Starting phenix.real_space_refine (version: dev) on Mon May 16 17:11:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/05_2022/6gve_0071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/05_2022/6gve_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_0071/05_2022/6gve_0071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/05_2022/6gve_0071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/05_2022/6gve_0071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/05_2022/6gve_0071_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 15, 'TRANS': 302, 'PCIS': 1} 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: {'PTRANS': 15, 'TRANS': 302, 'PCIS': 1} 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: {'PTRANS': 15, 'TRANS': 302, 'PCIS': 1} 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: {'PTRANS': 15, 'TRANS': 302, 'PCIS': 1} 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: 19.71, per 1000 atoms: 0.59 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: 13.80 Conformation dependent library (CDL) restraints added in 5.4 seconds 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... 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: 3.85 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: 11.63 Time building geometry restraints manager: 14.85 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: 19093 15.12 - 30.24: 1031 30.24 - 45.35: 184 45.35 - 60.47: 28 60.47 - 75.59: 16 Dihedral angle restraints: 20352 sinusoidal: 8028 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 20349 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 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. 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: 2.910 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: 0.030 Extract box with map and model: 12.510 Check model and map are aligned: 0.560 Convert atoms to be neutral: 0.320 Process input model: 87.000 Find NCS groups from input model: 2.580 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 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 : 10.072 75.588 12384 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 % 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 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1006 time to evaluate : 4.307 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 outliers start: 4 outliers final: 4 residues processed: 1010 average time/residue: 0.4684 time to fit residues: 759.0384 Evaluate side-chains 528 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 524 time to evaluate : 4.145 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3059 time to fit residues: 7.5870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 107 optimal weight: 0.9990 chunk 212 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 326 optimal weight: 20.0000 chunk 126 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 377 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 181 HIS A 15 ASN A 45 HIS A 173 GLN A 181 HIS A 187 GLN E 15 ASN E 181 HIS E 249 GLN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN F 45 HIS F 181 HIS F 291 ASN I 15 ASN I 181 HIS I 240 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 ASN K 45 HIS K 173 GLN K 181 HIS K 187 GLN K 258 GLN K 276 HIS K 290 HIS K 291 ASN N 15 ASN N 173 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 181 HIS ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN O 45 HIS O 181 HIS O 290 HIS ** O 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN J 114 HIS J 206 GLN B 90 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN G 90 ASN G 206 GLN L 90 ASN L 189 GLN L 279 ASN C 10 GLN C 64 ASN H 64 ASN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 HIS M 64 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 34096 Z= 0.231 Angle : 0.614 8.024 46328 Z= 0.318 Chirality : 0.047 0.161 5220 Planarity : 0.006 0.105 5980 Dihedral : 6.432 59.265 4680 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer Outliers : 3.08 % 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: -1.03 (0.13), residues: 1440 sheet: -2.02 (0.16), residues: 872 loop : -1.66 (0.13), residues: 1928 *********************** 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 771 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 662 time to evaluate : 4.281 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 outliers start: 109 outliers final: 74 residues processed: 724 average time/residue: 0.4092 time to fit residues: 495.7921 Evaluate side-chains 594 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 520 time to evaluate : 4.276 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.3063 time to fit residues: 48.3707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 257 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 378 optimal weight: 9.9990 chunk 408 optimal weight: 1.9990 chunk 337 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 303 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 226 GLN A 276 HIS E 45 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 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** ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 HIS ** 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** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN O 187 GLN O 276 HIS O 290 HIS ** O 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN B 106 HIS B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN ** L 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 34096 Z= 0.409 Angle : 0.712 8.728 46328 Z= 0.365 Chirality : 0.050 0.233 5220 Planarity : 0.006 0.110 5980 Dihedral : 6.484 58.113 4680 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer Outliers : 3.50 % 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: -1.91 (0.13), residues: 4240 helix: -0.43 (0.14), residues: 1452 sheet: -1.75 (0.16), residues: 928 loop : -1.55 (0.14), residues: 1860 *********************** 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 660 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 536 time to evaluate : 4.203 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 