Starting phenix.real_space_refine on Mon Apr 15 02:23:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/04_2024/6gve_0071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/04_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_0071/04_2024/6gve_0071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/04_2024/6gve_0071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/04_2024/6gve_0071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/04_2024/6gve_0071_updated.pdb" } 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-5288/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: 16.86, per 1000 atoms: 0.50 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: 13.44 Conformation dependent library (CDL) restraints added in 6.6 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... running ksdssp... Secondary structure from input PDB file: 136 helices and 32 sheets defined 31.5% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.47 Creating SS restraints... Processing helix chain 'P' and resid 3 through 21 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 27 through 51 Processing helix chain 'P' and resid 57 through 63 removed outlier: 4.253A pdb=" N ASP P 62 " --> pdb=" O GLN P 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 22 Processing helix chain 'D' and resid 40 through 48 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 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 106 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 154 through 169 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 256 through 269 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 284 through 287 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 320 through 334 Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 40 through 48 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 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 106 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 154 through 169 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 256 through 269 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 284 through 287 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'E' and resid 11 through 22 Processing helix chain 'E' and resid 40 through 48 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 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 106 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 154 through 169 Proline residue: E 161 - end of helix Processing helix chain 'E' and resid 216 through 221 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 256 through 269 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 284 through 287 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 320 through 334 Processing helix chain 'F' and resid 11 through 22 Processing helix chain 'F' and resid 40 through 48 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 83 through 85 No H-bonds generated for 'chain 'F' and resid 83 through 85' Processing helix chain 'F' and resid 106 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 154 through 169 Proline residue: F 161 - end of helix Processing helix chain 'F' and resid 216 through 221 Processing helix chain 'F' and resid 223 through 225 No H-bonds generated for 'chain 'F' and resid 223 through 225' Processing helix chain 'F' and resid 256 through 269 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 284 through 287 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 320 through 334 Processing helix chain 'I' and resid 11 through 22 Processing helix chain 'I' and resid 40 through 48 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 83 through 85 No H-bonds generated for 'chain 'I' and resid 83 through 85' Processing helix chain 'I' and resid 106 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 154 through 169 Proline residue: I 161 - end of helix Processing helix chain 'I' and resid 216 through 221 Processing helix chain 'I' and resid 223 through 225 No H-bonds generated for 'chain 'I' and resid 223 through 225' Processing helix chain 'I' and resid 256 through 269 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 284 through 287 Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 320 through 334 Processing helix chain 'K' and resid 11 through 22 Processing helix chain 'K' and resid 40 through 48 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 83 through 85 No H-bonds generated for 'chain 'K' and resid 83 through 85' Processing helix chain 'K' and resid 106 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 154 through 169 Proline residue: K 161 - end of helix Processing helix chain 'K' and resid 216 through 221 Processing helix chain 'K' and resid 223 through 225 No H-bonds generated for 'chain 'K' and resid 223 through 225' Processing helix chain 'K' and resid 256 through 269 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 284 through 287 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 320 through 334 Processing helix chain 'N' and resid 11 through 22 Processing helix chain 'N' and resid 40 through 48 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 83 through 85 No H-bonds generated for 'chain 'N' and resid 83 through 85' Processing helix chain 'N' and resid 106 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 154 through 169 Proline residue: N 161 - end of helix Processing helix chain 'N' and resid 216 through 221 Processing helix chain 'N' and resid 223 through 225 No H-bonds generated for 'chain 'N' and resid 223 through 225' Processing helix chain 'N' and resid 256 through 269 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 284 through 287 Processing helix chain 'N' and resid 298 through 300 No H-bonds generated for 'chain 'N' and resid 298 through 300' Processing helix chain 'N' and resid 320 through 334 Processing helix chain 'O' and resid 11 through 22 Processing helix chain 'O' and resid 40 through 48 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 83 through 85 No H-bonds generated for 'chain 'O' and resid 83 through 85' Processing helix chain 'O' and resid 106 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 154 through 169 Proline residue: O 161 - end of helix Processing helix chain 'O' and resid 216 through 221 Processing helix chain 'O' and resid 223 through 225 No H-bonds generated for 'chain 'O' and resid 223 through 225' Processing helix chain 'O' and resid 256 through 269 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 284 through 287 Processing helix chain 'O' and resid 298 through 300 No H-bonds generated for 'chain 'O' and resid 298 through 300' Processing helix chain 'O' and resid 320 through 334 Processing helix chain 'J' and resid 23 through 31 Processing helix chain 'J' and resid 50 through 56 Processing helix chain 'J' and resid 68 through 79 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) Processing helix chain 'J' and resid 135 through 148 removed outlier: 3.519A pdb=" N LYS J 144 " --> pdb=" O ALA J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 171 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 175 No H-bonds generated for 'chain 'J' and resid 173 through 175' Processing helix chain 'J' and resid 268 through 274 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 287 through 293 Processing helix chain 'J' and resid 304 through 324 removed outlier: 3.572A pdb=" N VAL J 310 " --> pdb=" O GLY J 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 31 Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 68 through 79 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) Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.519A pdb=" N LYS B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 171 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 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 268 through 274 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 287 through 293 Processing helix chain 'B' and resid 304 through 324 removed outlier: 3.572A pdb=" N VAL B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 31 Processing helix chain 'G' and resid 50 through 56 Processing helix chain 'G' and resid 68 through 79 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) Processing helix chain 'G' and resid 135 through 148 removed outlier: 3.519A pdb=" N LYS G 144 " --> pdb=" O ALA G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 171 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 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 268 through 274 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 287 through 293 Processing helix chain 'G' and resid 304 through 324 removed outlier: 3.572A pdb=" N VAL G 310 " --> pdb=" O GLY G 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 31 Processing helix chain 'L' and resid 50 through 56 Processing helix chain 'L' and resid 68 through 79 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) Processing helix chain 'L' and resid 135 through 148 removed outlier: 3.519A pdb=" N LYS L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 171 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 175 No H-bonds generated for 'chain 'L' and resid 173 through 175' Processing helix chain 'L' and resid 268 through 274 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 287 through 293 Processing helix chain 'L' and resid 304 through 324 removed outlier: 3.572A pdb=" N VAL L 310 " --> pdb=" O GLY L 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 21 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 27 through 51 Processing helix chain 'C' and resid 57 through 63 removed outlier: 4.252A pdb=" N ASP C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 21 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 27 through 51 Processing helix chain 'H' and resid 57 through 63 removed outlier: 4.253A pdb=" N ASP H 62 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 21 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 27 through 51 Processing helix chain 'M' and resid 57 through 63 removed outlier: 4.253A pdb=" N ASP M 62 " --> pdb=" O GLN M 58 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL D 120 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN D 151 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE D 122 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 95 " --> pdb=" O ARG D 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE D 6 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE D 34 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA D 74 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE D 34 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS D 76 " --> pdb=" O ILE D 34 " (cutoff:3.500A) Processing sheet with id= B, 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: 9.189A pdb=" N ASN D 230 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY D 175 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE D 232 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET D 177 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU D 234 " --> pdb=" O MET D 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR D 179 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL D 236 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS D 181 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN D 249 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY D 175 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 247 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET D 177 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP D 245 " --> pdb=" O MET D 177 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR D 179 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL D 243 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N HIS D 181 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL D 241 " --> pdb=" O HIS D 181 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 275 through 278 removed outlier: 6.259A pdb=" N SER D 294 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER D 278 " --> pdb=" O SER D 294 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU D 296 " --> pdb=" O SER D 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL A 120 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN A 151 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 122 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 95 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE A 6 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE A 34 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA A 74 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE A 34 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS A 76 " --> pdb=" O ILE A 34 " (cutoff:3.500A) Processing sheet with id= E, 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: 9.189A pdb=" N ASN A 230 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY A 175 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE A 232 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET A 177 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU A 234 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR A 179 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL A 236 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS A 181 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN A 249 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY A 175 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 247 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET A 177 " --> pdb=" O ASP A 245 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP A 245 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR A 179 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 243 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS A 181 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A 241 " --> pdb=" O HIS A 181 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 275 through 278 removed outlier: 6.258A pdb=" N SER A 294 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER A 278 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A 296 " --> pdb=" O SER A 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL E 120 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN E 151 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE E 122 " --> pdb=" O ASN E 151 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 95 " --> pdb=" O ARG E 3 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE E 6 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE E 34 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ALA E 74 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE E 34 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS E 76 " --> pdb=" O ILE E 34 " (cutoff:3.500A) Processing sheet with id= H, 