Starting phenix.real_space_refine on Sat Dec 16 01:56:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/12_2023/6gve_0071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/12_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_0071/12_2023/6gve_0071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/12_2023/6gve_0071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/12_2023/6gve_0071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gve_0071/12_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 16.99, per 1000 atoms: 0.51 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: 15.14 Conformation dependent library (CDL) restraints added in 6.5 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: 6.84 Creating SS restraints... Processing helix chain 'P' and resid 3 through 21 removed outlier: 4.057A pdb=" N GLU P 9 " --> pdb=" O GLU P 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS P 19 " --> pdb=" O ALA P 15 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP P 20 " --> pdb=" O HIS P 16 " (cutoff:3.500A) Processing helix chain 'P' and resid 27 through 51 Processing helix chain 'P' and resid 57 through 63 removed outlier: 4.253A pdb=" N ASP P 62 " --> pdb=" O GLN P 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 22 Processing helix chain 'D' and resid 40 through 48 removed outlier: 3.914A pdb=" N ALA D 44 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS D 45 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 106 through 115 removed outlier: 3.812A pdb=" N LYS D 111 " --> pdb=" O GLU D 107 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 169 Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 223 through 225 No H-bonds generated for 'chain 'D' and resid 223 through 225' Processing helix chain 'D' and resid 256 through 269 removed outlier: 3.626A pdb=" N ASN D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 287 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 320 through 334 Processing helix chain 'A' and resid 11 through 22 Processing helix chain 'A' and resid 40 through 48 removed outlier: 3.914A pdb=" N ALA A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 106 through 115 removed outlier: 3.811A pdb=" N LYS A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 169 Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.627A pdb=" N ASN A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 320 through 334 Processing helix chain 'E' and resid 11 through 22 Processing helix chain 'E' and resid 40 through 48 removed outlier: 3.914A pdb=" N ALA E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 106 through 115 removed outlier: 3.811A pdb=" N LYS E 111 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 169 Proline residue: E 161 - end of helix Processing helix chain 'E' and resid 216 through 221 Processing helix chain 'E' and resid 223 through 225 No H-bonds generated for 'chain 'E' and resid 223 through 225' Processing helix chain 'E' and resid 256 through 269 removed outlier: 3.627A pdb=" N ASN E 260 " --> pdb=" O ALA E 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 287 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 320 through 334 Processing helix chain 'F' and resid 11 through 22 Processing helix chain 'F' and resid 40 through 48 removed outlier: 3.914A pdb=" N ALA F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS F 45 " --> pdb=" O ARG F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 85 No H-bonds generated for 'chain 'F' and resid 83 through 85' Processing helix chain 'F' and resid 106 through 115 removed outlier: 3.812A pdb=" N LYS F 111 " --> pdb=" O GLU F 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS F 112 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 169 Proline residue: F 161 - end of helix Processing helix chain 'F' and resid 216 through 221 Processing helix chain 'F' and resid 223 through 225 No H-bonds generated for 'chain 'F' and resid 223 through 225' Processing helix chain 'F' and resid 256 through 269 removed outlier: 3.627A pdb=" N ASN F 260 " --> pdb=" O ALA F 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 287 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 320 through 334 Processing helix chain 'I' and resid 11 through 22 Processing helix chain 'I' and resid 40 through 48 removed outlier: 3.913A pdb=" N ALA I 44 " --> pdb=" O PRO I 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 85 No H-bonds generated for 'chain 'I' and resid 83 through 85' Processing helix chain 'I' and resid 106 through 115 removed outlier: 3.812A pdb=" N LYS I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS I 112 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 154 through 169 Proline residue: I 161 - end of helix Processing helix chain 'I' and resid 216 through 221 Processing helix chain 'I' and resid 223 through 225 No H-bonds generated for 'chain 'I' and resid 223 through 225' Processing helix chain 'I' and resid 256 through 269 removed outlier: 3.627A pdb=" N ASN I 260 " --> pdb=" O ALA I 256 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU I 268 " --> pdb=" O LYS I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 287 Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 320 through 334 Processing helix chain 'K' and resid 11 through 22 Processing helix chain 'K' and resid 40 through 48 removed outlier: 3.914A pdb=" N ALA K 44 " --> pdb=" O PRO K 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS K 45 " --> pdb=" O ARG