outliers start: 124 outliers final: 77 residues processed: 627 average time/residue: 0.4195 time to fit residues: 441.5329 Evaluate side-chains 534 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 457 time to evaluate : 3.836 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 0 residues processed: 77 average time/residue: 0.3077 time to fit residues: 50.3149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 373 optimal weight: 0.0670 chunk 284 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 254 optimal weight: 0.7980 chunk 379 optimal weight: 0.7980 chunk 402 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 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 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 ASN I 260 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 331 HIS K 335 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** O 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 34096 Z= 0.169 Angle : 0.590 12.736 46328 Z= 0.297 Chirality : 0.045 0.221 5220 Planarity : 0.005 0.089 5980 Dihedral : 5.847 64.230 4680 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 1.52 % 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: -1.38 (0.13), residues: 4240 helix: 0.11 (0.14), residues: 1436 sheet: -1.38 (0.16), residues: 912 loop : -1.40 (0.14), residues: 1892 *********************** 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 654 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 600 time to evaluate : 4.511 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 outliers start: 54 outliers final: 27 residues processed: 623 average time/residue: 0.4164 time to fit residues: 434.5221 Evaluate side-chains 517 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 490 time to evaluate : 3.866 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3206 time to fit residues: 20.8773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 5 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 343 optimal weight: 10.0000 chunk 277 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 360 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN ** O 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.080 34096 Z= 0.332 Angle : 0.668 14.092 46328 Z= 0.342 Chirality : 0.048 0.322 5220 Planarity : 0.005 0.106 5980 Dihedral : 6.011 65.024 4680 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer Outliers : 2.74 % 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: 0.14 (0.14), residues: 1432 sheet: -1.15 (0.16), residues: 896 loop : -1.38 (0.14), residues: 1912 *********************** 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 586 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 489 time to evaluate : 3.852 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 outliers start: 97 outliers final: 54 residues processed: 555 average time/residue: 0.4325 time to fit residues: 402.0061 Evaluate side-chains 501 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 447 time to evaluate : 4.433 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.3254 time to fit residues: 38.9880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 135 optimal weight: 9.9990 chunk 362 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 402 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 186 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 chunk 133 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 ASN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 HIS ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS G 295 HIS M 10 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.105 34096 Z= 0.211 Angle : 0.614 11.226 46328 Z= 0.309 Chirality : 0.046 0.285 5220 Planarity : 0.005 0.127 5980 Dihedral : 5.738 62.027 4680 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 1.41 % 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: -1.10 (0.13), residues: 4240 helix: 0.28 (0.14), residues: 1432 sheet: -1.13 (0.17), residues: 912 loop : -1.22 (0.14), residues: 1896 *********************** 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 594 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 544 time to evaluate : 4.272 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 outliers start: 50 outliers final: 27 residues processed: 571 average time/residue: 0.4193 time to fit residues: 400.5405 Evaluate side-chains 505 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 478 time to evaluate : 4.059 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2989 time to fit residues: 20.6517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 388 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 293 optimal weight: 5.9990 chunk 227 optimal weight: 0.5980 chunk 338 optimal weight: 0.0870 chunk 224 optimal weight: 6.9990 chunk 400 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 185 optimal weight: 10.0000 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 ASN A 15 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 331 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 173 GLN J 90 ASN J 279 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN B 284 HIS B 295 HIS M 10 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.101 34096 Z= 0.246 Angle : 0.629 12.880 46328 Z= 0.317 Chirality : 0.047 0.293 5220 Planarity : 0.005 0.097 5980 Dihedral : 5.664 66.007 4680 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 1.50 % 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: -1.02 (0.13), residues: 4240 helix: 0.31 (0.14), residues: 1432 sheet: -1.07 (0.17), residues: 928 loop : -1.15 (0.15), residues: 1880 *********************** 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 551 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 498 time to evaluate : 4.710 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 outliers start: 53 outliers final: 35 residues processed: 529 average time/residue: 0.4313 time to fit residues: 381.6682 Evaluate side-chains 499 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 464 time to evaluate : 4.201 