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: 9.190A pdb=" N ASN E 230 " --> pdb=" O GLN E 173 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY E 175 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ILE E 232 " --> pdb=" O GLY E 175 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N MET E 177 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU E 234 " --> pdb=" O MET E 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR E 179 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL E 236 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS E 181 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN E 249 " --> pdb=" O GLN E 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY E 175 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL E 247 " --> pdb=" O GLY E 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET E 177 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP E 245 " --> pdb=" O MET E 177 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR E 179 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL E 243 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS E 181 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL E 241 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 275 through 278 removed outlier: 6.259A pdb=" N SER E 294 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER E 278 " --> pdb=" O SER E 294 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU E 296 " --> pdb=" O SER E 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'F' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL F 120 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN F 151 " --> pdb=" O VAL F 120 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE F 122 " --> pdb=" O ASN F 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU F 95 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE F 6 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE F 34 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA F 74 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE F 34 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS F 76 " --> pdb=" O ILE F 34 " (cutoff:3.500A) Processing sheet with id= K, 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: 9.190A pdb=" N ASN F 230 " --> pdb=" O GLN F 173 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY F 175 " --> pdb=" O ASN F 230 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE F 232 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET F 177 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU F 234 " --> pdb=" O MET F 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR F 179 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL F 236 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS F 181 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN F 249 " --> pdb=" O GLN F 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY F 175 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL F 247 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET F 177 " --> pdb=" O ASP F 245 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP F 245 " --> pdb=" O MET F 177 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR F 179 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL F 243 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS F 181 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL F 241 " --> pdb=" O HIS F 181 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 275 through 278 removed outlier: 6.258A pdb=" N SER F 294 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N SER F 278 " --> pdb=" O SER F 294 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU F 296 " --> pdb=" O SER F 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'I' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL I 120 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN I 151 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE I 122 " --> pdb=" O ASN I 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU I 95 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE I 6 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE I 34 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ALA I 74 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE I 34 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS I 76 " --> pdb=" O ILE I 34 " (cutoff:3.500A) Processing sheet with id= N, 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: 9.189A pdb=" N ASN I 230 " --> pdb=" O GLN I 173 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY I 175 " --> pdb=" O ASN I 230 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE I 232 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET I 177 " --> pdb=" O ILE I 232 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU I 234 " --> pdb=" O MET I 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR I 179 " --> pdb=" O LEU I 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL I 236 " --> pdb=" O THR I 179 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS I 181 " --> pdb=" O VAL I 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN I 249 " --> pdb=" O GLN I 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY I 175 " --> pdb=" O VAL I 247 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL I 247 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET I 177 " --> pdb=" O ASP I 245 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP I 245 " --> pdb=" O MET I 177 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR I 179 " --> pdb=" O VAL I 243 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL I 243 " --> pdb=" O THR I 179 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS I 181 " --> pdb=" O VAL I 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL I 241 " --> pdb=" O HIS I 181 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 275 through 278 removed outlier: 6.258A pdb=" N SER I 294 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER I 278 " --> pdb=" O SER I 294 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU I 296 " --> pdb=" O SER I 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'K' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL K 120 " --> pdb=" O VAL K 149 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN K 151 " --> pdb=" O VAL K 120 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE K 122 " --> pdb=" O ASN K 151 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU K 95 " --> pdb=" O ARG K 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE K 6 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE K 34 " --> pdb=" O ILE K 6 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ALA K 74 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE K 34 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS K 76 " --> pdb=" O ILE K 34 " (cutoff:3.500A) Processing sheet with id= Q, 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: 9.190A pdb=" N ASN K 230 " --> pdb=" O GLN K 173 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY K 175 " --> pdb=" O ASN K 230 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ILE K 232 " --> pdb=" O GLY K 175 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET K 177 " --> pdb=" O ILE K 232 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU K 234 " --> pdb=" O MET K 177 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR K 179 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL K 236 " --> pdb=" O THR K 179 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS K 181 " --> pdb=" O VAL K 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN K 249 " --> pdb=" O GLN K 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY K 175 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL K 247 " --> pdb=" O GLY K 175 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET K 177 " --> pdb=" O ASP K 245 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP K 245 " --> pdb=" O MET K 177 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR K 179 " --> pdb=" O VAL K 243 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL K 243 " --> pdb=" O THR K 179 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS K 181 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL K 241 " --> pdb=" O HIS K 181 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'K' and resid 275 through 278 removed outlier: 6.258A pdb=" N SER K 294 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER K 278 " --> pdb=" O SER K 294 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU K 296 " --> pdb=" O SER K 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'N' and resid 148 through 151 removed outlier: 6.267A pdb=" N VAL N 120 " --> pdb=" O VAL N 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN N 151 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE N 122 " --> pdb=" O ASN N 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU N 95 " --> pdb=" O ARG N 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE N 6 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE N 34 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA N 74 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE N 34 " --> pdb=" O ALA N 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS N 76 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing sheet with id= T, 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: 9.189A pdb=" N ASN N 230 " --> pdb=" O GLN N 173 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY N 175 " --> pdb=" O ASN N 230 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ILE N 232 " --> pdb=" O GLY N 175 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET N 177 " --> pdb=" O ILE N 232 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU N 234 " --> pdb=" O MET N 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR N 179 " --> pdb=" O LEU N 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL N 236 " --> pdb=" O THR N 179 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS N 181 " --> pdb=" O VAL N 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN N 249 " --> pdb=" O GLN N 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY N 175 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL N 247 " --> pdb=" O GLY N 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET N 177 " --> pdb=" O ASP N 245 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP N 245 " --> pdb=" O MET N 177 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR N 179 " --> pdb=" O VAL N 243 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL N 243 " --> pdb=" O THR N 179 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS N 181 " --> pdb=" O VAL N 241 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL N 241 " --> pdb=" O HIS N 181 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'N' and resid 275 through 278 removed outlier: 6.258A pdb=" N SER N 294 " --> pdb=" O HIS N 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER N 278 " --> pdb=" O SER N 294 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU N 296 " --> pdb=" O SER N 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'O' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL O 120 " --> pdb=" O VAL O 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN O 151 " --> pdb=" O VAL O 120 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE O 122 " --> pdb=" O ASN O 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU O 95 " --> pdb=" O ARG O 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE O 6 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE O 34 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ALA O 74 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE O 34 " --> pdb=" O ALA O 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS O 76 " --> pdb=" O ILE O 34 " (cutoff:3.500A) Processing sheet with id= W, 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: 9.189A pdb=" N ASN O 230 " --> pdb=" O GLN O 173 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY O 175 " --> pdb=" O ASN O 230 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE O 232 " --> pdb=" O GLY O 175 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET O 177 " --> pdb=" O ILE O 232 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU O 234 " --> pdb=" O MET O 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR O 179 " --> pdb=" O LEU O 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL O 236 " --> pdb=" O THR O 179 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS O 181 " --> pdb=" O VAL O 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN O 249 " --> pdb=" O GLN O 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY O 175 " --> pdb=" O VAL O 247 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL O 247 " --> pdb=" O GLY O 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET O 177 " --> pdb=" O ASP O 245 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP O 245 " --> pdb=" O MET O 177 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR O 179 " --> pdb=" O VAL O 243 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL O 243 " --> pdb=" O THR O 179 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS O 181 " --> pdb=" O VAL O 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL O 241 " --> pdb=" O HIS O 181 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 275 through 278 removed outlier: 6.258A pdb=" N SER O 294 " --> pdb=" O HIS O 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER O 278 " --> pdb=" O SER O 294 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU O 296 " --> pdb=" O SER O 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'J' and resid 107 through 112 removed outlier: 6.169A pdb=" N VAL J 9 " --> pdb=" O ILE J 108 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE J 110 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE J 11 " --> pdb=" O ILE J 110 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY J 112 " --> pdb=" O ILE J 11 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL J 13 " --> pdb=" O GLY J 112 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE J 127 " --> pdb=" O GLY J 12 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ALA J 14 " --> pdb=" O PHE J 127 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL J 129 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL J 181 " --> pdb=" O TYR J 130 " (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= Z, first strand: chain 'J' and resid 84 through 86 Processing sheet with id= AA, first strand: chain 'B' and resid 107 through 112 removed outlier: 6.169A pdb=" N VAL B 9 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE B 110 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE B 11 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLY B 112 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 13 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE B 127 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ALA B 14 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 129 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL B 181 " --> pdb=" O TYR B 130 " (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= AB, first strand: chain 'B' and resid 84 through 86 Processing sheet with id= AC, first strand: chain 'G' and resid 107 through 112 removed outlier: 6.169A pdb=" N VAL G 9 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE G 110 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE G 11 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY G 112 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 13 " --> pdb=" O GLY G 112 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE G 127 " --> pdb=" O GLY G 12 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ALA G 14 " --> pdb=" O PHE G 127 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL G 129 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL G 181 " --> pdb=" O TYR G 130 " (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= AD, first strand: chain 'G' and resid 84 through 86 Processing sheet with id= AE, first strand: chain 'L' and resid 107 through 112 removed outlier: 6.169A pdb=" N VAL L 9 " --> pdb=" O ILE L 108 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE L 110 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE L 11 " --> pdb=" O ILE L 110 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY L 112 " --> pdb=" O ILE L 11 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL L 13 " --> pdb=" O GLY L 112 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE L 127 " --> pdb=" O GLY L 12 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ALA L 14 " --> pdb=" O PHE L 127 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL L 129 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL L 181 " --> pdb=" O TYR L 130 " (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= AF, first strand: chain 'L' and resid 84 through 86 1016 hydrogen bonds defined for protein. 