K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 85 No H-bonds generated for 'chain 'K' and resid 83 through 85' Processing helix chain 'K' and resid 106 through 115 removed outlier: 3.812A pdb=" N LYS K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS K 112 " --> pdb=" O GLY K 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU K 113 " --> pdb=" O ALA K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 154 through 169 Proline residue: K 161 - end of helix Processing helix chain 'K' and resid 216 through 221 Processing helix chain 'K' and resid 223 through 225 No H-bonds generated for 'chain 'K' and resid 223 through 225' Processing helix chain 'K' and resid 256 through 269 removed outlier: 3.627A pdb=" N ASN K 260 " --> pdb=" O ALA K 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU K 268 " --> pdb=" O LYS K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 287 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 320 through 334 Processing helix chain 'N' and resid 11 through 22 Processing helix chain 'N' and resid 40 through 48 removed outlier: 3.914A pdb=" N ALA N 44 " --> pdb=" O PRO N 40 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS N 45 " --> pdb=" O ARG N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 85 No H-bonds generated for 'chain 'N' and resid 83 through 85' Processing helix chain 'N' and resid 106 through 115 removed outlier: 3.812A pdb=" N LYS N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS N 112 " --> pdb=" O GLY N 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 154 through 169 Proline residue: N 161 - end of helix Processing helix chain 'N' and resid 216 through 221 Processing helix chain 'N' and resid 223 through 225 No H-bonds generated for 'chain 'N' and resid 223 through 225' Processing helix chain 'N' and resid 256 through 269 removed outlier: 3.627A pdb=" N ASN N 260 " --> pdb=" O ALA N 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU N 268 " --> pdb=" O LYS N 264 " (cutoff:3.500A) Processing helix chain 'N' and resid 284 through 287 Processing helix chain 'N' and resid 298 through 300 No H-bonds generated for 'chain 'N' and resid 298 through 300' Processing helix chain 'N' and resid 320 through 334 Processing helix chain 'O' and resid 11 through 22 Processing helix chain 'O' and resid 40 through 48 removed outlier: 3.914A pdb=" N ALA O 44 " --> pdb=" O PRO O 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS O 45 " --> pdb=" O ARG O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 85 No H-bonds generated for 'chain 'O' and resid 83 through 85' Processing helix chain 'O' and resid 106 through 115 removed outlier: 3.812A pdb=" N LYS O 111 " --> pdb=" O GLU O 107 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS O 112 " --> pdb=" O GLY O 108 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 169 Proline residue: O 161 - end of helix Processing helix chain 'O' and resid 216 through 221 Processing helix chain 'O' and resid 223 through 225 No H-bonds generated for 'chain 'O' and resid 223 through 225' Processing helix chain 'O' and resid 256 through 269 removed outlier: 3.627A pdb=" N ASN O 260 " --> pdb=" O ALA O 256 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU O 268 " --> pdb=" O LYS O 264 " (cutoff:3.500A) Processing helix chain 'O' and resid 284 through 287 Processing helix chain 'O' and resid 298 through 300 No H-bonds generated for 'chain 'O' and resid 298 through 300' Processing helix chain 'O' and resid 320 through 334 Processing helix chain 'J' and resid 23 through 31 Processing helix chain 'J' and resid 50 through 56 Processing helix chain 'J' and resid 68 through 79 removed outlier: 3.563A pdb=" N TYR J 72 " --> pdb=" O PHE J 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 148 removed outlier: 3.519A pdb=" N LYS J 144 " --> pdb=" O ALA J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 157 through 171 removed outlier: 3.708A pdb=" N ASN J 162 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA J 163 " --> pdb=" O ALA J 159 " (cutoff:3.500A) Proline residue: J 166 - end of helix Processing helix chain 'J' and resid 173 through 175 No H-bonds generated for 'chain 'J' and resid 173 through 175' Processing helix chain 'J' and resid 268 through 274 removed outlier: 3.824A pdb=" N ILE J 273 " --> pdb=" O GLU J 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU J 274 " --> pdb=" O LEU J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 293 Processing helix chain 'J' and resid 304 through 324 removed outlier: 3.572A pdb=" N VAL J 310 " --> pdb=" O GLY J 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 31 Processing helix chain 'B' and resid 50 through 56 Processing helix chain 'B' and resid 68 through 79 removed outlier: 3.563A pdb=" N TYR B 72 " --> pdb=" O PHE B 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 79 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.519A pdb=" N LYS B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 171 removed outlier: 3.707A pdb=" N ASN B 162 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Proline residue: B 166 - end of helix Processing helix chain 'B' and resid 173 through 175 No H-bonds generated for 'chain 'B' and resid 173 through 175' Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.824A pdb=" N ILE B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 304 through 324 removed outlier: 3.572A pdb=" N VAL B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 31 Processing helix chain 'G' and resid 50 