Starting phenix.real_space_refine on Tue Nov 21 09:56:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/11_2023/6gve_0071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/11_2023/6gve_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_0071/11_2023/6gve_0071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/11_2023/6gve_0071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/11_2023/6gve_0071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/11_2023/6gve_0071_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 180 5.16 5 C 20896 2.51 5 N 5880 2.21 5 O 6440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 12": "NH1" <-> "NH2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 198": "NH1" <-> "NH2" Residue "D ARG 199": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 288": "NH1" <-> "NH2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 199": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "E TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "E ARG 199": "NH1" <-> "NH2" Residue "E ARG 235": "NH1" <-> "NH2" Residue "E ARG 288": "NH1" <-> "NH2" Residue "F TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 199": "NH1" <-> "NH2" Residue "F ARG 235": "NH1" <-> "NH2" Residue "F ARG 288": "NH1" <-> "NH2" Residue "I TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 198": "NH1" <-> "NH2" Residue "I ARG 199": "NH1" <-> "NH2" Residue "I ARG 235": "NH1" <-> "NH2" Residue "I ARG 288": "NH1" <-> "NH2" Residue "K TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 198": "NH1" <-> "NH2" Residue "K ARG 199": "NH1" <-> "NH2" Residue "K ARG 235": "NH1" <-> "NH2" Residue "K ARG 288": "NH1" <-> "NH2" Residue "N TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 198": "NH1" <-> "NH2" Residue "N ARG 199": "NH1" <-> "NH2" Residue "N ARG 235": "NH1" <-> "NH2" Residue "N ARG 288": "NH1" <-> "NH2" Residue "O TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 198": "NH1" <-> "NH2" Residue "O ARG 199": "NH1" <-> "NH2" Residue "O ARG 235": "NH1" <-> "NH2" Residue "O ARG 288": "NH1" <-> "NH2" Residue "J ARG 27": "NH1" <-> "NH2" Residue "J ARG 145": "NH1" <-> "NH2" Residue "B ARG 27": "NH1" <-> "NH2" Residue "B ARG 145": "NH1" <-> "NH2" Residue "G ARG 27": "NH1" <-> "NH2" Residue "G ARG 145": "NH1" <-> "NH2" Residue "L ARG 27": "NH1" <-> "NH2" Residue "L ARG 145": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "H ARG 12": "NH1" <-> "NH2" Residue "M ARG 12": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 33412 Number of models: 1 Model: "" Number of chains: 24 Chain: "P" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 590 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "D" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "A" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "E" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "F" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "I" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "K" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "N" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "O" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2571 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "J" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2533 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 302} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2533 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 302} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "G" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2533 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 302} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "L" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2533 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 302} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 590 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "H" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 590 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "M" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 590 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.66, per 1000 atoms: 0.50 Number of scatterers: 33412 At special positions: 0 Unit cell: (143.439, 114.123, 213.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 16 15.00 O 6440 8.00 N 5880 7.00 C 20896 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS P 19 " - pdb=" SG CYS P 29 " distance=2.05 Simple disulfide: pdb=" SG CYS P 61 " - pdb=" SG CYS P 70 " distance=2.02 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 41 " distance=2.03 Simple disulfide: pdb=" SG CYS J 230 " - pdb=" SG CYS J 236 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 41 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 236 " distance=2.02 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 41 " distance=2.03 Simple disulfide: pdb=" SG CYS G 230 " - pdb=" SG CYS G 236 " distance=2.02 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 41 " distance=2.03 Simple disulfide: pdb=" SG CYS L 230 " - pdb=" SG CYS L 236 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 29 " distance=2.05 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 70 " distance=2.02 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 29 " distance=2.05 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 70 " distance=2.02 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 29 " distance=2.05 Simple disulfide: pdb=" SG CYS M 61 " - pdb=" SG CYS M 70 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.20 Conformation dependent library (CDL) restraints added in 5.8 seconds 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 32 sheets defined 31.5% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.88 