10) REVERT: A 176 MET cc_start: 0.8521 (mmt) cc_final: 0.7642 (mmp) REVERT: A 268 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8269 (pp20) REVERT: A 284 SER cc_start: 0.8785 (OUTLIER) cc_final: 0.8385 (m) REVERT: A 302 MET cc_start: 0.7529 (ptp) cc_final: 0.6205 (ptp) REVERT: A 323 GLN cc_start: 0.9299 (mm-40) cc_final: 0.8532 (mt0) REVERT: A 327 ASP cc_start: 0.9028 (m-30) cc_final: 0.8621 (m-30) REVERT: E 196 ASP cc_start: 0.8680 (t0) cc_final: 0.8298 (t0) REVERT: E 240 ASN cc_start: 0.7752 (t0) cc_final: 0.7210 (t0) REVERT: E 246 PHE cc_start: 0.8412 (t80) cc_final: 0.7949 (t80) REVERT: E 295 ILE cc_start: 0.8688 (mm) cc_final: 0.8137 (mm) REVERT: E 297 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8487 (m-30) REVERT: E 323 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8281 (mm-40) REVERT: F 1 MET cc_start: 0.8005 (pmm) cc_final: 0.7441 (pmm) REVERT: F 20 TRP cc_start: 0.8420 (t60) cc_final: 0.7947 (t60) REVERT: F 65 ASP cc_start: 0.8515 (p0) cc_final: 0.7842 (t0) REVERT: F 176 MET cc_start: 0.8546 (mmt) cc_final: 0.7406 (mmt) REVERT: F 284 SER cc_start: 0.8840 (p) cc_final: 0.8537 (p) REVERT: F 302 MET cc_start: 0.7332 (ptp) cc_final: 0.6606 (ptp) REVERT: F 323 GLN cc_start: 0.9160 (mm110) cc_final: 0.8715 (mm-40) REVERT: F 327 ASP cc_start: 0.8694 (m-30) cc_final: 0.8369 (m-30) REVERT: I 142 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6461 (p90) REVERT: I 249 GLN cc_start: 0.7347 (tp40) cc_final: 0.7075 (tp-100) REVERT: I 260 ASN cc_start: 0.8909 (m-40) cc_final: 0.8592 (m-40) REVERT: I 295 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8346 (mm) REVERT: I 314 TRP cc_start: 0.9346 (m100) cc_final: 0.8665 (m100) REVERT: K 17 MET cc_start: 0.9103 (tpt) cc_final: 0.8848 (tpt) REVERT: K 21 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9212 (mp) REVERT: K 65 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.7695 (t0) REVERT: K 93 ILE cc_start: 0.8892 (mm) cc_final: 0.8585 (tp) REVERT: K 176 MET cc_start: 0.8488 (mmt) cc_final: 0.7714 (mmt) REVERT: K 177 MET cc_start: 0.8982 (ppp) cc_final: 0.8687 (tmm) REVERT: K 240 ASN cc_start: 0.8601 (t0) cc_final: 0.8348 (t0) REVERT: K 302 MET cc_start: 0.7379 (ptp) cc_final: 0.6033 (ptp) REVERT: K 323 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8767 (tt0) REVERT: N 228 LYS cc_start: 0.8469 (mttt) cc_final: 0.8082 (mtmm) REVERT: N 240 ASN cc_start: 0.8012 (t0) cc_final: 0.7683 (t0) REVERT: N 295 ILE cc_start: 0.9100 (mp) cc_final: 0.8597 (mt) REVERT: N 297 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8738 (m-30) REVERT: N 314 TRP cc_start: 0.9356 (m100) cc_final: 0.8389 (m100) REVERT: N 323 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8230 (mm-40) REVERT: O 17 MET cc_start: 0.8799 (tpt) cc_final: 0.8467 (tpt) REVERT: O 20 TRP cc_start: 0.8450 (t60) cc_final: 0.7493 (t60) REVERT: O 26 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.7873 (t0) REVERT: O 65 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.8048 (t0) REVERT: O 93 ILE cc_start: 0.8772 (mm) cc_final: 0.8536 (tp) REVERT: O 176 MET cc_start: 0.8137 (mmt) cc_final: 0.7114 (mmt) REVERT: O 261 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8498 (pp30) REVERT: O 265 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: O 284 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8640 (m) REVERT: O 323 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8631 (mt0) REVERT: O 327 ASP cc_start: 0.9014 (m-30) cc_final: 0.8614 (m-30) REVERT: J 46 HIS cc_start: 0.7220 (m90) cc_final: 0.6741 (m90) REVERT: J 84 ILE cc_start: 0.7954 (tp) cc_final: 0.7721 (tp) REVERT: J 241 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8223 (tp) REVERT: J 279 ASN cc_start: 0.8686 (m-40) cc_final: 0.8221 (t0) REVERT: B 46 HIS cc_start: 0.7199 (m170) cc_final: 0.6622 (m170) REVERT: B 66 ASN cc_start: 0.7681 (m-40) cc_final: 0.6883 (m110) REVERT: B 131 LEU cc_start: 0.9348 (tt) cc_final: 0.9073 (mm) REVERT: B 241 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8269 (tp) REVERT: G 46 HIS cc_start: 0.7579 (m170) cc_final: 0.7213 (m170) REVERT: G 69 ASP cc_start: 0.7940 (m-30) cc_final: 0.7224 (t70) REVERT: G 80 ASN cc_start: 0.6852 (m-40) cc_final: 0.5676 (t0) REVERT: G 127 PHE cc_start: 0.8178 (t80) cc_final: 0.7510 (t80) REVERT: G 279 ASN cc_start: 0.8720 (t0) cc_final: 0.8307 (t0) REVERT: L 69 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7143 (t70) REVERT: L 78 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8540 (mm) REVERT: L 110 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8244 (tt) REVERT: L 124 LEU cc_start: 0.8655 (tp) cc_final: 0.8374 (tt) REVERT: L 180 ASP cc_start: 0.8019 (m-30) cc_final: 0.7584 (m-30) REVERT: L 214 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7498 (mp0) REVERT: L 241 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8264 (tp) REVERT: C 28 GLN cc_start: 0.8706 (mp10) cc_final: 0.8385 (mp10) REVERT: C 63 ASP cc_start: 0.6990 (p0) cc_final: 0.6788 (p0) REVERT: H 63 ASP cc_start: 0.6420 (p0) cc_final: 0.6186 (p0) REVERT: M 47 ARG cc_start: 0.8285 (mmm160) cc_final: 0.7903 (tpt-90) outliers start: 175 outliers final: 130 residues processed: 670 average time/residue: 0.4291 time to fit residues: 481.3982 Evaluate side-chains 675 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 526 time to evaluate : 4.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 2 SER Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain P residue 62 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 4 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 43 ASN Chi-restraints excluded: chain N residue 112 HIS Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 297 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 288 VAL Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 241 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain M residue 22 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 8.9990 chunk 384 optimal weight: 0.0570 chunk 350 optimal weight: 5.9990 chunk 373 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 293 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 337 optimal weight: 6.9990 chunk 353 optimal weight: 0.9980 chunk 372 optimal weight: 10.0000 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 46 GLN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 260 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 HIS N 112 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 206 ASN O 290 HIS ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 GLN M 10 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 34096 Z= 0.170 Angle : 0.627 15.293 46328 Z= 0.314 Chirality : 0.047 0.320 5220 Planarity : 0.004 0.048 5980 Dihedral : 6.232 57.463 5084 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.20 % Allowed : 17.95 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.42 (0.13), residues: 4240 helix: 0.51 (0.14), residues: 1472 sheet: -0.46 (0.17), residues: 888 loop : -0.71 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP K 20 HIS 0.012 0.001 HIS O 290 PHE 0.032 0.001 PHE G 68 TYR 0.017 0.001 TYR N 142 ARG 0.004 0.000 ARG B 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 570 time to evaluate : 3.991 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: P 12 ARG cc_start: 0.7928 (ttt180) cc_final: 0.7603 (ttt180) REVERT: P 54 LYS cc_start: 0.7700 (pmmt) cc_final: 0.7110 (tptp) REVERT: P 63 ASP cc_start: 0.7311 (p0) cc_final: 0.6990 (p0) REVERT: P 64 ASN cc_start: 0.8553 (t0) cc_final: 0.8312 (t0) REVERT: P 69 GLU cc_start: 0.7057 (mp0) cc_final: 0.6679 (mp0) REVERT: D 228 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7695 (mtmm) REVERT: D 271 MET cc_start: 0.8302 (mmt) cc_final: 0.8037 (mmm) REVERT: D 295 ILE cc_start: 0.9094 (mp) cc_final: 0.8623 (mt) REVERT: D 301 THR cc_start: 0.8978 (m) cc_final: 0.8774 (m) REVERT: D 323 GLN cc_start: 0.8527 (mm-40) cc_final: 0.7993 (mm-40) REVERT: A 64 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7969 (p0) REVERT: A 65 ASP cc_start: 0.8631 (p0) cc_final: 0.8204 (t0) REVERT: A 147 ASP cc_start: 0.8915 (p0) cc_final: 0.8555 (p0) REVERT: A 173 GLN cc_start: 0.8489 (mt0) cc_final: 0.8210 (mp10) REVERT: A 176 MET cc_start: 0.8484 (mmt) cc_final: 0.8221 (mmt) REVERT: A 268 