2916 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: 11.89 Time building geometry restraints manager: 14.54 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: 1223 2.69 - 3.24: 32240 3.24 - 3.79: 56680 3.79 - 4.35: 70432 4.35 - 4.90: 116484 Nonbonded interactions: 277059 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 277054 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 11.030 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 88.670 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.390 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: 109.100 ------------------------------------------------------------------------------- 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= 0.632 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 : 3.769 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: 0.4875 time to fit residues: 785.5159 Evaluate side-chains 577 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 573 time to evaluate : 4.002 ------------------------------------------------------------------------------- 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: 2.9990 chunk 174 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 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: 0.9990 chunk 242 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 181 HIS ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN F 45 HIS F 181 HIS ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 ASN I 173 GLN I 181 HIS I 240 ASN K 7 ASN K 15 ASN K 45 HIS K 173 GLN K 181 HIS K 187 GLN K 276 HIS K 290 HIS ** K 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** O 331 HIS J 90 ASN ** 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 ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN G 206 GLN L 90 ASN 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: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2489 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= 0.197 Angle : 0.584 8.065 46328 Z= 0.302 Chirality : 0.046 0.162 5220 Planarity : 0.005 0.054 5980 Dihedral : 7.245 59.814 5084 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.82 % Allowed : 11.17 % Favored : 86.00 % 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 (0.12), residues: 4240 helix: -1.04 (0.13), residues: 1440 sheet: -1.99 (0.16), residues: 888 loop : -1.65 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 20 HIS 0.010 0.001 HIS J 46 PHE 0.020 0.002 PHE L 68 TYR 0.020 0.002 TYR F 321 ARG 0.006 0.000 ARG D 81 *********************** 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 799 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 699 time to evaluate : 4.166 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: P 12 ARG cc_start: 0.7656 (ttt180) cc_final: 0.7405 (ttt180) REVERT: P 54 LYS cc_start: 0.7682 (pmmt) cc_final: 0.7154 (tptp) REVERT: P 63 ASP cc_start: 0.6483 (p0) cc_final: 0.6174 (p0) REVERT: D 52 MET cc_start: 0.7943 (tpp) cc_final: 0.7279 (tpt) REVERT: D 173 GLN cc_start: 0.8542 (mt0) cc_final: 0.8220 (mp10) REVERT: D 176 MET cc_start: 0.7560 (mmm) cc_final: 0.6956 (mmm) REVERT: D 177 MET cc_start: 0.8250 (ppp) cc_final: 0.7917 (ttp) REVERT: D 179 THR cc_start: 0.7947 (t) cc_final: 0.7711 (t) REVERT: D 249 GLN cc_start: 0.7735 (tt0) cc_final: 0.6791 (tt0) REVERT: D 285 SER cc_start: 0.8481 (t) cc_final: 0.8195 (t) REVERT: D 295 ILE cc_start: 0.9103 (mp) cc_final: 0.8626 (mt) REVERT: D 323 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8160 (mm-40) REVERT: A 49 TYR cc_start: 0.8528 (m-80) cc_final: 0.8092 (m-10) REVERT: A 67 CYS cc_start: 0.8445 (m) cc_final: 0.7825 (t) REVERT: A 85 ASN cc_start: 0.8907 (m-40) cc_final: 0.8658 (m110) REVERT: A 93 ILE cc_start: 0.8837 (mm) cc_final: 0.8304 (tp) REVERT: A 147 ASP cc_start: 0.8616 (p0) cc_final: 0.8151 (p0) REVERT: A 173 GLN cc_start: 0.8673 (mt0) cc_final: 0.8320 (mm-40) REVERT: A 176 MET cc_start: 0.8495 (mmt) cc_final: 0.8228 (mmt) REVERT: A 216 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8363 (mtpt) REVERT: A 268 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8294 (pp20) REVERT: A 302 MET cc_start: 0.7407 (ptp) cc_final: 0.7025 (ptp) REVERT: A 327 ASP cc_start: 0.8968 (m-30) cc_final: 0.8620 (m-30) REVERT: A 332 MET cc_start: 0.8527 (ttm) cc_final: 0.8017 (tmm) REVERT: E 95 LEU cc_start: 0.9158 (tp) cc_final: 0.8942 (mm) REVERT: E 188 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7504 (mmm-85) REVERT: E 196 ASP cc_start: 0.8487 (t0) cc_final: 0.8080 (t0) REVERT: E 205 MET cc_start: 0.8290 (mtp) cc_final: 0.7936 (mtp) REVERT: E 295 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8184 (mm) REVERT: E 302 MET cc_start: 0.8240 (ptp) cc_final: 0.7937 (ptp) REVERT: E 323 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8190 (mm-40) REVERT: F 1 MET cc_start: 0.7927 (pmm) cc_final: 0.7683 (pmm) REVERT: F 16 PHE cc_start: 0.9274 (t80) cc_final: 0.8967 (t80) REVERT: F 20 TRP cc_start: 0.8468 (t60) cc_final: 0.7936 (t60) REVERT: F 40 PRO cc_start: 0.9063 (Cg_exo) cc_final: 0.8789 (Cg_endo) REVERT: F 52 MET cc_start: 0.8103 (mmm) cc_final: 0.7809 (mmm) REVERT: F 65 ASP cc_start: 0.8634 (p0) cc_final: 0.7389 (t0) REVERT: F 67 CYS cc_start: 0.8400 (m) cc_final: 0.7850 (p) REVERT: F 69 TYR cc_start: 0.8650 (m-80) cc_final: 0.8447 (m-80) REVERT: F 173 GLN cc_start: 0.8687 (mt0) cc_final: 0.8268 (mm-40) REVERT: F 176 MET cc_start: 0.8670 (mmt) cc_final: 0.8326 (mmt) REVERT: F 261 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8595 (pp30) REVERT: F 284 SER cc_start: 0.8815 (p) cc_final: 0.8312 (m) REVERT: F 302 MET cc_start: 0.7287 (ptp) cc_final: 0.6679 (ptp) REVERT: F 323 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8903 (mm-40) REVERT: F 327 ASP cc_start: 0.8724 (m-30) cc_final: 0.8275 (m-30) REVERT: I 173 GLN cc_start: 0.8642 (mt0) cc_final: 0.8025 (mp10) REVERT: I 249 GLN cc_start: 0.7791 (tt0) cc_final: 0.6926 (tt0) REVERT: K 20 TRP cc_start: 0.8429 (t60) cc_final: 0.7934 (t60) REVERT: K 49 TYR cc_start: 0.8708 (m-80) cc_final: 0.8489 (m-10) REVERT: K 93 ILE cc_start: 0.8810 (mm) cc_final: 0.8471 (tp) REVERT: K 176 MET cc_start: 0.8459 (mmt) cc_final: 0.8155 (mmt) REVERT: K 207 ILE cc_start: 0.9169 (mt) cc_final: 0.8811 (mp) REVERT: K 240 ASN cc_start: 0.8200 (t0) cc_final: 0.7973 (t0) REVERT: K 246 PHE cc_start: 0.9033 (t80) cc_final: 0.8760 (t80) REVERT: K 284 SER cc_start: 0.8945 (p) cc_final: 0.8497 (m) REVERT: K 302 MET cc_start: 0.7277 (ptp) cc_final: 0.6118 (ptp) REVERT: K 318 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8172 (mt-10) REVERT: K 323 GLN cc_start: 0.9225 (mm-40) cc_final: 0.8562 (mt0) REVERT: K 327 ASP cc_start: 0.8712 (m-30) cc_final: 0.8427 (m-30) REVERT: N 55 ILE cc_start: 0.8827 (mt) cc_final: 0.8569 (mt) REVERT: N 142 TYR cc_start: 0.7218 (p90) cc_final: 0.6754 (p90) REVERT: N 177 MET cc_start: 0.7782 (ttp) cc_final: 0.7570 (ttp) REVERT: N 196 ASP cc_start: 0.8534 (t0) cc_final: 0.8154 (t0) REVERT: N 228 LYS cc_start: 0.8739 (mttt) cc_final: 0.8347 (mtmm) REVERT: N 240 ASN cc_start: 0.8156 (t0) cc_final: 0.7557 (t0) REVERT: N 295 ILE cc_start: 0.9095 (mp) cc_final: 0.8568 (mt) REVERT: N 323 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8233 (mm-40) REVERT: O 17 MET cc_start: 0.8786 (tpt) cc_final: 0.8501 (tpt) REVERT: O 20 TRP cc_start: 0.8413 (t60) cc_final: 0.7561 (t60) REVERT: O 93 ILE cc_start: 0.8910 (mm) cc_final: 0.8676 (tp) REVERT: O 129 ASN cc_start: 0.8039 (m-40) cc_final: 0.7819 (p0) REVERT: O 159 LEU cc_start: 0.8872 (tp) cc_final: 0.8600 (tp) REVERT: O 174 GLN cc_start: 0.8522 (mm110) cc_final: 0.7351 (mm110) REVERT: O 176 MET cc_start: 0.8463 (mmt) cc_final: 0.7425 (mmt) REVERT: O 249 GLN cc_start: 0.8578 (tt0) cc_final: 0.8278 (tm-30) REVERT: O 284 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8393 (m) REVERT: O 323 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8727 (mt0) REVERT: O 327 ASP cc_start: 0.9065 (m-30) cc_final: 0.8658 (m-30) REVERT: J 46 HIS cc_start: 0.7450 (m170) cc_final: 0.7232 (m170) REVERT: J 156 ASP cc_start: 0.7937 (t0) cc_final: 0.7263 (t0) REVERT: B 116 LEU cc_start: 0.8958 (tp) cc_final: 0.8617 (tt) REVERT: B 180 ASP cc_start: 0.7570 (m-30) cc_final: 0.7143 (m-30) REVERT: B 204 MET cc_start: 0.8223 (ptm) cc_final: 0.8007 (ptm) REVERT: B 270 LEU cc_start: 0.9436 (OUTLIER) cc_final: 0.9190 (tt) REVERT: B 279 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8424 (t0) REVERT: G 127 PHE cc_start: 0.8235 (t80) cc_final: 0.7533 (t80) REVERT: L 279 ASN cc_start: 0.8993 (OUTLIER) cc_final: 0.8395 (t0) REVERT: L 309 GLN cc_start: 0.8840 (mt0) cc_final: 0.8286 (mp10) REVERT: C 28 GLN cc_start: 0.8849 (mp-120) cc_final: 0.8506 (mp10) REVERT: C 54 LYS cc_start: 0.7109 (pmmt) cc_final: 0.6717 (tptp) REVERT: C 63 ASP cc_start: 0.6827 (p0) cc_final: 0.6521 (p0) REVERT: H 28 GLN cc_start: 0.8359 (mp-120) cc_final: 0.7918 (mt0) REVERT: M 12 ARG cc_start: 0.7557 (ttt180) cc_final: 0.7328 (ttt180) REVERT: M 28 GLN cc_start: 0.8317 (mp-120) cc_final: 0.7687 (tm-30) REVERT: M 42 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8280 (mm-30) outliers start: 100 outliers final: 70 residues processed: 757 average time/residue: 0.4523 time to fit residues: 581.0670 Evaluate side-chains 633 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 557 time to evaluate : 3.833 ------------------------------------------------------------------------------- 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 149 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 245 ASP 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 216 LYS 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 282 LEU Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain E residue 325 VAL 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 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 228 LYS Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain I residue 325 VAL 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 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 232 ILE Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 39 ASP 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 162 ASN Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain B residue 28 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 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 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 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 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 288 VAL 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: 9.9990 chunk 314 optimal weight: 6.9990 chunk 257 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 378 optimal weight: 0.1980 chunk 408 optimal weight: 4.9990 chunk 337 optimal weight: 10.0000 chunk 375 optimal weight: 0.0370 chunk 129 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 overall best weight: 1.6464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN E 173 GLN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 GLN ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 15 ASN O 187 GLN O 249 GLN ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN ** 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 279 ASN G 309 GLN L 106 HIS L 206 GLN L 279 ASN ** L 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34096 Z= 0.225 Angle : 0.576 12.298 46328 Z= 0.294 Chirality : 0.046 0.240 5220 Planarity : 0.004 0.055 5980 Dihedral : 6.932 58.970 5084 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.01 % Allowed : 12.95 % Favored : 83.04 % 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: -1.67 (0.12), residues: 4240 helix: -0.30 (0.14), residues: 1432 sheet: -1.66 (0.17), residues: 872 loop : -1.36 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP P 33 HIS 0.016 0.001 HIS O 290 PHE 0.019 0.001 PHE B 127 TYR 0.014 0.002 TYR F 321 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 736 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 594 time to evaluate : 4.144 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: P 12 ARG cc_start: 0.7501 (ttt180) cc_final: 0.7295 (ttt180) REVERT: P 54 LYS cc_start: 0.7932 (pmmt) cc_final: 0.7420 (tptp) REVERT: P 63 ASP cc_start: 0.6758 (p0) cc_final: 0.6453 (p0) REVERT: D 142 TYR cc_start: 0.7573 (p90) cc_final: 0.7269 (p90) REVERT: D 173 GLN cc_start: 0.8679 (mt0) cc_final: 0.8170 (mp10) REVERT: D 176 MET cc_start: 0.7589 (mmm) cc_final: 0.7347 (mmm) REVERT: D 177 MET cc_start: 0.8256 (ppp) cc_final: 0.7953 (ttp) REVERT: D 179 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7823 (t) REVERT: D 249 GLN cc_start: 0.7780 (tt0) cc_final: 0.6759 (tt0) REVERT: D 285 SER cc_start: 0.8752 (t) cc_final: 0.8434 (t) REVERT: D 295 ILE cc_start: 0.9083 (mp) cc_final: 0.8532 (mt) REVERT: D 323 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8150 (mm-40) REVERT: A 20 TRP cc_start: 0.8434 (t60) cc_final: 0.7709 (t60) REVERT: A 67 CYS cc_start: 0.8395 (m) cc_final: 0.7815 (t) REVERT: A 85 ASN cc_start: 0.8937 (m-40) cc_final: 0.8636 (m110) REVERT: A 147 ASP cc_start: 0.8724 (p0) cc_final: 0.8277 (p0) REVERT: A 173 GLN cc_start: 0.8683 (mt0) cc_final: 0.8197 (mm-40) REVERT: A 268 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8241 (pp20) REVERT: A 284 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8284 (m) REVERT: A 327 ASP cc_start: 0.9018 (m-30) cc_final: 0.8616 (m-30) REVERT: E 177 MET cc_start: 0.8101 (ttp) cc_final: 0.7729 (ttp) REVERT: E 182 SER cc_start: 0.9044 (p) cc_final: 0.8805 (t) REVERT: E 196 ASP cc_start: 0.8557 (t0) cc_final: 0.8194 (t0) REVERT: E 228 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8155 (mtmm) REVERT: E 295 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8180 (mm) REVERT: E 302 MET cc_start: 0.8252 (ptp) cc_final: 0.7858 (ptp) REVERT: E 323 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8211 (mm-40) REVERT: F 3 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7176 (ttm-80) REVERT: F 20 TRP cc_start: 0.8526 (t60) cc_final: 0.7918 (t60) REVERT: F 65 ASP cc_start: 0.8606 (p0) cc_final: 0.7548 (t0) REVERT: F 67 CYS cc_start: 0.8417 (m) cc_final: 0.7903 (p) REVERT: F 69 TYR cc_start: 0.8795 (m-80) cc_final: 0.8541 (m-80) REVERT: F 176 MET cc_start: 0.8553 (mmt) cc_final: 0.8282 (mmt) REVERT: F 284 SER cc_start: 0.8808 (p) cc_final: 0.8343 (m) REVERT: F 323 GLN cc_start: 0.9257 (mm-40) cc_final: 0.8903 (mm-40) REVERT: F 327 ASP cc_start: 0.8700 (m-30) cc_final: 0.8312 (m-30) REVERT: I 57 GLN cc_start: 0.7976 (pp30) cc_final: 0.7025 (pp30) REVERT: I 142 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6937 (p90) REVERT: I 173 GLN cc_start: 0.8657 (mt0) cc_final: 0.8198 (mp10) REVERT: I 249 GLN cc_start: 0.7747 (tt0) cc_final: 0.6752 (tt0) REVERT: I 295 ILE cc_start: 0.8509 (mm) cc_final: 0.8307 (mm) REVERT: K 17 MET cc_start: 0.8964 (tpt) cc_final: 0.8720 (tpt) REVERT: K 20 TRP cc_start: 0.8322 (t60) cc_final: 0.8051 (t60) REVERT: K 93 ILE cc_start: 0.8826 (mm) cc_final: 0.8561 (tp) REVERT: K 147 ASP cc_start: 0.8541 (p0) cc_final: 0.8302 (p0) REVERT: K 173 GLN cc_start: 0.8467 (mt0) cc_final: 0.8247 (mp10) REVERT: K 176 MET cc_start: 0.8456 (mmt) cc_final: 0.8111 (mmt) REVERT: K 207 ILE cc_start: 0.9132 (mt) cc_final: 0.8783 (mp) REVERT: K 246 PHE cc_start: 0.9103 (t80) cc_final: 0.8834 (t80) REVERT: K 261 GLN cc_start: 0.8515 (tt0) cc_final: 0.8216 (pp30) REVERT: K 284 SER cc_start: 0.8952 (p) cc_final: 0.8504 (m) REVERT: K 302 MET cc_start: 0.7143 (ptp) cc_final: 0.6252 (ptp) REVERT: K 318 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8071 (mt-10) REVERT: K 323 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8631 (mt0) REVERT: K 327 ASP cc_start: 0.8790 (m-30) cc_final: 0.8553 (m-30) REVERT: N 228 LYS cc_start: 0.8665 (mttt) cc_final: 0.8248 (mtmm) REVERT: N 240 ASN cc_start: 0.8156 (t0) cc_final: 0.7811 (t0) REVERT: N 295 ILE cc_start: 0.9116 (mp) cc_final: 0.8613 (mm) REVERT: N 297 ASP cc_start: 0.9325 (OUTLIER) cc_final: 0.8860 (m-30) REVERT: N 323 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8314 (mm-40) REVERT: O 17 MET cc_start: 0.8905 (tpt) cc_final: 0.8666 (tpt) REVERT: O 20 TRP cc_start: 0.8478 (t60) cc_final: 0.7570 (t60) REVERT: O 65 ASP cc_start: 0.8823 (OUTLIER) cc_final: 0.7545 (t0) REVERT: O 93 ILE cc_start: 0.8888 (mm) cc_final: 0.8680 (tp) REVERT: O 176 MET cc_start: 0.8482 (mmt) cc_final: 0.7359 (mmt) REVERT: O 249 GLN cc_start: 0.8601 (tt0) cc_final: 0.8319 (tm-30) REVERT: O 284 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8323 (m) REVERT: O 323 GLN cc_start: 0.9235 (mm-40) cc_final: 0.8951 (mm-40) REVERT: O 327 ASP cc_start: 0.9005 (m-30) cc_final: 0.8674 (m-30) REVERT: J 46 HIS cc_start: 0.7515 (m170) cc_final: 0.7286 (m170) REVERT: B 204 MET cc_start: 0.8148 (ptm) cc_final: 0.7891 (ptm) REVERT: B 279 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8375 (t0) REVERT: G 46 HIS cc_start: 0.7583 (m-70) cc_final: 0.7238 (m-70) REVERT: G 127 PHE cc_start: 0.8236 (t80) cc_final: 0.7556 (t80) REVERT: G 279 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8407 (t0) REVERT: L 279 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8334 (t0) REVERT: L 309 GLN cc_start: 0.8844 (mt0) cc_final: 0.8205 (mp10) REVERT: C 28 GLN cc_start: 0.8925 (mp-120) cc_final: 0.8516 (mp10) REVERT: C 54 LYS cc_start: 0.7594 (pmmt) cc_final: 0.6863 (tptp) REVERT: C 63 ASP cc_start: 0.6938 (p0) cc_final: 0.6677 (p0) REVERT: H 28 GLN cc_start: 0.8497 (mp-120) cc_final: 0.8006 (mt0) REVERT: H 63 ASP cc_start: 0.6437 (p0) cc_final: 0.6122 (p0) REVERT: M 28 GLN cc_start: 0.8300 (mp-120) cc_final: 0.7653 (tm-30) REVERT: M 46 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8160 (pt0) REVERT: M 54 LYS cc_start: 0.7495 (pmmt) cc_final: 0.7247 (tptp) outliers start: 142 outliers final: 92 residues processed: 683 average time/residue: 0.4332 time to fit residues: 491.3376 Evaluate side-chains 627 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 523 time to evaluate : 4.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 228 LYS 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 39 ASP 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 208 VAL Chi-restraints excluded: chain E residue 228 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 282 LEU 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 245 ASP 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 228 LYS Chi-restraints excluded: chain I residue 245 ASP 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 259 VAL Chi-restraints excluded: chain K residue 286 ASP 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 245 ASP Chi-restraints excluded: chain N residue 297 ASP Chi-restraints excluded: chain N residue 325 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 220 LEU 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 286 ASP Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 78 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 204 MET Chi-restraints excluded: chain J residue 216 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 67 ASN 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 257 VAL Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 70 LEU 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 225 ILE Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 279 ASN Chi-restraints excluded: chain G residue 288 VAL 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 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 Chi-restraints excluded: chain M residue 46 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 373 optimal weight: 9.9990 chunk 284 optimal weight: 0.2980 chunk 196 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 254 optimal weight: 0.6980 chunk 379 optimal weight: 0.9990 chunk 402 optimal weight: 10.0000 chunk 198 optimal weight: 6.9990 chunk 359 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 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 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 249 GLN O 290 HIS ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN J 206 GLN B 279 ASN L 106 HIS L 279 ASN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3386 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= 0.171 Angle : 0.558 10.939 46328 Z= 0.280 Chirality : 0.045 0.223 5220 Planarity : 0.004 0.056 5980 Dihedral : 6.540 59.824 5084 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.06 % Allowed : 14.67 % Favored : 81.26 % 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: -1.27 (0.13), residues: 4240 helix: 0.06 (0.14), residues: 1452 sheet: -1.38 (0.17), residues: 872 loop : -1.18 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 20 HIS 0.005 0.001 HIS P 16 PHE 0.021 0.001 PHE J 127 TYR 0.017 0.001 TYR K 49 ARG 0.004 0.000 ARG M 47 *********************** 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 741 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 597 time to evaluate : 3.709 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: P 54 LYS cc_start: 0.7934 (pmmt) cc_final: 0.7330 (tptp) REVERT: P 63 ASP cc_start: 0.6968 (p0) cc_final: 0.6618 (p0) REVERT: D 142 TYR cc_start: 0.7636 (p90) cc_final: 0.7415 (p90) REVERT: D 173 GLN cc_start: 0.8689 (mt0) cc_final: 0.8130 (mp10) REVERT: D 176 MET cc_start: 0.7556 (mmm) cc_final: 0.7279 (mmm) REVERT: D 177 MET cc_start: 0.8174 (ppp) cc_final: 0.7877 (ttp) REVERT: D 179 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7704 (t) REVERT: D 249 GLN cc_start: 0.7786 (tt0) cc_final: 0.6751 (tt0) REVERT: D 271 MET cc_start: 0.8363 (mmt) cc_final: 0.8090 (mmm) REVERT: D 284 SER cc_start: 0.8722 (p) cc_final: 0.8008 (m) REVERT: D 285 SER cc_start: 0.8710 (t) cc_final: 0.7935 (t) REVERT: D 295 ILE cc_start: 0.9014 (mp) cc_final: 0.8646 (mt) REVERT: D 323 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8112 (mm-40) REVERT: A 20 TRP cc_start: 0.8395 (t60) cc_final: 0.7638 (t60) REVERT: A 40 PRO cc_start: 0.9108 (Cg_exo) cc_final: 0.8898 (Cg_endo) REVERT: A 65 ASP cc_start: 0.8738 (p0) cc_final: 0.7698 (t0) REVERT: A 67 CYS cc_start: 0.8371 (m) cc_final: 0.7421 (p) REVERT: A 85 ASN cc_start: 0.8897 (m-40) cc_final: 0.8685 (m110) REVERT: A 93 ILE cc_start: 0.8827 (mm) cc_final: 0.8370 (tp) REVERT: A 147 ASP cc_start: 0.8698 (p0) cc_final: 0.8324 (p0) REVERT: A 176 MET cc_start: 0.8368 (mmt) cc_final: 0.7798 (mmt) REVERT: A 268 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8285 (pp20) REVERT: A 284 SER cc_start: 0.8856 (OUTLIER) cc_final: 0.8292 (m) REVERT: A 323 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8363 (tt0) REVERT: A 327 ASP cc_start: 0.9018 (m-30) cc_final: 0.8591 (m-30) REVERT: E 52 MET cc_start: 0.7332 (mmm) cc_final: 0.7117 (tpt) REVERT: E 133 TYR cc_start: 0.8057 (m-80) cc_final: 0.7842 (m-80) REVERT: E 177 MET cc_start: 0.8107 (ttp) cc_final: 0.7710 (ttp) REVERT: E 182 SER cc_start: 0.8992 (p) cc_final: 0.8784 (t) REVERT: E 196 ASP cc_start: 0.8596 (t0) cc_final: 0.8209 (t0) REVERT: E 205 MET cc_start: 0.8655 (mtp) cc_final: 0.8376 (mtp) REVERT: E 295 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8118 (mm) REVERT: E 302 MET cc_start: 0.8307 (ptp) cc_final: 0.7948 (ptp) REVERT: E 323 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8219 (mm-40) REVERT: F 1 MET cc_start: 0.7728 (pmm) cc_final: 0.6983 (pmm) REVERT: F 20 TRP cc_start: 0.8512 (t60) cc_final: 0.7997 (t60) REVERT: F 65 ASP cc_start: 0.8520 (p0) cc_final: 0.7558 (t0) REVERT: F 173 GLN cc_start: 0.8684 (mt0) cc_final: 0.8380 (mp10) REVERT: F 176 MET cc_start: 0.8630 (mmt) cc_final: 0.8259 (mmt) REVERT: F 240 ASN cc_start: 0.8487 (t0) cc_final: 0.8277 (t0) REVERT: F 284 SER cc_start: 0.8829 (p) cc_final: 0.8405 (m) REVERT: F 302 MET cc_start: 0.7404 (ptp) cc_final: 0.6921 (ptp) REVERT: F 323 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8830 (mm-40) REVERT: F 327 ASP cc_start: 0.8821 (m-30) cc_final: 0.8430 (m-30) REVERT: I 142 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6998 (p90) REVERT: I 173 GLN cc_start: 0.8694 (mt0) cc_final: 0.8119 (mp10) REVERT: I 249 GLN cc_start: 0.7772 (tt0) cc_final: 0.6725 (tt0) REVERT: I 295 ILE cc_start: 0.8358 (mm) cc_final: 0.8123 (mm) REVERT: K 20 TRP cc_start: 0.8250 (t60) cc_final: 0.7992 (t60) REVERT: K 65 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.7513 (t0) REVERT: K 93 ILE cc_start: 0.8793 (mm) cc_final: 0.8483 (tp) REVERT: K 147 ASP cc_start: 0.8685 (p0) cc_final: 0.8477 (p0) REVERT: K 174 GLN cc_start: 0.8814 (mm110) cc_final: 0.7630 (mm-40) REVERT: K 176 MET cc_start: 0.8470 (mmt) cc_final: 0.8222 (mmt) REVERT: K 261 GLN cc_start: 0.8518 (tt0) cc_final: 0.8211 (pp30) REVERT: K 284 SER cc_start: 0.8972 (p) cc_final: 0.8547 (m) REVERT: K 302 MET cc_start: 0.7060 (ptp) cc_final: 0.6662 (ptp) REVERT: K 323 GLN cc_start: 0.9236 (mm-40) cc_final: 0.8524 (mt0) REVERT: K 327 ASP cc_start: 0.8801 (m-30) cc_final: 0.8536 (m-30) REVERT: N 265 GLU cc_start: 0.8453 (pt0) cc_final: 0.8245 (pp20) REVERT: N 295 ILE cc_start: 0.9022 (mp) cc_final: 0.8473 (mt) REVERT: N 323 GLN cc_start: 0.8703 (mm-40) cc_final: 0.8263 (mm-40) REVERT: O 17 MET cc_start: 0.8906 (tpt) cc_final: 0.8649 (tpt) REVERT: O 20 TRP cc_start: 0.8422 (t60) cc_final: 0.7452 (t60) REVERT: O 26 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.7771 (t0) REVERT: O 65 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.7573 (t0) REVERT: O 93 ILE cc_start: 0.8815 (mm) cc_final: 0.8588 (tp) REVERT: O 174 GLN cc_start: 0.8658 (mm110) cc_final: 0.7427 (mm110) REVERT: O 176 MET cc_start: 0.8363 (mmt) cc_final: 0.7944 (mmt) REVERT: O 207 ILE cc_start: 0.8946 (mp) cc_final: 0.8708 (mp) REVERT: O 240 ASN cc_start: 0.8065 (t0) cc_final: 0.7864 (t0) REVERT: O 249 GLN cc_start: 0.8642 (tt0) cc_final: 0.8321 (tm-30) REVERT: O 261 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8411 (tm-30) REVERT: O 284 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8352 (m) REVERT: O 323 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8855 (mm-40) REVERT: O 327 ASP cc_start: 0.9019 (m-30) cc_final: 0.8596 (m-30) REVERT: J 46 HIS cc_start: 0.7458 (m170) cc_final: 0.7219 (m170) REVERT: J 67 ASN cc_start: 0.8248 (p0) cc_final: 0.8048 (t0) REVERT: J 131 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9063 (mm) REVERT: B 46 HIS cc_start: 0.7582 (m170) cc_final: 0.7170 (m170) REVERT: B 66 ASN cc_start: 0.7542 (m-40) cc_final: 0.6603 (m-40) REVERT: B 279 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8384 (t0) REVERT: G 46 HIS cc_start: 0.7597 (m-70) cc_final: 0.7117 (m-70) REVERT: G 69 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7907 (m-30) REVERT: G 127 PHE cc_start: 0.8126 (t80) cc_final: 0.7502 (t80) REVERT: G 131 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9153 (mm) REVERT: G 279 ASN cc_start: 0.8973 (t0) cc_final: 0.8626 (t0) REVERT: L 127 PHE cc_start: 0.7944 (t80) cc_final: 0.7643 (t80) REVERT: L 279 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8408 (t0) REVERT: L 309 GLN cc_start: 0.8823 (mt0) cc_final: 0.8065 (mp10) REVERT: C 28 GLN cc_start: 0.8874 (mp-120) cc_final: 0.8547 (mp10) REVERT: C 54 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.6865 (tptp) REVERT: H 28 GLN cc_start: 0.8531 (mp-120) cc_final: 0.8034 (mt0) REVERT: H 63 ASP cc_start: 0.6397 (p0) cc_final: 0.6082 (p0) REVERT: M 28 GLN cc_start: 0.8246 (mp-120) cc_final: 0.7672 (tm-30) REVERT: M 39 LEU cc_start: 0.8395 (mp) cc_final: 0.7967 (tp) REVERT: M 46 