through 56 Processing helix chain 'G' and resid 68 through 79 removed outlier: 3.563A pdb=" N TYR G 72 " --> pdb=" O PHE G 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 148 removed outlier: 3.519A pdb=" N LYS G 144 " --> pdb=" O ALA G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 171 removed outlier: 3.708A pdb=" N ASN G 162 " --> pdb=" O ILE G 158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA G 163 " --> pdb=" O ALA G 159 " (cutoff:3.500A) Proline residue: G 166 - end of helix Processing helix chain 'G' and resid 173 through 175 No H-bonds generated for 'chain 'G' and resid 173 through 175' Processing helix chain 'G' and resid 268 through 274 removed outlier: 3.824A pdb=" N ILE G 273 " --> pdb=" O GLU G 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU G 274 " --> pdb=" O LEU G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 287 through 293 Processing helix chain 'G' and resid 304 through 324 removed outlier: 3.572A pdb=" N VAL G 310 " --> pdb=" O GLY G 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 31 Processing helix chain 'L' and resid 50 through 56 Processing helix chain 'L' and resid 68 through 79 removed outlier: 3.563A pdb=" N TYR L 72 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS L 79 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 148 removed outlier: 3.519A pdb=" N LYS L 144 " --> pdb=" O ALA L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 171 removed outlier: 3.708A pdb=" N ASN L 162 " --> pdb=" O ILE L 158 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA L 163 " --> pdb=" O ALA L 159 " (cutoff:3.500A) Proline residue: L 166 - end of helix Processing helix chain 'L' and resid 173 through 175 No H-bonds generated for 'chain 'L' and resid 173 through 175' Processing helix chain 'L' and resid 268 through 274 removed outlier: 3.824A pdb=" N ILE L 273 " --> pdb=" O GLU L 269 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU L 274 " --> pdb=" O LEU L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 293 Processing helix chain 'L' and resid 304 through 324 removed outlier: 3.572A pdb=" N VAL L 310 " --> pdb=" O GLY L 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 21 removed outlier: 4.057A pdb=" N GLU C 9 " --> pdb=" O GLU C 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS C 19 " --> pdb=" O ALA C 15 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP C 20 " --> pdb=" O HIS C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 51 Processing helix chain 'C' and resid 57 through 63 removed outlier: 4.252A pdb=" N ASP C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 21 removed outlier: 4.057A pdb=" N GLU H 9 " --> pdb=" O GLU H 5 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP H 20 " --> pdb=" O HIS H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 51 Processing helix chain 'H' and resid 57 through 63 removed outlier: 4.253A pdb=" N ASP H 62 " --> pdb=" O GLN H 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 21 removed outlier: 4.057A pdb=" N GLU M 9 " --> pdb=" O GLU M 5 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS M 19 " --> pdb=" O ALA M 15 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP M 20 " --> pdb=" O HIS M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 51 Processing helix chain 'M' and resid 57 through 63 removed outlier: 4.253A pdb=" N ASP M 62 " --> pdb=" O GLN M 58 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL D 120 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN D 151 " --> pdb=" O VAL D 120 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE D 122 " --> pdb=" O ASN D 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU D 95 " --> pdb=" O ARG D 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE D 6 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE D 34 " --> pdb=" O ILE D 6 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA D 74 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE D 34 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS D 76 " --> pdb=" O ILE D 34 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 208 through 212 removed outlier: 3.960A pdb=" N THR D 212 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY D 231 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ASN D 230 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY D 175 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE D 232 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET D 177 " --> pdb=" O ILE D 232 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU D 234 " --> pdb=" O MET D 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR D 179 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL D 236 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS D 181 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN D 249 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY D 175 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL D 247 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET D 177 " --> pdb=" O ASP D 245 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP D 245 " --> pdb=" O MET D 177 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR D 179 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL D 243 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N HIS D 181 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL D 241 " --> pdb=" O HIS D 181 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 275 through 278 removed outlier: 6.259A pdb=" N SER D 294 