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: 10.52 Time building geometry restraints manager: 13.25 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 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.790 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 83.110 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.067 34096 Z= 0.632 Angle : 0.986 10.513 46328 Z= 0.530 Chirality : 0.064 0.364 5220 Planarity : 0.008 0.077 5980 Dihedral : 10.072 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 % Allowed : 3.19 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.10), residues: 4240 helix: -2.67 (0.10), residues: 1412 sheet: -2.27 (0.15), residues: 896 loop : -2.26 (0.12), residues: 1932 *********************** 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 : 4.233 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: 0.4663 time to fit residues: 755.1051 Evaluate side-chains 531 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 527 time to evaluate : 3.806 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2930 time to fit residues: 7.4678 ------------------------------------------------------------------------------- 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: 10.0000 chunk 168 optimal weight: 3.9990 chunk 326 optimal weight: 4.9990 chunk 126 optimal weight: 0.5980 chunk 198 optimal weight: 1.9990 chunk 242 optimal weight: 0.9990 chunk 377 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 A 276 HIS 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 206 GLN B 90 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN G 206 GLN L 90 ASN L 189 GLN L 279 ASN C 10 GLN C 16 HIS 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: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34096 Z= 0.223 Angle : 0.608 7.991 46328 Z= 0.316 Chirality : 0.046 0.162 5220 Planarity : 0.005 0.055 5980 Dihedral : 6.446 59.599 4680 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.05 % Allowed : 11.65 % Favored : 85.30 % 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: -1.02 (0.13), residues: 1440 sheet: -2.02 (0.16), residues: 872 loop : -1.65 (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 763 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 655 time to evaluate : 3.903 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 outliers start: 108 outliers final: 71 residues processed: 717 average time/residue: 0.4186 time to fit residues: 502.6079 Evaluate side-chains 584 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 513 time to evaluate : 3.649 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.2944 time to fit residues: 44.4889 ------------------------------------------------------------------------------- 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: 1.9990 chunk 117 optimal weight: 9.9990 chunk 314 optimal weight: 9.9990 chunk 257 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 378 optimal weight: 10.0000 chunk 408 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 303 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 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 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 GLN ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 ASN K 7 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 184 GLN ** B 206 GLN ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34096 Z= 0.293 Angle : 0.628 8.318 46328 Z= 0.322 Chirality : 0.048 0.241 5220 Planarity : 0.005 0.057 5980 Dihedral : 6.193 59.493 4680 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.93 % Allowed : 13.97 % Favored : 83.10 % 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: -1.69 (0.13), residues: 4240 helix: -0.20 (0.14), residues: 1408 sheet: -1.65 (0.16), residues: 936 loop : -1.44 (0.14), residues: 1896 *********************** 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 659 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 555 time to evaluate : 3.736 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: 104 outliers final: 59 residues processed: 631 average time/residue: 0.4427 time to fit residues: 470.5851 Evaluate side-chains 540 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 481 time to evaluate : 3.814 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.3195 time to fit residues: 40.9844 ------------------------------------------------------------------------------- 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: 0.3980 chunk 284 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 254 optimal weight: 7.9990 chunk 379 optimal weight: 0.6980 chunk 402 optimal weight: 10.0000 chunk 198 optimal weight: 0.6980 chunk 359 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** I 260 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 GLN ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** O 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN B 90 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS B 309 GLN G 309 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34096 Z= 0.173 Angle : 0.576 13.164 46328 Z= 0.291 Chirality : 0.045 0.215 5220 Planarity : 0.004 0.055 5980 Dihedral : 5.758 59.438 4680 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.69 % Allowed : 16.70 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 4240 helix: 0.08 (0.14), residues: 1444 sheet: -1.34 (0.16), residues: 912 loop : -1.31 (0.14), residues: 1884 *********************** 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 638 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 578 time to evaluate : 4.201 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: 60 outliers final: 32 residues processed: 604 average time/residue: 0.4283 