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7904 (pt0) outliers start: 144 outliers final: 94 residues processed: 684 average time/residue: 0.4348 time to fit residues: 496.0067 Evaluate side-chains 639 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 530 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 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 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 65 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 228 LYS Chi-restraints excluded: chain E residue 282 LEU 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 244 VAL Chi-restraints excluded: chain F residue 245 ASP 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 228 LYS Chi-restraints excluded: chain I residue 245 ASP 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 244 VAL 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 166 LEU Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 282 LEU 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 85 ASN Chi-restraints excluded: chain O residue 193 SER Chi-restraints excluded: chain O residue 220 LEU Chi-restraints excluded: chain O residue 245 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 286 ASP Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 78 LEU 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 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 67 ASN 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 236 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 70 LEU 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 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 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 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 257 VAL 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 C residue 54 LYS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain M residue 2 SER Chi-restraints excluded: chain M residue 46 GLN Chi-restraints excluded: chain M residue 54 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 0.9980 chunk 228 optimal weight: 0.6980 chunk 5 optimal weight: 0.0060 chunk 299 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 360 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN E 45 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 GLN ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 HIS N 112 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN 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 90 ASN B 279 ASN L 106 HIS L 279 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 34096 Z= 0.161 Angle : 0.556 11.565 46328 Z= 0.277 Chirality : 0.045 0.283 5220 Planarity : 0.004 0.052 5980 Dihedral : 6.279 59.082 5084 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.18 % Allowed : 15.69 % Favored : 80.14 % 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: -1.01 (0.13), residues: 4240 helix: 0.25 (0.14), residues: 1456 sheet: -1.12 (0.16), residues: 928 loop : -1.05 (0.14), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 20 HIS 0.013 0.001 HIS O 290 PHE 0.032 0.001 PHE K 246 TYR 0.016 0.001 TYR N 142 ARG 0.003 0.000 ARG C 47 *********************** 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 717 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 569 time to evaluate : 4.073 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: P 8 ILE cc_start: 0.8492 (mt) cc_final: 0.8266 (mm) REVERT: P 37 GLU cc_start: 0.8040 (tp30) cc_final: 0.7831 (tp30) REVERT: P 39 LEU cc_start: 0.8138 (mp) cc_final: 0.7902 (tp) REVERT: P 54 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7233 (tptp) REVERT: P 63 ASP cc_start: 0.6899 (p0) cc_final: 0.6513 (p0) REVERT: D 173 GLN cc_start: 0.8722 (mt0) cc_final: 0.8244 (mp10) REVERT: D 177 MET cc_start: 0.8027 (ppp) cc_final: 0.7826 (ttp) REVERT: D 179 THR cc_start: 0.7947 (OUTLIER) cc_final: 0.7706 (t) REVERT: D 205 MET cc_start: 0.8758 (mtp) cc_final: 0.8557 (mtp) REVERT: D 249 GLN cc_start: 0.7721 (tt0) cc_final: 0.6614 (tt0) REVERT: D 271 MET cc_start: 0.8343 (mmt) cc_final: 0.8042 (mmm) REVERT: D 285 SER cc_start: 0.8681 (t) cc_final: 0.8216 (t) REVERT: D 295 ILE cc_start: 0.8981 (mp) cc_final: 0.8684 (mt) REVERT: D 302 MET cc_start: 0.8124 (ptp) cc_final: 0.7681 (ptt) REVERT: A 40 PRO cc_start: 0.9092 (Cg_exo) cc_final: 0.8879 (Cg_endo) REVERT: A 65 ASP cc_start: 0.8725 (p0) cc_final: 0.7693 (t0) REVERT: A 67 CYS cc_start: 0.8391 (m) cc_final: 0.7489 (p) REVERT: A 85 ASN cc_start: 0.8855 (m-40) cc_final: 0.8654 (m110) REVERT: A 147 ASP cc_start: 0.8763 (p0) cc_final: 0.8422 (p0) REVERT: A 176 MET cc_start: 0.8371 (mmt) cc_final: 0.7756 (mmt) REVERT: A 268 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8287 (pp20) REVERT: A 284 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8286 (m) REVERT: A 302 MET cc_start: 0.8112 (ptp) cc_final: 0.7494 (ptp) REVERT: A 323 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8347 (mt0) REVERT: A 327 ASP cc_start: 0.9006 (m-30) cc_final: 0.8631 (m-30) REVERT: E 133 TYR cc_start: 0.8117 (m-80) cc_final: 0.7871 (m-80) REVERT: E 177 MET cc_start: 0.8109 (ttp) cc_final: 0.7744 (ttp) REVERT: E 179 THR cc_start: 0.8437 (t) cc_final: 0.8213 (t) REVERT: E 196 ASP cc_start: 0.8630 (t0) cc_final: 0.8249 (t0) REVERT: E 205 MET cc_start: 0.8725 (mtp) cc_final: 0.8524 (mtp) REVERT: E 228 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8192 (mtmm) REVERT: E 295 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.7983 (mm) REVERT: E 302 MET cc_start: 0.8349 (ptp) cc_final: 0.7850 (ptp) REVERT: E 304 LEU cc_start: 0.8161 (mt) cc_final: 0.7878 (tp) REVERT: E 323 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8182 (mm-40) REVERT: E 332 MET cc_start: 0.8097 (mmp) cc_final: 0.7815 (mmm) REVERT: F 1 MET cc_start: 0.7806 (pmm) cc_final: 0.7185 (pmm) REVERT: F 20 TRP cc_start: 0.8454 (t60) cc_final: 0.8028 (t60) REVERT: F 65 ASP cc_start: 0.8531 (p0) cc_final: 0.7614 (t0) REVERT: F 173 GLN cc_start: 0.8603 (mt0) cc_final: 0.8290 (mp10) REVERT: F 176 MET cc_start: 0.8639 (mmt) cc_final: 0.8333 (mmt) REVERT: F 261 GLN cc_start: 0.8786 (pp30) cc_final: 0.8408 (pp30) REVERT: F 265 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8423 (tp30) REVERT: F 284 SER cc_start: 0.8829 (p) cc_final: 0.8392 (m) REVERT: F 302 MET cc_start: 0.7385 (ptp) cc_final: 0.6870 (ptp) REVERT: F 323 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8827 (mm-40) REVERT: F 327 ASP cc_start: 0.8807 (m-30) cc_final: 0.8429 (m-30) REVERT: I 177 MET cc_start: 0.8227 (ttp) cc_final: 0.8006 (ttp) REVERT: I 295 ILE cc_start: 0.8326 (mm) cc_final: 0.8082 (mm) REVERT: K 65 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.7536 (t0) REVERT: K 93 ILE cc_start: 0.8785 (mm) cc_final: 0.8459 (tp) REVERT: K 147 ASP cc_start: 0.8723 (p0) cc_final: 0.8460 (p0) REVERT: K 174 GLN cc_start: 0.8822 (mm110) cc_final: 0.7718 (mm-40) REVERT: K 261 GLN cc_start: 0.8541 (tt0) cc_final: 0.8224 (pp30) REVERT: K 284 SER cc_start: 0.9010 (p) cc_final: 0.8463 (m) REVERT: K 302 MET cc_start: 0.6996 (ptp) cc_final: 0.6568 (ptp) REVERT: K 323 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8453 (mt0) REVERT: K 327 ASP cc_start: 0.8795 (m-30) cc_final: 0.8591 (m-30) REVERT: N 196 ASP cc_start: 0.8532 (t0) cc_final: 0.8205 (t0) REVERT: N 228 LYS cc_start: 0.8663 (mttt) cc_final: 0.8302 (mtmm) REVERT: N 295 ILE cc_start: 0.8975 (mp) cc_final: 0.8406 (mt) REVERT: N 323 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8243 (mm-40) REVERT: O 17 MET cc_start: 0.8835 (tpt) cc_final: 0.8558 (tpt) REVERT: O 20 TRP cc_start: 0.8438 (t60) cc_final: 0.7539 (t60) REVERT: O 26 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.7791 (t0) REVERT: O 65 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.7954 (t0) REVERT: O 93 ILE cc_start: 0.8757 (mm) cc_final: 0.8524 (tp) REVERT: O 174 GLN cc_start: 0.8663 (mm110) cc_final: 0.7485 (mm110) REVERT: O 176 MET cc_start: 0.8356 (mmt) cc_final: 0.7929 (mmt) REVERT: O 249 GLN cc_start: 0.8527 (tt0) cc_final: 0.8270 (tm-30) REVERT: O 284 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8466 (m) REVERT: O 323 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8826 (mm-40) REVERT: O 327 ASP cc_start: 0.9020 (m-30) cc_final: 0.8601 (m-30) REVERT: J 46 HIS cc_start: 0.7300 (m170) cc_final: 0.7061 (m170) REVERT: J 69 ASP cc_start: 0.7729 (m-30) cc_final: 0.6327 (t70) REVERT: J 241 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8192 (tp) REVERT: B 46 HIS cc_start: 0.7439 (m170) cc_final: 0.7032 (m170) REVERT: B 69 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: B 71 MET cc_start: 0.8200 (ptp) cc_final: 0.7900 (ptp) REVERT: G 69 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7347 (t0) REVERT: G 127 PHE cc_start: 0.8120 (t80) cc_final: 0.7498 (t80) REVERT: G 279 ASN cc_start: 0.8949 (t0) cc_final: 0.8601 (t0) REVERT: L 66 ASN cc_start: 0.7407 (m-40) cc_final: 0.7180 (m-40) REVERT: L 279 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8506 (t0) REVERT: C 28 GLN cc_start: 0.8736 (mp-120) cc_final: 0.8266 (mp10) REVERT: C 54 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.6892 (tptp) REVERT: C 69 GLU cc_start: 0.7304 (mp0) cc_final: 0.6785 (mp0) REVERT: H 63 ASP cc_start: 0.6440 (p0) cc_final: 0.6095 (p0) REVERT: M 28 GLN cc_start: 0.8276 (mp-120) cc_final: 0.7755 (tm-30) REVERT: M 46 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8100 (pt0) REVERT: M 47 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7639 (tpp80) REVERT: M 54 LYS cc_start: 0.7680 (pmmt) cc_final: 0.7205 (tptp) outliers start: 148 outliers final: 98 residues processed: 661 average time/residue: 0.4275 time to fit residues: 472.4038 Evaluate side-chains 623 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 509 time to evaluate : 3.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 179 THR 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 247 VAL 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 244 VAL 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 208 VAL Chi-restraints excluded: chain E residue 228 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 295 ILE Chi-restraints excluded: chain F residue 17 MET 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 244 VAL Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 166 LEU 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 251 GLU 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 244 VAL 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 112 HIS 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 247 VAL Chi-restraints excluded: chain N residue 282 LEU 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 85 ASN Chi-restraints excluded: chain O residue 98 GLU Chi-restraints excluded: chain O residue 149 VAL 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 286 ASP Chi-restraints excluded: chain J residue 113 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 216 VAL 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 67 ASN 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 236 CYS Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 70 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 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 G residue 292 LEU Chi-restraints excluded: chain L residue 28 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 279 ASN Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain M residue 46 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 6.9990 chunk 362 optimal weight: 0.0870 chunk 79 optimal weight: 10.0000 chunk 236 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 402 optimal weight: 0.3980 chunk 334 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 211 optimal weight: 1.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 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 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 GLN ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 249 GLN O 290 HIS ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN G 67 ASN L 279 ASN M 10 GLN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34096 Z= 0.159 Angle : 0.563 12.820 46328 Z= 0.279 Chirality : 0.045 0.239 5220 Planarity : 0.004 0.051 5980 Dihedral : 6.112 58.749 5084 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.43 % Allowed : 15.80 % Favored : 79.77 % 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: -0.80 (0.13), residues: 4240 helix: 0.34 (0.14), residues: 1460 sheet: -0.94 (0.17), residues: 928 loop : -0.89 (0.15), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 20 HIS 0.009 0.001 HIS N 112 PHE 0.024 0.001 PHE J 127 TYR 0.016 0.001 TYR N 142 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 700 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 543 time to evaluate : 3.827 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: P 37 GLU cc_start: 0.8047 (tp30) cc_final: 0.7845 (tp30) REVERT: P 54 LYS cc_start: 0.7756 (pmmt) cc_final: 0.7207 (tptp) REVERT: P 63 ASP cc_start: 0.6826 (p0) cc_final: 0.6346 (p0) REVERT: D 142 TYR cc_start: 0.7416 (p90) cc_final: 0.7194 (p90) REVERT: D 173 GLN cc_start: 0.8814 (mt0) cc_final: 0.8326 (mp10) REVERT: D 177 MET cc_start: 0.8112 (ppp) cc_final: 0.7783 (ttp) REVERT: D 179 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7678 (t) REVERT: D 240 ASN cc_start: 0.7664 (t0) cc_final: 0.6808 (t0) REVERT: D 249 GLN cc_start: 0.7637 (tt0) cc_final: 0.6569 (tt0) REVERT: D 271 MET cc_start: 0.8324 (mmt) cc_final: 0.8008 (mmm) REVERT: D 285 SER cc_start: 0.8740 (t) cc_final: 0.8260 (t) REVERT: D 295 ILE cc_start: 0.8958 (mp) cc_final: 0.8487 (mt) REVERT: D 323 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8064 (mm-40) REVERT: A 40 PRO cc_start: 0.9094 (Cg_exo) cc_final: 0.8876 (Cg_endo) REVERT: A 64 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.7591 (p0) REVERT: A 65 ASP cc_start: 0.8666 (p0) cc_final: 0.8010 (t0) REVERT: A 67 CYS cc_start: 0.8383 (m) cc_final: 0.7775 (p) REVERT: A 147 ASP cc_start: 0.8779 (p0) cc_final: 0.8487 (p0) REVERT: A 173 GLN cc_start: 0.8538 (mt0) cc_final: 0.8227 (mp10) REVERT: A 176 MET cc_start: 0.8436 (mmt) cc_final: 0.8184 (mmt) REVERT: A 268 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8305 (pp20) REVERT: A 284 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8258 (m) REVERT: A 302 MET cc_start: 0.8201 (ptp) cc_final: 0.7582 (ptt) REVERT: A 323 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8371 (mt0) REVERT: A 327 ASP cc_start: 0.9020 (m-30) cc_final: 0.8568 (m-30) REVERT: E 177 MET cc_start: 0.8083 (ttp) cc_final: 0.7724 (ttp) REVERT: E 179 THR cc_start: 0.8382 (t) cc_final: 0.8170 (t) REVERT: E 196 ASP cc_start: 0.8666 (t0) cc_final: 0.8301 (t0) REVERT: E 295 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.7974 (mm) REVERT: E 304 LEU cc_start: 0.8214 (mt) cc_final: 