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER D 278 " --> pdb=" O SER D 294 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU D 296 " --> pdb=" O SER D 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL A 120 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN A 151 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE A 122 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 95 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE A 6 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE A 34 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA A 74 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE A 34 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS A 76 " --> pdb=" O ILE A 34 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR A 212 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A 231 " --> pdb=" O THR A 212 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ASN A 230 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY A 175 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE A 232 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET A 177 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU A 234 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR A 179 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL A 236 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS A 181 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN A 249 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY A 175 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 247 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET A 177 " --> pdb=" O ASP A 245 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP A 245 " --> pdb=" O MET A 177 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR A 179 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 243 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS A 181 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL A 241 " --> pdb=" O HIS A 181 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 275 through 278 removed outlier: 6.258A pdb=" N SER A 294 " --> pdb=" O HIS A 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER A 278 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A 296 " --> pdb=" O SER A 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'E' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL E 120 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN E 151 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE E 122 " --> pdb=" O ASN E 151 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 95 " --> pdb=" O ARG E 3 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE E 6 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE E 34 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ALA E 74 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE E 34 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS E 76 " --> pdb=" O ILE E 34 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR E 212 " --> pdb=" O GLY E 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY E 231 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N ASN E 230 " --> pdb=" O GLN E 173 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY E 175 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ILE E 232 " --> pdb=" O GLY E 175 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N MET E 177 " --> pdb=" O ILE E 232 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU E 234 " --> pdb=" O MET E 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR E 179 " --> pdb=" O LEU E 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL E 236 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS E 181 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN E 249 " --> pdb=" O GLN E 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY E 175 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL E 247 " --> pdb=" O GLY E 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET E 177 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP E 245 " --> pdb=" O MET E 177 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR E 179 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL E 243 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS E 181 " --> pdb=" O VAL E 241 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL E 241 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 275 through 278 removed outlier: 6.259A pdb=" N SER E 294 " --> pdb=" O HIS E 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER E 278 " --> pdb=" O SER E 294 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU E 296 " --> pdb=" O SER E 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'F' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL F 120 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN F 151 " --> pdb=" O VAL F 120 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE F 122 " --> pdb=" O ASN F 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU F 95 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE F 6 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE F 34 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA F 74 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE F 34 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS F 76 " --> pdb=" O ILE F 34 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR F 212 " --> pdb=" O GLY F 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY F 231 " --> pdb=" O THR F 212 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N