time to fit residues: 433.3223 Evaluate side-chains 517 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 485 time to evaluate : 3.824 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3126 time to fit residues: 23.9861 ------------------------------------------------------------------------------- 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: 6.9990 chunk 228 optimal weight: 0.4980 chunk 5 optimal weight: 7.9990 chunk 299 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 343 optimal weight: 0.8980 chunk 277 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 360 optimal weight: 10.0000 chunk 101 optimal weight: 0.7980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 226 GLN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 HIS N 112 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN J 90 ASN B 90 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS G 67 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34096 Z= 0.185 Angle : 0.579 10.090 46328 Z= 0.293 Chirality : 0.045 0.262 5220 Planarity : 0.004 0.053 5980 Dihedral : 5.603 56.896 4680 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.83 % Allowed : 17.58 % Favored : 80.59 % 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: -1.05 (0.13), residues: 4240 helix: 0.24 (0.14), residues: 1440 sheet: -1.11 (0.17), residues: 912 loop : -1.12 (0.14), residues: 1888 *********************** 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 596 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 531 time to evaluate : 3.727 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 outliers start: 65 outliers final: 34 residues processed: 574 average time/residue: 0.4127 time to fit residues: 399.9026 Evaluate side-chains 511 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 477 time to evaluate : 4.165 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3115 time to fit residues: 26.0354 ------------------------------------------------------------------------------- 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: 5.9990 chunk 362 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 402 optimal weight: 10.0000 chunk 334 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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** A 15 ASN ** A 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 129 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** O 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** 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 10 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 34096 Z= 0.402 Angle : 0.717 12.380 46328 Z= 0.364 Chirality : 0.049 0.284 5220 Planarity : 0.005 0.052 5980 Dihedral : 6.130 65.259 4680 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 2.43 % Allowed : 18.91 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 4240 helix: -0.02 (0.14), residues: 1468 sheet: -1.18 (0.17), residues: 928 loop : -1.27 (0.14), residues: 1844 *********************** 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 575 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 489 time to evaluate : 3.889 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: 86 outliers final: 52 residues processed: 544 average time/residue: 0.4221 time to fit residues: 389.4801 Evaluate side-chains 499 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 447 time to evaluate : 3.994 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.3174 time to fit residues: 36.1176 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 227 optimal weight: 0.4980 chunk 338 optimal weight: 1.9990 chunk 224 optimal weight: 0.9990 chunk 400 optimal weight: 2.9990 chunk 250 optimal weight: 8.9990 chunk 244 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 ASN A 174 GLN ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** 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 240 ASN ** 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 15 ASN J 90 ASN J 279 ASN J 284 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN G 279 ASN G 295 HIS ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34096 Z= 0.174 Angle : 0.614 13.914 46328 Z= 0.306 Chirality : 0.046 0.316 5220 Planarity : 0.004 0.051 5980 Dihedral : 5.663 61.608 4680 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.24 % Allowed : 19.44 % Favored : 79.32 % 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: 0.24 (0.14), residues: 1440 sheet: -0.99 (0.17), residues: 920 loop : -1.00 (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 587 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 543 time to evaluate : 3.696 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: 44 outliers final: 22 residues processed: 563 average time/residue: 0.4297 time to fit residues: 408.8881 Evaluate side-chains 498 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 476 time to evaluate : 3.804 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3143 time to fit residues: 18.2539 ------------------------------------------------------------------------------- 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: 8.9990 chunk 160 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 254 optimal weight: 0.7980 chunk 273 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 315 optimal weight: 0.9980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** I 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN ** O 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS G 67 ASN ** C 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 34096 Z= 0.186 Angle : 0.617 14.656 46328 Z= 0.308 Chirality : 0.046 0.296 5220 Planarity : 0.004 0.051 5980 Dihedral : 5.402 56.757 4680 