0.7876 (tp) REVERT: E 323 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8149 (mm-40) REVERT: E 332 MET cc_start: 0.8182 (mmp) cc_final: 0.7969 (tpp) REVERT: F 1 MET cc_start: 0.7846 (pmm) cc_final: 0.7227 (pmm) REVERT: F 20 TRP cc_start: 0.8474 (t60) cc_final: 0.7973 (t60) REVERT: F 65 ASP cc_start: 0.8483 (p0) cc_final: 0.7769 (t0) REVERT: F 173 GLN cc_start: 0.8628 (mt0) cc_final: 0.8365 (mp10) REVERT: F 176 MET cc_start: 0.8626 (mmt) cc_final: 0.8289 (mmt) REVERT: F 261 GLN cc_start: 0.8818 (pp30) cc_final: 0.8468 (pp30) REVERT: F 265 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8401 (tp30) REVERT: F 284 SER cc_start: 0.8858 (p) cc_final: 0.8375 (m) REVERT: F 302 MET cc_start: 0.7438 (ptp) cc_final: 0.7104 (ptp) REVERT: F 323 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8754 (mm-40) REVERT: F 327 ASP cc_start: 0.8844 (m-30) cc_final: 0.8481 (m-30) REVERT: I 295 ILE cc_start: 0.8382 (mm) cc_final: 0.8112 (mm) REVERT: K 65 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.7557 (t0) REVERT: K 93 ILE cc_start: 0.8810 (mm) cc_final: 0.8514 (tp) REVERT: K 173 GLN cc_start: 0.8260 (mt0) cc_final: 0.7736 (mp10) REVERT: K 174 GLN cc_start: 0.8813 (mm110) cc_final: 0.7772 (mm110) REVERT: K 261 GLN cc_start: 0.8530 (tt0) cc_final: 0.8208 (pp30) REVERT: K 302 MET cc_start: 0.6957 (ptp) cc_final: 0.6556 (ptp) REVERT: K 323 GLN cc_start: 0.9247 (mm-40) cc_final: 0.8523 (mt0) REVERT: K 327 ASP cc_start: 0.8919 (m-30) cc_final: 0.8625 (m-30) REVERT: N 196 ASP cc_start: 0.8492 (t0) cc_final: 0.8217 (t0) REVERT: N 205 MET cc_start: 0.8802 (mtp) cc_final: 0.8522 (mtp) REVERT: N 228 LYS cc_start: 0.8699 (mttt) cc_final: 0.8272 (mtmm) REVERT: N 284 SER cc_start: 0.8937 (p) cc_final: 0.8432 (m) REVERT: N 295 ILE cc_start: 0.8956 (mp) cc_final: 0.8381 (mt) REVERT: N 323 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8226 (mm-40) REVERT: O 17 MET cc_start: 0.8829 (tpt) cc_final: 0.8533 (tpt) REVERT: O 20 TRP cc_start: 0.8505 (t60) cc_final: 0.7588 (t60) REVERT: O 26 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.7878 (t0) REVERT: O 34 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8896 (mp) REVERT: O 65 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.7873 (t0) REVERT: O 174 GLN cc_start: 0.8642 (mm110) cc_final: 0.7433 (mm110) REVERT: O 176 MET cc_start: 0.8307 (mmt) cc_final: 0.7878 (mmt) REVERT: O 249 GLN cc_start: 0.8573 (tt0) cc_final: 0.8344 (tm-30) REVERT: O 284 SER cc_start: 0.9050 (OUTLIER) cc_final: 0.8486 (m) REVERT: O 323 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8849 (mm-40) REVERT: O 327 ASP cc_start: 0.9023 (m-30) cc_final: 0.8603 (m-30) REVERT: J 69 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.6641 (t70) REVERT: J 241 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8209 (tp) REVERT: B 46 HIS cc_start: 0.7317 (m170) cc_final: 0.7040 (m170) REVERT: B 71 MET cc_start: 0.8137 (ptp) cc_final: 0.7905 (ptp) REVERT: B 269 GLU cc_start: 0.8408 (pp20) cc_final: 0.7755 (pp20) REVERT: G 46 HIS cc_start: 0.7531 (m-70) cc_final: 0.6855 (m-70) REVERT: G 69 ASP cc_start: 0.8211 (m-30) cc_final: 0.7479 (t0) REVERT: G 127 PHE cc_start: 0.8114 (t80) cc_final: 0.7483 (t80) REVERT: G 279 ASN cc_start: 0.8961 (t0) cc_final: 0.8616 (t0) REVERT: L 66 ASN cc_start: 0.7465 (m-40) cc_final: 0.7238 (m-40) REVERT: L 69 ASP cc_start: 0.7981 (m-30) cc_final: 0.6965 (t70) REVERT: L 78 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8379 (mm) REVERT: L 180 ASP cc_start: 0.7726 (m-30) cc_final: 0.7431 (m-30) REVERT: L 279 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8565 (t0) REVERT: C 28 GLN cc_start: 0.8751 (mp-120) cc_final: 0.8468 (mp10) REVERT: C 54 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.6900 (tptp) REVERT: H 28 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8008 (mt0) REVERT: H 63 ASP cc_start: 0.6462 (p0) cc_final: 0.6082 (p0) REVERT: M 28 GLN cc_start: 0.8193 (mp-120) cc_final: 0.7712 (tm-30) REVERT: M 39 LEU cc_start: 0.8209 (mp) cc_final: 0.7845 (tp) REVERT: M 46 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8132 (pt0) REVERT: M 47 ARG cc_start: 0.8092 (mmm160) cc_final: 0.7737 (tpp80) REVERT: M 54 LYS cc_start: 0.7659 (pmmt) cc_final: 0.7210 (tptp) outliers start: 157 outliers final: 111 residues processed: 642 average time/residue: 0.4199 time to fit residues: 452.1835 Evaluate side-chains 634 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 507 time to evaluate : 4.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 GLU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 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 43 ASN Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 122 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 241 VAL Chi-restraints excluded: chain A residue 244 VAL 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 208 VAL Chi-restraints excluded: chain E residue 228 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 282 LEU 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 220 LEU Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 166 LEU 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 251 GLU 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 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 241 VAL Chi-restraints excluded: chain K residue 244 VAL 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 166 LEU Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 282 LEU 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 85 ASN Chi-restraints excluded: chain O residue 98 GLU Chi-restraints excluded: chain O residue 149 VAL 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 286 ASP Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 113 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 216 VAL 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 67 ASN 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 G residue 28 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 70 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 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 78 LEU 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 279 ASN Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain M residue 46 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 388 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 227 optimal weight: 4.9990 chunk 338 optimal weight: 5.9990 chunk 224 optimal weight: 5.9990 chunk 400 optimal weight: 4.9990 chunk 250 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 240 ASN ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 HIS O 290 HIS ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN B 106 HIS B 184 GLN B 279 ASN G 46 HIS G 67 ASN L 279 ASN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 34096 Z= 0.369 Angle : 0.688 13.658 46328 Z= 0.347 Chirality : 0.048 0.264 5220 Planarity : 0.005 0.051 5980 Dihedral : 7.220 58.820 5084 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.80 % Allowed : 16.17 % Favored : 79.03 % 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: -0.93 (0.13), residues: 4240 helix: 0.21 (0.14), residues: 1444 sheet: -0.96 (0.17), residues: 920 loop : -0.98 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP K 20 HIS 0.015 0.001 HIS O 290 PHE 0.028 0.002 PHE O 246 TYR 0.021 0.002 TYR D 133 ARG 0.007 0.001 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 688 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 518 time to evaluate : 3.556 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: P 4 LEU cc_start: 0.7995 (tt) cc_final: 0.7756 (mt) REVERT: P 37 GLU cc_start: 0.8113 (tp30) cc_final: 0.7881 (tp30) REVERT: P 54 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7676 (tptp) REVERT: D 142 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6987 (p90) REVERT: D 173 GLN cc_start: 0.8706 (mt0) cc_final: 0.8059 (mp10) REVERT: D 240 ASN cc_start: 0.8334 (t0) cc_final: 0.7996 (t0) REVERT: D 249 GLN cc_start: 0.7956 (tt0) cc_final: 0.6933 (tt0) REVERT: D 295 ILE cc_start: 0.9153 (mp) cc_final: 0.8680 (mt) REVERT: D 323 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8068 (mm-40) REVERT: A 49 TYR cc_start: 0.8513 (m-80) cc_final: 0.8108 (m-80) REVERT: A 64 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8239 (p0) REVERT: A 147 ASP cc_start: 0.8948 (p0) cc_final: 0.8637 (p0) REVERT: A 173 GLN cc_start: 0.8575 (mt0) cc_final: 0.8223 (mp10) REVERT: A 268 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8325 (pp20) REVERT: A 302 MET cc_start: 0.8020 (ptp) cc_final: 0.6714 (ptp) REVERT: A 327 ASP cc_start: 0.9025 (m-30) cc_final: 0.8600 (m-30) REVERT: E 177 MET cc_start: 0.8141 (ttp) cc_final: 0.7868 (ttp) REVERT: E 205 MET cc_start: 0.8928 (mtp) cc_final: 0.8641 (mtp) REVERT: E 228 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8020 (mtmm) REVERT: E 323 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8130 (mm-40) REVERT: F 1 MET cc_start: 0.8015 (pmm) cc_final: 0.7319 (pmm) REVERT: F 20 TRP cc_start: 0.8658 (t60) cc_final: 0.7993 (t60) REVERT: F 65 ASP cc_start: 0.8660 (p0) cc_final: 0.7865 (t0) REVERT: F 176 MET cc_start: 0.8780 (mmt) cc_final: 0.7716 (mmt) REVERT: F 177 MET cc_start: 0.8157 (tmm) cc_final: 0.7938 (tmm) REVERT: F 261 GLN cc_start: 0.8784 (pp30) cc_final: 0.8474 (pp30) REVERT: F 265 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8416 (tp30) REVERT: F 302 MET cc_start: 0.7282 (ptp) cc_final: 0.7046 (ptp) REVERT: F 323 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8878 (mm-40) REVERT: F 327 ASP cc_start: 0.8738 (m-30) cc_final: 0.8332 (m-30) REVERT: I 142 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.6291 (p90) REVERT: I 176 MET cc_start: 0.8052 (ttm) cc_final: 0.7791 (mtt) REVERT: I 240 ASN cc_start: 0.7942 (t0) cc_final: 0.7678 (t0) REVERT: I 295 ILE cc_start: 0.8889 (mm) cc_final: 0.8505 (mm) REVERT: K 65 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.7780 (t0) REVERT: K 93 ILE cc_start: 0.8964 (mm) cc_final: 0.8666 (tp) REVERT: K 177 MET cc_start: 0.9081 (ppp) cc_final: 0.8020 (ppp) REVERT: K 207 ILE cc_start: 0.9073 (mt) cc_final: 0.8690 (mp) REVERT: K 261 GLN cc_start: 0.8520 (tt0) cc_final: 0.8216 (pp30) REVERT: K 302 MET cc_start: 0.6962 (ptp) cc_final: 0.5723 (ptp) REVERT: K 323 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8895 (mm-40) REVERT: K 327 ASP cc_start: 0.8848 (m-30) cc_final: 0.8613 (m-30) REVERT: N 133 TYR cc_start: 0.8230 (m-80) cc_final: 0.8014 (m-80) REVERT: N 228 LYS cc_start: 0.8389 (mttt) cc_final: 0.7937 (mtmm) REVERT: N 284 SER cc_start: 0.8991 (p) cc_final: 0.8395 (m) REVERT: N 295 ILE cc_start: 0.9118 (mp) cc_final: 0.8556 (mm) REVERT: N 323 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8339 (mm-40) REVERT: O 65 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8099 (t0) REVERT: O 176 MET cc_start: 0.8537 (mmt) cc_final: 0.7534 (mmt) REVERT: O 249 GLN cc_start: 0.8620 (tt0) cc_final: 0.8300 (tm-30) REVERT: O 284 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8441 (m) REVERT: O 323 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8920 (mm-40) REVERT: O 327 ASP cc_start: 0.8955 (m-30) cc_final: 0.8579 (m-30) REVERT: J 90 ASN cc_start: 0.8229 (t0) cc_final: 0.7976 (t0) REVERT: J 309 GLN cc_start: 0.9014 (mt0) cc_final: 0.8306 (mp10) REVERT: B 46 HIS cc_start: 0.7367 (m170) cc_final: 0.7159 (m170) REVERT: G 46 HIS cc_start: 0.7589 (m170) cc_final: 0.7222 (m-70) REVERT: G 127 PHE cc_start: 0.8230 (t80) cc_final: 0.7692 (t80) REVERT: L 78 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8426 (mm) REVERT: L 279 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8452 (t0) REVERT: C 28 GLN cc_start: 0.8824 (mp-120) cc_final: 0.8485 (mp10) REVERT: C 50 GLN cc_start: 0.7928 (mm110) cc_final: 0.7643 (mm110) REVERT: C 63 ASP cc_start: 0.7098 (p0) cc_final: 0.6711 (p0) REVERT: H 28 GLN cc_start: 0.8754 (mm-40) cc_final: 0.8198 (mt0) REVERT: H 63 ASP cc_start: 0.6801 (p0) cc_final: 0.6355 (p0) REVERT: M 28 GLN cc_start: 0.8254 (mp-120) cc_final: 0.7749 (pp30) REVERT: M 39 LEU cc_start: 0.8250 (mp) cc_final: 0.7904 (tp) REVERT: M 42 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8246 (mm-30) REVERT: M 46 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8042 (pt0) REVERT: M 47 ARG cc_start: 0.8243 (mmm160) cc_final: 0.7783 (tpp80) outliers start: 170 outliers final: 130 residues processed: 628 average time/residue: 0.4084 time to fit residues: 433.5345 Evaluate side-chains 625 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 483 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 GLU 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 142 TYR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 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 280 LEU Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain A residue 43 ASN 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 166 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 228 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain F residue 265 GLU 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 228 LYS Chi-restraints excluded: chain I residue 243 VAL Chi-restraints excluded: chain I residue 245 ASP Chi-restraints excluded: chain I residue 247 VAL 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 149 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 245 ASP 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 37 THR Chi-restraints excluded: chain N residue 43 ASN 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 241 VAL Chi-restraints excluded: chain N residue 243 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 282 LEU 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 39 ASP Chi-restraints excluded: chain O residue 65 ASP Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 98 GLU Chi-restraints excluded: chain O residue 149 VAL 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 265 GLU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 286 ASP Chi-restraints excluded: chain O residue 290 HIS Chi-restraints excluded: chain J residue 69 ASP Chi-restraints excluded: chain J residue 80 ASN Chi-restraints excluded: chain J residue 113 LEU 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 216 VAL 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 67 ASN 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 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 G residue 28 LEU Chi-restraints excluded: chain G residue 110 ILE Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 155 GLU 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 200 LEU Chi-restraints excluded: chain G residue 225 ILE 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 G residue 289 THR 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 