ASN F 230 " --> pdb=" O GLN F 173 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY F 175 " --> pdb=" O ASN F 230 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE F 232 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET F 177 " --> pdb=" O ILE F 232 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU F 234 " --> pdb=" O MET F 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR F 179 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL F 236 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS F 181 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN F 249 " --> pdb=" O GLN F 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY F 175 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL F 247 " --> pdb=" O GLY F 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET F 177 " --> pdb=" O ASP F 245 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP F 245 " --> pdb=" O MET F 177 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR F 179 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL F 243 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS F 181 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL F 241 " --> pdb=" O HIS F 181 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 275 through 278 removed outlier: 6.258A pdb=" N SER F 294 " --> pdb=" O HIS F 276 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N SER F 278 " --> pdb=" O SER F 294 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU F 296 " --> pdb=" O SER F 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'I' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL I 120 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN I 151 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE I 122 " --> pdb=" O ASN I 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU I 95 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE I 6 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE I 34 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ALA I 74 " --> pdb=" O VAL I 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE I 34 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS I 76 " --> pdb=" O ILE I 34 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 208 through 212 removed outlier: 3.958A pdb=" N THR I 212 " --> pdb=" O GLY I 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY I 231 " --> pdb=" O THR I 212 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ASN I 230 " --> pdb=" O GLN I 173 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY I 175 " --> pdb=" O ASN I 230 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE I 232 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET I 177 " --> pdb=" O ILE I 232 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU I 234 " --> pdb=" O MET I 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR I 179 " --> pdb=" O LEU I 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL I 236 " --> pdb=" O THR I 179 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS I 181 " --> pdb=" O VAL I 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN I 249 " --> pdb=" O GLN I 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY I 175 " --> pdb=" O VAL I 247 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL I 247 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET I 177 " --> pdb=" O ASP I 245 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP I 245 " --> pdb=" O MET I 177 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR I 179 " --> pdb=" O VAL I 243 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL I 243 " --> pdb=" O THR I 179 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS I 181 " --> pdb=" O VAL I 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL I 241 " --> pdb=" O HIS I 181 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 275 through 278 removed outlier: 6.258A pdb=" N SER I 294 " --> pdb=" O HIS I 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER I 278 " --> pdb=" O SER I 294 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU I 296 " --> pdb=" O SER I 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'K' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL K 120 " --> pdb=" O VAL K 149 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN K 151 " --> pdb=" O VAL K 120 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE K 122 " --> pdb=" O ASN K 151 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU K 95 " --> pdb=" O ARG K 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE K 6 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE K 34 " --> pdb=" O ILE K 6 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ALA K 74 " --> pdb=" O VAL K 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE K 34 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS K 76 " --> pdb=" O ILE K 34 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'K' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR K 212 " --> pdb=" O GLY K 231 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY K 231 " --> pdb=" O THR K 212 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N ASN K 230 " --> pdb=" O GLN K 173 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY K 175 " --> pdb=" O ASN K 230 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ILE K 232 " --> pdb=" O GLY K 175 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET K 177 " --> pdb=" O ILE K 232 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU K 234 " --> pdb=" O MET K 177 