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8266 (pp20) REVERT: A 284 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8351 (m) REVERT: A 302 MET cc_start: 0.7497 (ptp) cc_final: 0.6186 (ptp) REVERT: A 323 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8860 (mm-40) REVERT: A 327 ASP cc_start: 0.9005 (m-30) cc_final: 0.8584 (m-30) REVERT: E 196 ASP cc_start: 0.8663 (t0) cc_final: 0.8277 (t0) REVERT: E 246 PHE cc_start: 0.8392 (t80) cc_final: 0.7899 (t80) REVERT: E 295 ILE cc_start: 0.8668 (mm) cc_final: 0.8092 (mm) REVERT: E 297 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8512 (m-30) REVERT: E 323 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8211 (mm-40) REVERT: F 1 MET cc_start: 0.7944 (pmm) cc_final: 0.7347 (pmm) REVERT: F 20 TRP cc_start: 0.8442 (t60) cc_final: 0.7985 (t60) REVERT: F 65 ASP cc_start: 0.8525 (p0) cc_final: 0.7843 (t0) REVERT: F 176 MET cc_start: 0.8605 (mmt) cc_final: 0.7530 (mmt) REVERT: F 284 SER cc_start: 0.8828 (p) cc_final: 0.8540 (p) REVERT: F 302 MET cc_start: 0.7354 (ptp) cc_final: 0.6768 (ptp) REVERT: F 323 GLN cc_start: 0.9138 (mm110) cc_final: 0.8668 (mm-40) REVERT: F 327 ASP cc_start: 0.8719 (m-30) cc_final: 0.8395 (m-30) REVERT: I 142 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6554 (p90) REVERT: I 228 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7762 (mtmm) REVERT: I 246 PHE cc_start: 0.8813 (t80) cc_final: 0.8570 (t80) REVERT: I 249 GLN cc_start: 0.7397 (tp40) cc_final: 0.7046 (tp40) REVERT: I 295 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8300 (mm) REVERT: I 314 TRP cc_start: 0.9326 (m100) cc_final: 0.8697 (m100) REVERT: K 17 MET cc_start: 0.8727 (tpt) cc_final: 0.8409 (tpt) REVERT: K 21 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.8967 (mp) REVERT: K 65 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.7680 (t0) REVERT: K 93 ILE cc_start: 0.8908 (mm) cc_final: 0.8615 (tp) REVERT: K 176 MET cc_start: 0.8529 (mmt) cc_final: 0.7746 (mmt) REVERT: K 177 MET cc_start: 0.8979 (ppp) cc_final: 0.8679 (tmm) REVERT: K 226 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8279 (mt0) REVERT: K 240 ASN cc_start: 0.8571 (t0) cc_final: 0.8341 (t0) REVERT: K 302 MET cc_start: 0.7426 (ptp) cc_final: 0.5883 (ptp) REVERT: K 323 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8767 (tt0) REVERT: N 52 MET cc_start: 0.7764 (tpt) cc_final: 0.7520 (tpt) REVERT: N 228 LYS cc_start: 0.8443 (mttt) cc_final: 0.8066 (mtmm) REVERT: N 240 ASN cc_start: 0.8008 (t0) cc_final: 0.7661 (t0) REVERT: N 295 ILE cc_start: 0.9090 (mp) cc_final: 0.8577 (mt) REVERT: N 297 ASP cc_start: 0.9047 (OUTLIER) cc_final: 0.8731 (m-30) REVERT: N 314 TRP cc_start: 0.9328 (m100) cc_final: 0.8372 (m100) REVERT: N 323 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8220 (mm-40) REVERT: O 17 MET cc_start: 0.8802 (tpt) cc_final: 0.8478 (tpt) REVERT: O 20 TRP cc_start: 0.8437 (t60) cc_final: 0.7473 (t60) REVERT: O 26 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.7844 (t0) REVERT: O 65 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8092 (t0) REVERT: O 93 ILE cc_start: 0.8758 (mm) cc_final: 0.8509 (tp) REVERT: O 176 MET cc_start: 0.8156 (mmt) cc_final: 0.7210 (mmt) REVERT: O 261 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8510 (pp30) REVERT: O 265 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: O 323 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8775 (mm-40) REVERT: O 327 ASP cc_start: 0.9020 (m-30) cc_final: 0.8650 (m-30) REVERT: J 46 HIS cc_start: 0.7251 (m90) cc_final: 0.6820 (m170) REVERT: J 84 ILE cc_start: 0.7887 (tp) cc_final: 0.7650 (tp) REVERT: J 131 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9016 (mp) REVERT: J 241 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8219 (tp) REVERT: J 279 ASN cc_start: 0.8621 (m-40) cc_final: 0.8141 (t0) REVERT: B 46 HIS cc_start: 0.7230 (m170) cc_final: 0.6740 (m170) REVERT: B 66 ASN cc_start: 0.7688 (m-40) cc_final: 0.6956 (m110) REVERT: B 131 LEU cc_start: 0.9345 (tt) cc_final: 0.9084 (mm) REVERT: B 241 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8247 (tp) REVERT: G 46 HIS cc_start: 0.7615 (m170) cc_final: 