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.13 % Allowed : 21.08 % Favored : 77.79 % 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: -0.82 (0.13), residues: 4240 helix: 0.26 (0.14), residues: 1448 sheet: -0.96 (0.17), residues: 928 loop : -0.84 (0.15), residues: 1864 *********************** 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 552 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 512 time to evaluate : 3.809 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 outliers start: 40 outliers final: 25 residues processed: 531 average time/residue: 0.4315 time to fit residues: 385.4140 Evaluate side-chains 501 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 476 time to evaluate : 3.998 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3276 time to fit residues: 20.5932 ------------------------------------------------------------------------------- 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: 0.5980 chunk 384 optimal weight: 4.9990 chunk 350 optimal weight: 4.9990 chunk 373 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 337 optimal weight: 8.9990 chunk 353 optimal weight: 5.9990 chunk 372 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 HIS A 15 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** 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 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 GLN ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN J 284 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS C 46 GLN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 34096 Z= 0.345 Angle : 0.709 15.645 46328 Z= 0.357 Chirality : 0.049 0.327 5220 Planarity : 0.004 0.060 5980 Dihedral : 5.757 71.682 4680 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.19 % Allowed : 20.97 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.13), residues: 4240 helix: 0.14 (0.14), residues: 1440 sheet: -1.02 (0.17), residues: 928 loop : -0.99 (0.15), residues: 1872 *********************** 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 519 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 477 time to evaluate : 4.034 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: 42 outliers final: 29 residues processed: 497 average time/residue: 0.4340 time to fit residues: 365.1016 Evaluate side-chains 479 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 450 time to evaluate : 3.729 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3130 time to fit residues: 22.5635 ------------------------------------------------------------------------------- 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: 2.9990 chunk 395 optimal weight: 9.9990 chunk 241 optimal weight: 0.3980 chunk 187 optimal weight: 0.4980 chunk 274 optimal weight: 2.9990 chunk 414 optimal weight: 0.7980 chunk 381 optimal weight: 0.0570 chunk 330 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** 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 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 GLN K 7 ASN N 15 ASN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 ASN ** O 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 335 HIS ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 284 HIS ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS G 67 ASN L 90 ASN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 34096 Z= 0.178 Angle : 0.672 15.685 46328 Z= 0.331 Chirality : 0.047 0.444 5220 Planarity : 0.004 0.049 5980 Dihedral : 5.347 61.890 4680 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.34 % Allowed : 21.90 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4240 helix: 0.33 (0.14), residues: 1436 sheet: -0.95 (0.17), residues: 928 loop : -0.82 (0.15), residues: 1876 ********************** 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 542 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 530 time to evaluate : 3.856 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 outliers start: 12 outliers final: 6 residues processed: 533 average time/residue: 0.4236 time to fit residues: 381.2740 Evaluate side-chains 487 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 481 time to evaluate : 3.898 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3179 time to fit residues: 8.6871 ------------------------------------------------------------------------------- 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: 8.9990 chunk 351 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 304 optimal weight: 0.9980 chunk 48 optimal weight: 0.0770 chunk 91 optimal weight: 4.9990 chunk 330 optimal weight: 0.8980 chunk 138 optimal weight: 3.9990 chunk 339 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** I 240 ASN ** I 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 7 ASN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS L 90 ASN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.107581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.084161 restraints weight = 87996.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.086743 restraints weight = 47660.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.088379 restraints weight = 32621.879| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 34096 Z= 0.180 Angle : 0.660 15.205 46328 Z= 0.324 Chirality : 0.047 0.495 5220 Planarity : 0.004 0.052 5980 Dihedral : 5.188 56.741 4680 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.59 % Allowed : 22.60 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.13), residues: 4240 helix: 0.33 (0.14), residues: 1436 sheet: -0.87 (0.17), residues: 928 loop : -0.76 (0.15), residues: 1876 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8122.86 seconds wall clock time: 148 minutes 53.36 seconds (8933.36 seconds total)