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR K 179 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL K 236 " --> pdb=" O THR K 179 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS K 181 " --> pdb=" O VAL K 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN K 249 " --> pdb=" O GLN K 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY K 175 " --> pdb=" O VAL K 247 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL K 247 " --> pdb=" O GLY K 175 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET K 177 " --> pdb=" O ASP K 245 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP K 245 " --> pdb=" O MET K 177 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR K 179 " --> pdb=" O VAL K 243 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL K 243 " --> pdb=" O THR K 179 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS K 181 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL K 241 " --> pdb=" O HIS K 181 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'K' and resid 275 through 278 removed outlier: 6.258A pdb=" N SER K 294 " --> pdb=" O HIS K 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER K 278 " --> pdb=" O SER K 294 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU K 296 " --> pdb=" O SER K 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'N' and resid 148 through 151 removed outlier: 6.267A pdb=" N VAL N 120 " --> pdb=" O VAL N 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN N 151 " --> pdb=" O VAL N 120 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE N 122 " --> pdb=" O ASN N 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU N 95 " --> pdb=" O ARG N 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE N 6 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE N 34 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA N 74 " --> pdb=" O VAL N 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE N 34 " --> pdb=" O ALA N 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS N 76 " --> pdb=" O ILE N 34 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'N' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR N 212 " --> pdb=" O GLY N 231 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY N 231 " --> pdb=" O THR N 212 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ASN N 230 " --> pdb=" O GLN N 173 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY N 175 " --> pdb=" O ASN N 230 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ILE N 232 " --> pdb=" O GLY N 175 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET N 177 " --> pdb=" O ILE N 232 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU N 234 " --> pdb=" O MET N 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR N 179 " --> pdb=" O LEU N 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL N 236 " --> pdb=" O THR N 179 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N HIS N 181 " --> pdb=" O VAL N 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN N 249 " --> pdb=" O GLN N 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY N 175 " --> pdb=" O VAL N 247 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL N 247 " --> pdb=" O GLY N 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET N 177 " --> pdb=" O ASP N 245 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP N 245 " --> pdb=" O MET N 177 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR N 179 " --> pdb=" O VAL N 243 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL N 243 " --> pdb=" O THR N 179 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HIS N 181 " --> pdb=" O VAL N 241 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL N 241 " --> pdb=" O HIS N 181 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'N' and resid 275 through 278 removed outlier: 6.258A pdb=" N SER N 294 " --> pdb=" O HIS N 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER N 278 " --> pdb=" O SER N 294 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU N 296 " --> pdb=" O SER N 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'O' and resid 148 through 151 removed outlier: 6.268A pdb=" N VAL O 120 " --> pdb=" O VAL O 149 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ASN O 151 " --> pdb=" O VAL O 120 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE O 122 " --> pdb=" O ASN O 151 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU O 95 " --> pdb=" O ARG O 3 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE O 6 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE O 34 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ALA O 74 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 9.062A pdb=" N ILE O 34 " --> pdb=" O ALA O 74 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LYS O 76 " --> pdb=" O ILE O 34 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'O' and resid 208 through 212 removed outlier: 3.959A pdb=" N THR O 212 " --> pdb=" O GLY O 231 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY O 231 " --> pdb=" O THR O 212 " (cutoff:3.500A) removed outlier: 9.189A pdb=" N ASN O 230 " --> pdb=" O GLN O 173 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY O 175 " --> pdb=" O ASN O 230 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ILE O 232 " --> pdb=" O GLY O 175 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET O 177 " --> pdb=" O ILE O 232 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU O 234 " --> pdb=" O MET O 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR O 179 " --> pdb=" O LEU O 234 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL O 236 " --> pdb=" O THR O 179 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS O 181 " --> pdb=" O VAL O 236 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN O 249 " --> pdb=" O GLN O 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY O 175 " --> pdb=" O VAL O 247 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL O 247 " --> pdb=" O GLY O 175 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET O 177 " --> pdb=" O ASP O 245 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASP O 245 " --> pdb=" O MET O 177 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR O 179 " --> pdb=" O VAL O 243 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL O 243 " --> pdb=" O THR O 179 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N HIS O 181 " --> pdb=" O VAL O 241 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N VAL O 241 " --> pdb=" O HIS O 181 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'O' and resid 275 through 278 removed outlier: 6.258A pdb=" N SER O 294 " --> pdb=" O HIS O 276 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER O 278 " --> pdb=" O SER O 294 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU O 296 " --> pdb=" O SER O 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'J' and resid 107 through 112 removed outlier: 6.169A pdb=" N VAL J 9 " --> pdb=" O ILE J 108 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE J 110 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE J 11 " --> pdb=" O ILE J 110 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY J 112 " --> pdb=" O ILE J 11 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL J 13 " --> pdb=" O GLY J 112 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE J 127 " --> pdb=" O GLY J 12 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ALA J 14 " --> pdb=" O PHE J 127 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL J 129 " --> pdb=" O ALA J 14 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL J 181 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU J 258 " --> pdb=" O MET J 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN J 206 " --> pdb=" O SER J 256 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 84 through 86 Processing sheet with id= AA, first strand: chain 'B' and resid 107 through 112 removed outlier: 6.169A pdb=" N VAL B 9 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE B 110 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE B 11 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLY B 112 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL B 13 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE B 127 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ALA B 14 " --> pdb=" O PHE B 127 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 129 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL B 181 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 258 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 206 " --> pdb=" O SER B 256 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 84 through 86 Processing sheet with id= AC, first strand: chain 'G' and resid 107 through 112 removed outlier: 6.169A pdb=" N VAL G 9 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE G 110 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE G 11 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY G 112 " --> pdb=" O ILE G 11 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 13 " --> pdb=" O GLY G 112 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE G 127 " --> pdb=" O GLY G 12 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ALA G 14 " --> pdb=" O PHE G 127 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL G 129 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL G 181 " --> pdb=" O TYR G 130 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU G 258 " --> pdb=" O MET G 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN G 206 " --> pdb=" O SER G 256 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 84 through 86 Processing sheet with id= AE, first strand: chain 'L' and resid 107 through 112 removed outlier: 6.169A pdb=" N VAL L 9 " --> pdb=" O ILE L 108 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ILE L 110 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE L 11 " --> pdb=" O ILE L 110 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY L 112 " --> pdb=" O ILE L 11 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL L 13 " --> pdb=" O GLY L 112 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE L 127 " --> pdb=" O GLY L 12 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ALA L 14 " --> pdb=" O PHE L 127 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL L 129 " --> pdb=" O ALA L 14 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL L 181 " --> pdb=" O TYR L 130 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 258 " --> pdb=" O MET L 204 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN L 206 " --> pdb=" O SER L 256 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'L' and resid 84 through 86 1016 hydrogen bonds defined for protein. 2916 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.84 Time building geometry restraints manager: 16.