0.7304 (m170) REVERT: G 69 ASP cc_start: 0.7922 (m-30) cc_final: 0.7234 (t70) REVERT: G 80 ASN cc_start: 0.6771 (m-40) cc_final: 0.5777 (t0) REVERT: G 127 PHE cc_start: 0.8170 (t80) cc_final: 0.7507 (t80) REVERT: G 241 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8167 (tp) REVERT: G 279 ASN cc_start: 0.8683 (t0) cc_final: 0.8292 (t0) REVERT: L 42 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8282 (mt) REVERT: L 69 ASP cc_start: 0.7985 (m-30) cc_final: 0.7349 (t70) REVERT: L 78 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8519 (mm) REVERT: L 110 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8301 (tt) REVERT: L 214 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7468 (mp0) REVERT: C 28 GLN cc_start: 0.8783 (mp10) cc_final: 0.8442 (mp10) REVERT: H 63 ASP cc_start: 0.6388 (p0) cc_final: 0.6104 (p0) REVERT: M 47 ARG cc_start: 0.8291 (mmm160) cc_final: 0.7919 (tpt-90) outliers start: 149 outliers final: 114 residues processed: 666 average time/residue: 0.4089 time to fit residues: 457.8629 Evaluate side-chains 664 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 530 time to evaluate : 3.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 62 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 85 ASN Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 297 ASP Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 224 THR Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain M residue 22 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 245 optimal weight: 7.9990 chunk 395 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 187 optimal weight: 0.7980 chunk 274 optimal weight: 0.0980 chunk 414 optimal weight: 0.8980 chunk 381 optimal weight: 2.9990 chunk 330 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 202 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 ASN ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 ASN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 206 ASN O 240 ASN O 249 GLN O 290 HIS ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34096 Z= 0.208 Angle : 0.656 17.286 46328 Z= 0.329 Chirality : 0.047 0.312 5220 Planarity : 0.004 0.047 5980 Dihedral : 6.342 58.923 5084 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.15 % Allowed : 18.62 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.39 (0.13), residues: 4240 helix: 0.53 (0.14), residues: 1472 sheet: -0.44 (0.17), residues: 896 loop : -0.68 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP K 20 HIS 0.009 0.001 HIS O 290 PHE 0.030 0.002 PHE G 68 TYR 0.018 0.001 TYR N 142 ARG 0.006 0.000 ARG I 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 532 time to evaluate : 4.358 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: P 12 ARG cc_start: 0.7959 (ttt180) cc_final: 0.7622 (ttt180) REVERT: P 54 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7322 (tptp) REVERT: P 63 ASP cc_start: 0.7313 (p0) cc_final: 0.7040 (p0) REVERT: P 64 ASN cc_start: 0.8563 (t0) cc_final: 0.8324 (t0) REVERT: P 69 GLU cc_start: 0.7168 (mp0) cc_final: 0.6819 (mp0) REVERT: D 228 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7615 (mtmm) REVERT: D 240 ASN cc_start: 0.7926 (t0) cc_final: 0.7484 (t0) REVERT: D 295 ILE cc_start: 0.9077 (mp) cc_final: 0.8578 (mt) REVERT: D 323 GLN cc_start: 0.8538 (mm-40) cc_final: 0.7986 (mm-40) REVERT: A 65 ASP cc_start: 0.8652 (p0) cc_final: 0.7935 (t0) REVERT: A 147 ASP cc_start: 0.8951 (p0) cc_final: 0.8606 (p0) REVERT: A 173 GLN cc_start: 0.8497 (mt0) cc_final: 0.8229 (mp10) REVERT: A 176 MET cc_start: 0.8714 (mmt) cc_final: 0.8051 (mmt) REVERT: A 268 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8285 (pp20) REVERT: A 302 MET cc_start: 0.7473 (ptp) cc_final: 0.6131 (ptp) REVERT: A 323 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8861 (mm-40) REVERT: A 327 ASP cc_start: 0.8989 (m-30) cc_final: 0.8532 (m-30) REVERT: E 196 ASP cc_start: 0.8676 (t0) cc_final: 0.8334 (t0) REVERT: E 240 ASN cc_start: 0.7838 (t0) cc_final: 0.7475 (t0) REVERT: E 246 PHE cc_start: 0.8447 (t80) cc_final: 0.7990 (t80) REVERT: E 295 ILE cc_start: 0.8690 (mm) cc_final: 0.8118 (mm) REVERT: E 297 