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 C residue 36 LEU Chi-restraints excluded: chain M residue 46 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 254 optimal weight: 0.7980 chunk 273 optimal weight: 4.9990 chunk 198 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 315 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 58 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 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 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 249 GLN O 290 HIS ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN J 284 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN G 67 ASN G 295 HIS L 279 ASN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34096 Z= 0.169 Angle : 0.603 14.210 46328 Z= 0.298 Chirality : 0.045 0.317 5220 Planarity : 0.004 0.049 5980 Dihedral : 6.547 61.305 5084 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.35 % Allowed : 18.06 % Favored : 77.60 % 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: -0.70 (0.13), residues: 4240 helix: 0.32 (0.14), residues: 1444 sheet: -0.83 (0.17), residues: 912 loop : -0.78 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP K 20 HIS 0.015 0.001 HIS O 290 PHE 0.025 0.001 PHE G 68 TYR 0.018 0.001 TYR N 142 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 703 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 549 time to evaluate : 3.984 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: P 1 MET cc_start: 0.6133 (tmm) cc_final: 0.5669 (tmm) REVERT: P 4 LEU cc_start: 0.7876 (tt) cc_final: 0.7549 (mt) REVERT: P 12 ARG cc_start: 0.7883 (ttt180) cc_final: 0.7665 (ttt180) REVERT: P 37 GLU cc_start: 0.8079 (tp30) cc_final: 0.7864 (tp30) REVERT: P 54 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7059 (tptp) REVERT: P 63 ASP cc_start: 0.7094 (p0) cc_final: 0.6657 (p0) REVERT: P 69 GLU cc_start: 0.6924 (mp0) cc_final: 0.6553 (mp0) REVERT: D 51 SER cc_start: 0.8383 (t) cc_final: 0.8106 (p) REVERT: D 173 GLN cc_start: 0.8783 (mt0) cc_final: 0.8348 (mp10) REVERT: D 228 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7439 (mtmm) REVERT: D 249 GLN cc_start: 0.7700 (tt0) cc_final: 0.6855 (tt0) REVERT: D 285 SER cc_start: 0.8745 (t) cc_final: 0.8422 (t) REVERT: D 295 ILE cc_start: 0.8978 (mp) cc_final: 0.8516 (mt) REVERT: D 323 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8187 (mm-40) REVERT: A 65 ASP cc_start: 0.8771 (p0) cc_final: 0.7877 (t0) REVERT: A 147 ASP cc_start: 0.8890 (p0) cc_final: 0.8550 (p0) REVERT: A 176 MET cc_start: 0.8636 (mmt) cc_final: 0.7604 (mmt) REVERT: A 268 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8268 (pp20) REVERT: A 284 SER cc_start: 0.8870 (OUTLIER) cc_final: 0.8392 (m) REVERT: A 302 MET cc_start: 0.8169 (ptp) cc_final: 0.7485 (ptt) REVERT: A 323 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8402 (mt0) REVERT: A 327 ASP cc_start: 0.8983 (m-30) cc_final: 0.8543 (m-30) REVERT: E 205 MET cc_start: 0.8707 (mtp) cc_final: 0.8472 (mtp) REVERT: E 295 ILE cc_start: 0.8478 (mm) cc_final: 0.7989 (mm) REVERT: E 304 LEU cc_start: 0.8433 (mt) cc_final: 0.7960 (tp) REVERT: E 323 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8118 (mm-40) REVERT: F 1 MET cc_start: 0.8051 (pmm) cc_final: 0.7401 (pmm) REVERT: F 20 TRP cc_start: 0.8528 (t60) cc_final: 0.8038 (t60) REVERT: F 65 ASP cc_start: 0.8481 (p0) cc_final: 0.7832 (t0) REVERT: F 129 ASN cc_start: 0.6715 (p0) cc_final: 0.6465 (p0) REVERT: F 173 GLN cc_start: 0.8559 (mt0) cc_final: 0.8157 (mm-40) REVERT: F 176 MET cc_start: 0.8752 (mmt) cc_final: 0.8237 (mmt) REVERT: F 177 MET cc_start: 0.8139 (tmm) cc_final: 0.7885 (tmm) REVERT: F 261 GLN cc_start: 0.8785 (pp30) cc_final: 0.8475 (pp30) REVERT: F 265 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8385 (tp30) REVERT: F 281 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8234 (mt-10) REVERT: F 302 MET cc_start: 0.7473 (ptp) cc_final: 0.6711 (ptp) REVERT: F 323 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8721 (mm-40) REVERT: F 327 ASP cc_start: 0.8796 (m-30) cc_final: 0.8460 (m-30) REVERT: I 177 MET cc_start: 0.8076 (ttp) cc_final: 0.7855 (ttp) REVERT: I 295 ILE cc_start: 0.8468 (mm) cc_final: 0.8147 (mm) REVERT: I 304 LEU cc_start: 0.8289 (mt) cc_final: 0.7545 (tp) REVERT: K 65 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.7748 (t0) REVERT: K 93 ILE cc_start: 0.8916 (mm) cc_final: 0.8600 (tp) REVERT: K 176 MET cc_start: 0.8660 (mmt) cc_final: 0.8139 (mmt) REVERT: K 177 MET cc_start: 0.9074 (ppp) cc_final: 0.8201 (ppp) REVERT: K 207 ILE cc_start: 0.9111 (mt) cc_final: 0.8767 (mp) REVERT: K 261 GLN cc_start: 0.8503 (tt0) cc_final: 0.8189 (pp30) REVERT: K 284 SER cc_start: 0.9063 (p) cc_final: 0.8465 (m) REVERT: K 302 MET cc_start: 0.6935 (ptp) cc_final: 0.6504 (ptp) REVERT: K 323 GLN cc_start: 0.9276 (mm-40) cc_final: 0.8481 (tt0) REVERT: K 327 ASP cc_start: 0.8846 (m-30) cc_final: 0.8573 (m-30) REVERT: N 189 LEU cc_start: 0.8950 (tp) cc_final: 0.8707 (tp) REVERT: N 228 LYS cc_start: 0.8429 (mttt) cc_final: 0.7832 (mtmm) REVERT: N 284 SER cc_start: 0.8954 (p) cc_final: 0.8264 (m) REVERT: N 295 ILE cc_start: 0.8922 (mp) cc_final: 0.8404 (mm) REVERT: N 323 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8219 (mm-40) REVERT: O 26 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.7907 (t0) REVERT: O 34 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8958 (mp) REVERT: O 65 ASP cc_start: 0.8771 (p0) cc_final: 0.7990 (t0) REVERT: O 176 MET cc_start: 0.8423 (mmt) cc_final: 0.8030 (mmt) REVERT: O 249 GLN cc_start: 0.8483 (tt0) cc_final: 0.8243 (tm-30) REVERT: O 284 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8425 (m) REVERT: O 323 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8535 (mt0) REVERT: O 327 ASP cc_start: 0.8996 (m-30) cc_final: 0.8584 (m-30) REVERT: J 69 ASP cc_start: 0.7938 (m-30) cc_final: 0.6660 (t70) REVERT: J 90 ASN cc_start: 0.8177 (t0) cc_final: 0.7853 (t0) REVERT: J 233 LYS cc_start: 0.9085 (mmtt) cc_final: 0.8846 (mttm) REVERT: J 279 ASN cc_start: 0.8858 (OUTLIER) cc_final: 0.8629 (t0) REVERT: J 309 GLN cc_start: 0.8918 (mt0) cc_final: 0.8163 (mp10) REVERT: B 46 HIS cc_start: 0.7135 (m170) cc_final: 0.6723 (m170) REVERT: B 66 ASN cc_start: 0.7797 (m-40) cc_final: 0.6670 (m110) REVERT: G 46 HIS cc_start: 0.7301 (m170) cc_final: 0.6971 (m-70) REVERT: G 69 ASP cc_start: 0.8504 (m-30) cc_final: 0.7796 (t0) REVERT: G 71 MET cc_start: 0.8105 (ptp) cc_final: 0.7626 (ptp) REVERT: G 80 ASN cc_start: 0.6898 (m110) cc_final: 0.5885 (t0) REVERT: G 127 PHE cc_start: 0.8189 (t80) cc_final: 0.7631 (t80) REVERT: G 279 ASN cc_start: 0.8973 (t0) cc_final: 0.8654 (t0) REVERT: L 66 ASN cc_start: 0.7668 (m-40) cc_final: 0.7216 (m-40) REVERT: L 85 MET cc_start: 0.7861 (tpt) cc_final: 0.7646 (tpt) REVERT: L 180 ASP cc_start: 0.7904 (m-30) cc_final: 0.7573 (m-30) REVERT: L 279 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8524 (t0) REVERT: C 28 GLN cc_start: 0.8737 (mp-120) cc_final: 0.8330 (mp10) REVERT: C 50 GLN cc_start: 0.7937 (mm110) cc_final: 0.7610 (mm110) REVERT: C 63 ASP cc_start: 0.6901 (p0) cc_final: 0.6577 (p0) REVERT: H 28 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8178 (mt0) REVERT: H 63 ASP cc_start: 0.6594 (p0) cc_final: 0.6083 (p0) REVERT: M 28 GLN cc_start: 0.8197 (mp-120) cc_final: 0.7696 (pp30) REVERT: M 42 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8160 (mm-30) REVERT: M 46 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8056 (pt0) REVERT: M 47 ARG cc_start: 0.8198 (mmm160) cc_final: 0.7817 (tpp80) REVERT: M 54 LYS cc_start: 0.7875 (pmmt) cc_final: 0.7446 (tptp) outliers start: 154 outliers final: 112 residues processed: 644 average time/residue: 0.4304 time to fit residues: 468.1504 Evaluate side-chains 635 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 512 time to evaluate : 4.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain D residue 4 VAL 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 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 A residue 64 ASP Chi-restraints excluded: chain A residue 122 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 65 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 228 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 205 MET Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 190 LEU 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 247 VAL Chi-restraints excluded: chain I residue 279 GLU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain K residue 17 MET 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 241 VAL 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 37 THR Chi-restraints excluded: chain N residue 137 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 241 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 98 GLU Chi-restraints excluded: chain O residue 149 VAL 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 265 GLU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 286 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 136 ASP 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 216 VAL 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 56 MET Chi-restraints excluded: chain B residue 67 ASN 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 289 THR Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 70 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 200 LEU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 288 VAL 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 206 GLN Chi-restraints excluded: chain L residue 225 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 C residue 36 LEU Chi-restraints excluded: chain C residue 54 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain M residue 46 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 10.0000 chunk 384 optimal weight: 2.9990 chunk 350 optimal weight: 0.5980 chunk 373 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 chunk 353 optimal weight: 0.9990 chunk 372 optimal weight: 0.2980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 58 GLN ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 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 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 GLN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN O 206 ASN O 249 GLN ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN G 67 ASN L 279 ASN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34096 Z= 0.234 Angle : 0.627 15.342 46328 Z= 0.311 Chirality : 0.046 0.286 5220 Planarity : 0.004 0.049 5980 Dihedral : 6.637 64.681 5084 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.06 % Allowed : 18.43 % Favored : 77.51 % 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: -0.71 (0.13), residues: 4240 helix: 0.27 (0.14), residues: 1444 sheet: -0.82 (0.17), residues: 912 loop : -0.73 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP K 20 HIS 0.009 0.001 HIS J 46 PHE 0.029 0.002 PHE B 127 TYR 0.025 0.002 TYR D 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 648 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 504 time to evaluate : 4.293 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 1 MET cc_start: 0.6344 (tmm) cc_final: 0.6136 (tmm) REVERT: P 54 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7157 (tptp) REVERT: P 69 GLU cc_start: 0.7281 (mp0) cc_final: 0.6881 (mp0) REVERT: D 173 GLN cc_start: 0.8835 (mt0) cc_final: 0.8285 (mp10) REVERT: D 240 ASN cc_start: 0.8143 (t0) cc_final: 0.7613 (t0) REVERT: D 249 GLN cc_start: 0.7796 (tt0) cc_final: 0.6865 (tt0) REVERT: D 285 SER cc_start: 0.8825 (t) cc_final: 0.8457 (t) REVERT: D 295 ILE cc_start: 0.8979 (mp) cc_final: 0.8595 (mt) REVERT: A 64 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.7865 (p0) REVERT: A 65 ASP cc_start: 0.8773 (p0) cc_final: 0.8101 (t0) REVERT: A 147 ASP cc_start: 0.8918 (p0) cc_final: 0.8595 (p0) REVERT: A 176 MET cc_start: 0.8672 (mmt) cc_final: 0.7641 (mmt) REVERT: A 268 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8314 (pp20) REVERT: A 284 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8402 (m) REVERT: A 302 MET cc_start: 0.8143 (ptp) cc_final: 0.6852 (ptt) REVERT: A 323 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8383 (mt0) REVERT: A 327 ASP cc_start: 0.8997 (m-30) cc_final: 0.8558 (m-30) REVERT: E 205 MET cc_start: 0.8797 (mtp) cc_final: 0.8596 (mtp) REVERT: E 228 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8116 (mtmm) REVERT: E 295 ILE cc_start: 0.8634 (mm) cc_final: 0.8157 (mm) REVERT: E 323 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8215 (mm-40) REVERT: F 20 TRP cc_start: 0.8587 (t60) cc_final: 0.8108 (t60) REVERT: F 65 ASP cc_start: 0.8498 (p0) cc_final: 0.7857 (t0) REVERT: F 176 MET cc_start: 0.8786 (mmt) cc_final: 0.7734 (mmt) REVERT: F 261 GLN cc_start: 0.8786 (pp30) cc_final: 0.8487 (pp30) REVERT: F 265 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8355 (tp30) REVERT: F 281 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8289 (mt-10) REVERT: F 302 MET cc_start: 0.7410 (ptp) cc_final: 0.6577 (ptp) REVERT: F 323 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8781 (mm-40) REVERT: F 327 ASP cc_start: 0.8810 (m-30) cc_final: 0.8497 (m-30) REVERT: I 142 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.6339 (p90) REVERT: I 176 MET cc_start: 0.7945 (ttm) cc_final: 0.7652 (mtt) REVERT: I 228 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7879 (mtmm) REVERT: I 295 ILE cc_start: 0.8630 (mm) cc_final: 0.8260 (mm) REVERT: I 304 LEU cc_start: 0.8266 (mt) cc_final: 0.7483 (tp) REVERT: K 65 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.7736 (t0) REVERT: K 176 MET cc_start: 0.8699 (mmt) cc_final: 0.8194 (mmt) REVERT: K 177 MET cc_start: 0.9095 (ppp) cc_final: 0.8254 (ppp) REVERT: K 207 ILE cc_start: 0.9088 (mt) cc_final: 0.8722 (mp) REVERT: K 261 GLN cc_start: 0.8504 (tt0) cc_final: 0.8190 (pp30) REVERT: K 302 MET cc_start: 0.7012 (ptp) cc_final: 0.5840 (ptp) REVERT: K 323 GLN cc_start: 0.9288 (mm-40) cc_final: 0.8813 (mm-40) REVERT: K 327 ASP cc_start: 0.8889 (m-30) cc_final: 0.8647 (m-30) REVERT: N 228 LYS cc_start: 0.8358 (mttt) cc_final: 0.7741 (mtmm) REVERT: N 284 SER cc_start: 0.9013 (p) cc_final: 0.8351 (m) REVERT: N 295 ILE cc_start: 0.8941 (mp) cc_final: 0.8412 (mm) REVERT: N 323 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8250 (mm-40) REVERT: O 26 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.7928 (t0) REVERT: O 65 ASP cc_start: 0.8759 (p0) cc_final: 0.8041 (t0) REVERT: O 176 MET cc_start: 0.8456 (mmt) cc_final: 0.7430 (mmt) REVERT: O 249 GLN cc_start: 0.8572 (tt0) cc_final: 0.8323 (tm-30) REVERT: O 284 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8398 (m) REVERT: O 323 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8781 (mm-40) REVERT: O 327 ASP cc_start: 0.8976 (m-30) cc_final: 0.8551 (m-30) REVERT: J 85 MET cc_start: 0.8305 (tpt) cc_final: 0.7973 (tpt) REVERT: J 90 ASN cc_start: 0.8223 (t0) cc_final: 0.8004 (t0) REVERT: J 233 LYS cc_start: 0.9110 (mmtt) cc_final: 0.8879 (mttm) REVERT: J 308 PHE cc_start: 0.8796 (m-10) cc_final: 0.8434 (m-10) REVERT: G 46 HIS cc_start: 0.7358 (m170) cc_final: 0.7075 (m-70) REVERT: G 69 ASP cc_start: 0.8507 (m-30) cc_final: 0.7760 (t0) REVERT: G 71 MET cc_start: 0.8102 (ptp) cc_final: 0.7686 (ptp) REVERT: G 80 ASN cc_start: 0.6944 (m110) cc_final: 0.5929 (t0) REVERT: G 127 PHE cc_start: 0.8260 (t80) cc_final: 0.7658 (t80) REVERT: L 66 ASN cc_start: 0.7786 (m-40) cc_final: 0.7427 (m-40) REVERT: L 71 MET cc_start: 0.8486 (ptp) cc_final: 0.7974 (ptp) REVERT: L 180 ASP cc_start: 0.7892 (m-30) cc_final: 0.7596 (m-30) REVERT: C 28 GLN cc_start: 0.8759 (mp-120) cc_final: 0.8403 (mp10) REVERT: C 50 GLN cc_start: 0.7964 (mm110) cc_final: 0.7639 (mm110) REVERT: C 63 ASP cc_start: 0.7037 (p0) cc_final: 0.6702 (p0) REVERT: H 28 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8171 (mt0) REVERT: H 63 ASP cc_start: 0.6746 (p0) cc_final: 0.6261 (p0) REVERT: H 69 GLU cc_start: 0.7336 (mp0) cc_final: 0.6955 (mp0) REVERT: M 28 GLN cc_start: 0.8186 (mp-120) cc_final: 0.7690 (tm-30) REVERT: M 46 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: M 47 ARG cc_start: 0.8281 (mmm160) cc_final: 0.7949 (tpt-90) REVERT: M 54 LYS cc_start: 0.7870 (pmmt) cc_final: 0.7472 (tptp) outliers start: 144 outliers final: 113 residues processed: 594 average time/residue: 0.4242 time to fit residues: 424.6861 Evaluate side-chains 617 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 493 time to evaluate : 4.