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3069 time to fit residues: 25.8511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 248 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 273 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 315 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 174 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 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN J 90 ASN J 284 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 295 HIS G 67 ASN M 10 GLN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.115 34096 Z= 0.225 Angle : 0.640 14.503 46328 Z= 0.320 Chirality : 0.047 0.297 5220 Planarity : 0.005 0.103 5980 Dihedral : 5.541 64.390 4680 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 1.07 % 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: -0.98 (0.13), residues: 4240 helix: 0.26 (0.14), residues: 1448 sheet: -1.03 (0.17), residues: 912 loop : -1.07 (0.15), residues: 1880 *********************** 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 557 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 519 time to evaluate : 4.377 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 outliers start: 38 outliers final: 22 residues processed: 536 average time/residue: 0.4296 time to fit residues: 385.9752 Evaluate side-chains 491 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 469 time to evaluate : 4.380 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3034 time to fit residues: 18.3139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 364 optimal weight: 0.0010 chunk 384 optimal weight: 0.9990 chunk 350 optimal weight: 4.9990 chunk 373 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 293 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 337 optimal weight: 4.9990 chunk 353 optimal weight: 2.9990 chunk 372 optimal weight: 0.0270 overall best weight: 1.4050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 174 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 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 295 HIS G 67 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.139 34096 Z= 0.242 Angle : 0.651 15.087 46328 Z= 0.328 Chirality : 0.047 0.308 5220 Planarity : 0.005 0.100 5980 Dihedral : 5.454 64.028 4680 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.90 % 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: -0.91 (0.13), residues: 4240 helix: 0.25 (0.14), residues: 1448 sheet: -0.92 (0.17), residues: 924 loop : -1.01 (0.15), residues: 1868 *********************** 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 523 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 491 time to evaluate : 4.195 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 outliers start: 32 outliers final: 19 residues processed: 509 average time/residue: 0.4313 time to fit residues: 368.3259 Evaluate side-chains 481 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 462 time to evaluate : 4.333 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3128 time to fit residues: 17.0834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 245 optimal weight: 4.9990 chunk 395 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 274 optimal weight: 0.0010 chunk 414 optimal weight: 1.9990 chunk 381 optimal weight: 3.9990 chunk 330 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 46 GLN ** E 174 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 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 261 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 295 HIS G 67 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.121 34096 Z= 0.251 Angle : 0.683 16.076 46328 Z= 0.340 Chirality : 0.047 0.324 5220 Planarity : 0.005 0.107 5980 Dihedral : 5.456 64.070 4680 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 4240 helix: 0.26 (0.14), residues: 1444 sheet: -0.90 (0.17), residues: 908 loop : -1.07 (0.15), residues: 1888 ********************** 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 503 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 483 time to evaluate : 4.245 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 outliers start: 20 outliers final: 14 residues processed: 496 average time/residue: 0.4328 time to fit residues: 361.3428 Evaluate side-chains 471 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 457 time to evaluate : 4.199 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3093 time to fit residues: 13.8508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 0.9990 chunk 351 optimal weight: 7.9990 chunk 101 optimal weight: 0.0010 chunk 304 optimal weight: 6.9990 chunk 48 optimal weight: 0.1980 chunk 91 optimal weight: 0.0970 chunk 330 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 339 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 129 ASN ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 HIS E 157 ASN ** E 174 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 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN J 279 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 295 HIS G 67 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 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 = 0.3741 r_free = 0.3741 target = 0.107964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085331 restraints weight = 86605.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.087968 restraints weight = 45357.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.089641 restraints weight = 30365.027| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.137 34096 Z= 0.200 Angle : 0.662 15.729 46328 Z= 0.330 Chirality : 0.046 0.313 5220 Planarity : 0.005 0.136 5980 Dihedral : 5.220 57.281 4680 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 0.59 % 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: -0.81 (0.13), residues: 4240 helix: 0.34 (0.14), residues: 1436 sheet: -0.77 (0.17), residues: 908 loop : -1.00 (0.15), residues: 1896 =============================================================================== Job complete usr+sys time: 7839.26 seconds wall clock time: 143 minutes 39.24 seconds (8619.24 seconds total)