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8493 (m-30) REVERT: E 323 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8250 (mm-40) REVERT: F 1 MET cc_start: 0.7849 (pmm) cc_final: 0.7258 (pmm) REVERT: F 20 TRP cc_start: 0.8440 (t60) cc_final: 0.7996 (t60) REVERT: F 65 ASP cc_start: 0.8503 (p0) cc_final: 0.7850 (t0) REVERT: F 176 MET cc_start: 0.8630 (mmt) cc_final: 0.7493 (mmt) REVERT: F 284 SER cc_start: 0.8865 (p) cc_final: 0.8565 (p) REVERT: F 302 MET cc_start: 0.7510 (ptp) cc_final: 0.6750 (ptp) REVERT: F 323 GLN cc_start: 0.9146 (mm110) cc_final: 0.8701 (mm-40) REVERT: F 327 ASP cc_start: 0.8719 (m-30) cc_final: 0.8378 (m-30) REVERT: I 142 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.6587 (p90) REVERT: I 228 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7755 (mtmm) REVERT: I 246 PHE cc_start: 0.8832 (t80) cc_final: 0.8587 (t80) REVERT: I 249 GLN cc_start: 0.7322 (tp40) cc_final: 0.7053 (tp40) REVERT: I 295 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8311 (mm) REVERT: I 314 TRP cc_start: 0.9345 (m100) cc_final: 0.8678 (m100) REVERT: K 17 MET cc_start: 0.8316 (tpt) cc_final: 0.7862 (tpt) REVERT: K 21 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9040 (mp) REVERT: K 65 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.7679 (t0) REVERT: K 176 MET cc_start: 0.8551 (mmt) cc_final: 0.7758 (mmt) REVERT: K 177 MET cc_start: 0.8984 (ppp) cc_final: 0.8773 (ppp) REVERT: K 226 GLN cc_start: 0.8795 (tp-100) cc_final: 0.8256 (mt0) REVERT: K 240 ASN cc_start: 0.8603 (t0) cc_final: 0.8326 (t0) REVERT: K 302 MET cc_start: 0.7356 (ptp) cc_final: 0.5923 (ptp) REVERT: K 323 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8835 (tt0) REVERT: N 52 MET cc_start: 0.7768 (tpt) cc_final: 0.7514 (tpt) REVERT: N 226 GLN cc_start: 0.8196 (tm-30) cc_final: 0.7958 (tm-30) REVERT: N 228 LYS cc_start: 0.8434 (mttt) cc_final: 0.8029 (mtmm) REVERT: N 240 ASN cc_start: 0.8040 (t0) cc_final: 0.7715 (t0) REVERT: N 295 ILE cc_start: 0.9125 (mp) cc_final: 0.8664 (mm) REVERT: N 297 ASP cc_start: 0.9000 (OUTLIER) cc_final: 0.8726 (m-30) REVERT: N 314 TRP cc_start: 0.9339 (m100) cc_final: 0.8393 (m100) REVERT: N 323 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8251 (mm-40) REVERT: O 17 MET cc_start: 0.8796 (tpt) cc_final: 0.8458 (tpt) REVERT: O 20 TRP cc_start: 0.8428 (t60) cc_final: 0.7492 (t60) REVERT: O 26 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.7980 (t0) REVERT: O 65 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8130 (t0) REVERT: O 93 ILE cc_start: 0.8776 (mm) cc_final: 0.8520 (tp) REVERT: O 176 MET cc_start: 0.8300 (mmt) cc_final: 0.7220 (mmt) REVERT: O 261 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8491 (pp30) REVERT: O 265 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: O 323 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8839 (mm-40) REVERT: O 327 ASP cc_start: 0.9021 (m-30) cc_final: 0.8635 (m-30) REVERT: J 46 HIS cc_start: 0.7182 (m90) cc_final: 0.6775 (m170) REVERT: J 84 ILE cc_start: 0.7909 (tp) cc_final: 0.7679 (tp) REVERT: J 131 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8971 (mp) REVERT: J 241 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8225 (tp) REVERT: J 279 ASN cc_start: 0.8621 (m-40) cc_final: 0.8131 (t0) REVERT: B 45 TYR cc_start: 0.7039 (m-80) cc_final: 0.6626 (m-80) REVERT: B 46 HIS cc_start: 0.7116 (m170) cc_final: 0.6584 (m170) REVERT: B 66 ASN cc_start: 0.7694 (m-40) cc_final: 0.6898 (m110) REVERT: B 131 LEU cc_start: 0.9361 (tt) cc_final: 0.9090 (mm) REVERT: B 241 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8264 (tp) REVERT: G 46 HIS cc_start: 0.7719 (m170) cc_final: 0.7340 (m170) REVERT: G 69 ASP cc_start: 0.8027 (m-30) cc_final: 0.7283 (t70) REVERT: G 80 ASN cc_start: 0.6819 (m-40) cc_final: 0.5819 (t0) REVERT: G 127 PHE cc_start: 0.8194 (t80) cc_final: 0.7716 (t80) REVERT: G 279 ASN cc_start: 0.8698 (t0) cc_final: 0.8334 (t0) REVERT: L 42 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8322 (mt) REVERT: L 69 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7306 (t70) REVERT: L 78 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8525 (mm) REVERT: L 110 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8253 (tp) REVERT: L 131 LEU cc_start: 0.9365 (tt) cc_final: 0.9019 (mp) REVERT: L 214 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7535 (mp0) REVERT: C 28 GLN cc_start: 0.8796 (mp10) cc_final: 0.8488 (mp10) REVERT: C 47 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7535 (tpp80) REVERT: H 63 ASP cc_start: 0.6423 (p0) cc_final: 0.6191 (p0) REVERT: M 47 ARG cc_start: 0.8303 (mmm160) cc_final: 0.7924 (tpt-90) outliers start: 147 outliers final: 118 residues processed: 628 average time/residue: 0.3954 time to fit residues: 417.3989 Evaluate side-chains 656 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 519 time to evaluate : 4.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain P residue 62 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 218 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 245 ASP Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 43 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 218 VAL Chi-restraints excluded: chain I residue 228 LYS Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain I residue 251 GLU Chi-restraints excluded: chain I residue 295 ILE Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 43 ASN Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 129 ASN Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 220 LEU Chi-restraints excluded: chain K residue 259 VAL Chi-restraints excluded: chain K residue 278 SER Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 137 VAL Chi-restraints excluded: chain N residue 218 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 245 ASP Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 297 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain O residue 22 GLN Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 244 VAL Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 110 ILE Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 162 ASN Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 204 MET Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 257 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 167 ASP Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 182 VAL Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 236 CYS Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 110 ILE Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 167 ASP Chi-restraints excluded: chain L residue 182 VAL Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 257 VAL Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain H residue 36 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 4.9990 chunk 351 optimal weight: 2.9990 chunk 101 optimal weight: 0.0470 chunk 304 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 330 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 339 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 GLN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 260 ASN ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 290 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 290 HIS ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.107269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.083149 restraints weight = 87056.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.085775 restraints weight = 46948.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.087422 restraints weight = 32144.600| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 34096 Z= 0.225 Angle : 0.671 17.389 46328 Z= 0.337 Chirality : 0.047 0.323 5220 Planarity : 0.004 0.047 5980 Dihedral : 6.443 59.903 5084 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.18 % Allowed : 18.71 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: -0.39 (0.13), residues: 4240 helix: 0.54 (0.14), residues: 1472 sheet: -0.46 (0.17), residues: 896 loop : -0.68 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.001 TRP K 20 HIS 0.011 0.001 HIS O 290 PHE 0.030 0.002 PHE G 68 TYR 0.019 0.001 TYR D 133 ARG 0.004 0.000 ARG I 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8618.67 seconds wall clock time: 154 minutes 7.73 seconds (9247.73 seconds total)