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 5 GLU Chi-restraints excluded: chain P residue 54 LYS Chi-restraints excluded: chain P residue 57 PHE Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 228 LYS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 280 LEU 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 A residue 286 ASP 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 142 TYR Chi-restraints excluded: chain E residue 147 ASP Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 228 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 85 ASN 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 265 GLU 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 166 LEU Chi-restraints excluded: chain I residue 190 LEU 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 247 VAL Chi-restraints excluded: chain I residue 279 GLU 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 241 VAL Chi-restraints excluded: chain K residue 259 VAL 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 155 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 241 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 98 GLU Chi-restraints excluded: chain O residue 149 VAL 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 265 GLU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 286 ASP Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 131 LEU Chi-restraints excluded: chain J residue 136 ASP Chi-restraints excluded: chain J residue 167 ASP Chi-restraints excluded: chain J residue 182 VAL 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 67 ASN 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 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 70 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 200 LEU Chi-restraints excluded: chain G residue 225 ILE Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 288 VAL 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 206 GLN 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 C residue 36 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain M residue 46 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 245 optimal weight: 0.4980 chunk 395 optimal weight: 0.7980 chunk 241 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 chunk 414 optimal weight: 6.9990 chunk 381 optimal weight: 3.9990 chunk 330 optimal weight: 5.9990 chunk 34 optimal weight: 0.3980 chunk 254 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 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 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN K 15 ASN K 174 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 249 GLN ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 GLN G 67 ASN C 46 GLN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34096 Z= 0.160 Angle : 0.613 15.646 46328 Z= 0.301 Chirality : 0.045 0.320 5220 Planarity : 0.004 0.048 5980 Dihedral : 6.278 60.263 5084 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.47 % Allowed : 19.24 % Favored : 77.29 % 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: -0.58 (0.13), residues: 4240 helix: 0.39 (0.14), residues: 1436 sheet: -0.78 (0.17), residues: 920 loop : -0.66 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP K 20 HIS 0.013 0.001 HIS B 46 PHE 0.046 0.001 PHE G 68 TYR 0.020 0.001 TYR D 142 ARG 0.004 0.000 ARG C 47 ********************** 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 674 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 551 time to evaluate : 3.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7481 (pmmt) cc_final: 0.7041 (tptp) REVERT: P 63 ASP cc_start: 0.7451 (p0) cc_final: 0.7116 (p0) REVERT: P 69 GLU cc_start: 0.6983 (mp0) cc_final: 0.6604 (mp0) REVERT: D 173 GLN cc_start: 0.8816 (mt0) cc_final: 0.8310 (mp10) REVERT: D 176 MET cc_start: 0.6754 (mtp) cc_final: 0.6342 (mtp) REVERT: D 240 ASN cc_start: 0.7849 (t0) cc_final: 0.7349 (t0) REVERT: D 249 GLN cc_start: 0.7694 (tt0) cc_final: 0.6867 (tt0) REVERT: D 285 SER cc_start: 0.8722 (t) cc_final: 0.8289 (t) REVERT: D 295 ILE cc_start: 0.8911 (mp) cc_final: 0.8406 (mt) REVERT: A 65 ASP cc_start: 0.8687 (p0) cc_final: 0.7970 (t0) REVERT: A 147 ASP cc_start: 0.8889 (p0) cc_final: 0.8599 (p0) REVERT: A 173 GLN cc_start: 0.8562 (mt0) cc_final: 0.8292 (mp10) REVERT: A 176 MET cc_start: 0.8683 (mmt) cc_final: 0.7637 (mmt) REVERT: A 284 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8372 (m) REVERT: A 302 MET cc_start: 0.8200 (ptp) cc_final: 0.7572 (ptt) REVERT: A 323 GLN cc_start: 0.9129 (mm-40) cc_final: 0.8430 (mt0) REVERT: A 327 ASP cc_start: 0.8973 (m-30) cc_final: 0.8510 (m-30) REVERT: E 295 ILE cc_start: 0.8425 (mm) cc_final: 0.7940 (mm) REVERT: E 323 GLN cc_start: 0.8577 (mm-40) cc_final: 0.8124 (mm-40) REVERT: F 20 TRP cc_start: 0.8488 (t60) cc_final: 0.8109 (t60) REVERT: F 65 ASP cc_start: 0.8420 (p0) cc_final: 0.7802 (t0) REVERT: F 176 MET cc_start: 0.8805 (mmt) cc_final: 0.8379 (mmt) REVERT: F 261 GLN cc_start: 0.8794 (pp30) cc_final: 0.8491 (pp30) REVERT: F 265 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8336 (tp30) REVERT: F 281 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8233 (mt-10) REVERT: F 302 MET cc_start: 0.7508 (ptp) cc_final: 0.6729 (ptp) REVERT: F 323 GLN cc_start: 0.9039 (mm-40) cc_final: 0.8683 (mm-40) REVERT: F 327 ASP cc_start: 0.8763 (m-30) cc_final: 0.8413 (m-30) REVERT: I 142 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6182 (p90) REVERT: I 176 MET cc_start: 0.7963 (ttm) cc_final: 0.7708 (mtt) REVERT: I 295 ILE cc_start: 0.8447 (mm) cc_final: 0.8152 (mm) REVERT: I 304 LEU cc_start: 0.8309 (mt) cc_final: 0.7485 (tp) REVERT: K 34 ILE cc_start: 0.9350 (OUTLIER) cc_final: 0.9054 (mp) REVERT: K 65 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.7755 (t0) REVERT: K 176 MET cc_start: 0.8607 (mmt) cc_final: 0.8196 (mtp) REVERT: K 177 MET cc_start: 0.9070 (ppp) cc_final: 0.8242 (ppp) REVERT: K 205 MET cc_start: 0.8805 (mtp) cc_final: 0.8566 (mtm) REVERT: K 261 GLN cc_start: 0.8535 (tt0) cc_final: 0.8187 (pp30) REVERT: K 302 MET cc_start: 0.7055 (ptp) cc_final: 0.6627 (ptp) REVERT: K 327 ASP cc_start: 0.8862 (m-30) cc_final: 0.8555 (m-30) REVERT: N 228 LYS cc_start: 0.8414 (mttt) cc_final: 0.7886 (mtmm) REVERT: N 284 SER cc_start: 0.8947 (p) cc_final: 0.8273 (m) REVERT: N 295 ILE cc_start: 0.8831 (mp) cc_final: 0.8223 (mt) REVERT: N 323 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8169 (mm-40) REVERT: O 26 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.7963 (t0) REVERT: O 34 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9005 (mp) REVERT: O 65 ASP cc_start: 0.8734 (p0) cc_final: 0.8124 (t0) REVERT: O 176 MET cc_start: 0.8418 (mmt) cc_final: 0.8047 (mmt) REVERT: O 246 PHE cc_start: 0.9120 (t80) cc_final: 0.8899 (t80) REVERT: O 249 GLN cc_start: 0.8450 (tt0) cc_final: 0.8245 (tm-30) REVERT: O 284 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8410 (m) REVERT: O 323 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8699 (mm-40) REVERT: O 327 ASP cc_start: 0.9003 (m-30) cc_final: 0.8625 (m-30) REVERT: J 69 ASP cc_start: 0.7809 (m-30) cc_final: 0.6406 (t70) REVERT: J 85 MET cc_start: 0.8253 (tpt) cc_final: 0.7997 (tpt) REVERT: J 90 ASN cc_start: 0.8059 (t0) cc_final: 0.7842 (t0) REVERT: J 233 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8833 (mttm) REVERT: J 241 ILE cc_start: 0.8460 (OUTLIER) cc_final: 0.8160 (tp) REVERT: J 308 PHE cc_start: 0.8767 (m-10) cc_final: 0.8494 (m-10) REVERT: B 66 ASN cc_start: 0.7838 (m-40) cc_final: 0.7017 (m110) REVERT: B 69 ASP cc_start: 0.7971 (m-30) cc_final: 0.6993 (t0) REVERT: B 241 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8187 (tp) REVERT: G 46 HIS cc_start: 0.7226 (m170) cc_final: 0.6988 (m-70) REVERT: G 69 ASP cc_start: 0.8447 (m-30) cc_final: 0.7865 (t0) REVERT: G 80 ASN cc_start: 0.6864 (m110) cc_final: 0.5985 (t0) REVERT: G 85 MET cc_start: 0.8381 (tpt) cc_final: 0.8123 (tpt) REVERT: G 127 PHE cc_start: 0.8192 (t80) cc_final: 0.7625 (t80) REVERT: G 279 ASN cc_start: 0.8966 (t0) cc_final: 0.8709 (t0) REVERT: L 69 ASP cc_start: 0.8058 (m-30) cc_final: 0.7234 (t70) REVERT: L 180 ASP cc_start: 0.7954 (m-30) cc_final: 0.7614 (m-30) REVERT: C 28 GLN cc_start: 0.8722 (mp-120) cc_final: 0.8348 (mp10) REVERT: C 50 GLN cc_start: 0.7973 (mm110) cc_final: 0.7647 (mm110) REVERT: C 54 LYS cc_start: 0.7947 (pmmt) cc_final: 0.7216 (tptp) REVERT: H 1 MET cc_start: 0.6831 (tmm) cc_final: 0.6543 (tmm) REVERT: H 12 ARG cc_start: 0.7586 (ttt180) cc_final: 0.7377 (ttt180) REVERT: H 28 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8040 (mt0) REVERT: H 63 ASP cc_start: 0.6610 (p0) cc_final: 0.6087 (p0) REVERT: H 69 GLU cc_start: 0.7078 (mp0) cc_final: 0.6741 (mp0) REVERT: M 1 MET cc_start: 0.7536 (tmm) cc_final: 0.3521 (mmm) REVERT: M 28 GLN cc_start: 0.8119 (mp-120) cc_final: 0.7637 (tm-30) REVERT: M 47 ARG cc_start: 0.8210 (mmm160) cc_final: 0.7884 (tpp80) REVERT: M 54 LYS cc_start: 0.7823 (pmmt) cc_final: 0.7419 (tptp) outliers start: 123 outliers final: 100 residues processed: 629 average time/residue: 0.4327 time to fit residues: 454.5081 Evaluate side-chains 619 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 509 time to evaluate : 4.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 57 PHE Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 142 TYR Chi-restraints excluded: chain D residue 166 LEU 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 247 VAL Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 122 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 A residue 286 ASP 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 142 TYR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 228 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 64 ASP 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 265 GLU Chi-restraints excluded: chain I residue 4 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 142 TYR Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 190 LEU 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 279 GLU Chi-restraints excluded: chain I residue 296 LEU Chi-restraints excluded: chain K residue 26 ASN Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain K residue 178 THR Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 259 VAL 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 155 THR Chi-restraints excluded: chain N residue 208 VAL Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 282 LEU Chi-restraints excluded: chain O residue 26 ASN Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 85 ASN Chi-restraints excluded: chain O residue 98 GLU Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 149 VAL 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 J residue 42 LEU Chi-restraints excluded: chain J residue 89 TYR Chi-restraints excluded: chain J residue 113 LEU Chi-restraints excluded: chain J residue 136 ASP 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 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 67 ASN 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 241 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 67 ASN 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 257 VAL Chi-restraints excluded: chain G residue 288 VAL 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 206 GLN 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 C residue 36 LEU Chi-restraints excluded: chain H residue 54 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 3.9990 chunk 351 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 chunk 304 optimal weight: 5.9990 chunk 48 optimal weight: 0.0470 chunk 91 optimal weight: 5.9990 chunk 330 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 339 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 45 HIS ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 ASN I 260 ASN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 174 GLN O 187 GLN O 249 GLN ** O 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 295 HIS ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.108013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084989 restraints weight = 86407.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.087665 restraints weight = 45468.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.089353 restraints weight = 30384.892| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 34096 Z= 0.161 Angle : 0.615 15.470 46328 Z= 0.303 Chirality : 0.045 0.337 5220 Planarity : 0.004 0.048 5980 Dihedral : 6.126 59.121 5084 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.47 % Allowed : 19.95 % Favored : 76.58 % 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: -0.52 (0.13), residues: 4240 helix: 0.40 (0.14), residues: 1436 sheet: -0.67 (0.17), residues: 920 loop : -0.63 (0.15), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.001 TRP K 20 HIS 0.008 0.001 HIS B 46 PHE 0.037 0.001 PHE G 68 TYR 0.020 0.001 TYR D 142 ARG 0.004 0.000 ARG N 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8633.73 seconds wall clock time: 158 minutes 10.54 seconds (9490.54 seconds total)