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10572 1.33 - 1.45: 5793 1.45 - 1.57: 17411 1.57 - 1.69: 32 1.69 - 1.81: 288 Bond restraints: 34096 Sorted by residual: bond pdb=" O3 NAD K1001 " pdb=" PA NAD K1001 " ideal model delta sigma weight residual 1.653 1.593 0.060 2.00e-02 2.50e+03 8.91e+00 bond pdb=" O3 NAD N1001 " pdb=" PA NAD N1001 " ideal model delta sigma weight residual 1.653 1.594 0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" O3 NAD I1001 " pdb=" PA NAD I1001 " ideal model delta sigma weight residual 1.653 1.594 0.059 2.00e-02 2.50e+03 8.85e+00 bond pdb=" O3 NAD A1001 " pdb=" PA NAD A1001 " ideal model delta sigma weight residual 1.653 1.594 0.059 2.00e-02 2.50e+03 8.82e+00 bond pdb=" O3 NAD D1001 " pdb=" PA NAD D1001 " ideal model delta sigma weight residual 1.653 1.594 0.059 2.00e-02 2.50e+03 8.81e+00 ... (remaining 34091 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.31: 744 105.31 - 112.53: 18087 112.53 - 119.75: 11906 119.75 - 126.96: 15166 126.96 - 134.18: 425 Bond angle restraints: 46328 Sorted by residual: angle pdb=" C TYR J 154 " pdb=" N GLU J 155 " pdb=" CA GLU J 155 " ideal model delta sigma weight residual 121.54 132.05 -10.51 1.91e+00 2.74e-01 3.03e+01 angle pdb=" C TYR G 154 " pdb=" N GLU G 155 " pdb=" CA GLU G 155 " ideal model delta sigma weight residual 121.54 132.03 -10.49 1.91e+00 2.74e-01 3.02e+01 angle pdb=" C TYR B 154 " pdb=" N GLU B 155 " pdb=" CA GLU B 155 " ideal model delta sigma weight residual 121.54 132.00 -10.46 1.91e+00 2.74e-01 3.00e+01 angle pdb=" C TYR L 154 " pdb=" N GLU L 155 " pdb=" CA GLU L 155 " ideal model delta sigma weight residual 121.54 131.99 -10.45 1.91e+00 2.74e-01 2.99e+01 angle pdb=" C LEU L 218 " pdb=" N PHE L 219 " pdb=" CA PHE L 219 " ideal model delta sigma weight residual 121.54 129.55 -8.01 1.91e+00 2.74e-01 1.76e+01 ... (remaining 46323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.12: 19389 15.12 - 30.24: 1095 30.24 - 45.35: 200 45.35 - 60.47: 52 60.47 - 75.59: 16 Dihedral angle restraints: 20752 sinusoidal: 8428 harmonic: 12324 Sorted by residual: dihedral pdb=" CB CYS H 19 " pdb=" SG CYS H 19 " pdb=" SG CYS H 29 " pdb=" CB CYS H 29 " ideal model delta sinusoidal sigma weight residual 93.00 19.46 73.54 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS P 19 " pdb=" SG CYS P 19 " pdb=" SG CYS P 29 " pdb=" CB CYS P 29 " ideal model delta sinusoidal sigma weight residual 93.00 19.46 73.54 1 1.00e+01 1.00e-02 6.88e+01 dihedral pdb=" CB CYS C 19 " pdb=" SG CYS C 19 " pdb=" SG CYS C 29 " pdb=" CB CYS C 29 " ideal model delta sinusoidal sigma weight residual 93.00 19.46 73.54 1 1.00e+01 1.00e-02 6.88e+01 ... (remaining 20749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4093 0.073 - 0.146: 988 0.146 - 0.218: 99 0.218 - 0.291: 28 0.291 - 0.364: 12 Chirality restraints: 5220 Sorted by residual: chirality pdb=" CB ILE K 148 " pdb=" CA ILE K 148 " pdb=" CG1 ILE K 148 " pdb=" CG2 ILE K 148 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE F 148 " pdb=" CA ILE F 148 " pdb=" CG1 ILE F 148 " pdb=" CG2 ILE F 148 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB ILE N 148 " pdb=" CA ILE N 148 " pdb=" CG1 ILE N 148 " pdb=" CG2 ILE N 148 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 5217 not shown) Planarity restraints: 5980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD E1001 " -0.013 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" C2N NAD E1001 " 0.049 2.00e-02 2.50e+03 pdb=" C3N NAD E1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD E1001 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD E1001 " -0.003 2.00e-02 2.50e+03 pdb=" C6N NAD E1001 " -0.027 2.00e-02 2.50e+03 pdb=" C7N NAD E1001 " -0.039 2.00e-02 2.50e+03 pdb=" N1N NAD E1001 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A1001 " -0.013 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" C2N NAD A1001 " 0.049 2.00e-02 2.50e+03 pdb=" C3N NAD A1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD A1001 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD A1001 " -0.003 2.00e-02 2.50e+03 pdb=" C6N NAD A1001 " -0.027 2.00e-02 2.50e+03 pdb=" C7N NAD A1001 " -0.039 2.00e-02 2.50e+03 pdb=" N1N NAD A1001 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD K1001 " -0.013 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" C2N NAD K1001 " 0.049 2.00e-02 2.50e+03 pdb=" C3N NAD K1001 " 0.006 2.00e-02 2.50e+03 pdb=" C4N NAD K1001 " 0.025 2.00e-02 2.50e+03 pdb=" C5N NAD K1001 " -0.003 2.00e-02 2.50e+03 pdb=" C6N NAD K1001 " -0.027 2.00e-02 2.50e+03 pdb=" C7N NAD K1001 " -0.039 2.00e-02 2.50e+03 pdb=" N1N NAD K1001 " 0.003 2.00e-02 2.50e+03 ... (remaining 5977 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1223 2.69 - 3.24: 32240 3.24 - 3.79: 56680 3.79 - 4.35: 70432 4.35 - 4.90: 116484 Nonbonded interactions: 277059 Sorted by model distance: nonbonded pdb=" OH TYR C 73 " pdb=" O1A NAD E1001 " model vdw 2.133 2.440 nonbonded pdb=" OG1 THR J 226 " pdb=" OG1 THR G 226 " model vdw 2.252 2.440 nonbonded pdb=" OH TYR M 73 " pdb=" O1A NAD N1001 " model vdw 2.263 2.440 nonbonded pdb=" NH1 ARG E 81 " pdb=" OD2 ASP C 66 " model vdw 2.264 2.520 nonbonded pdb=" OG1 THR B 226 " pdb=" OG1 THR L 226 " model vdw 2.270 2.440 ... (remaining 277054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 11.340 Check model and map are aligned: 0.460 Set scattering table: 0.290 Process input model: 89.530 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.067 34096 Z= 0.632 Angle : 0.986 10.513 46328 Z= 0.530 Chirality : 0.064 0.364 5220 Planarity : 0.008 0.077 5980 Dihedral : 10.439 75.588 12784 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.72 (0.10), residues: 4240 helix: -2.67 (0.10), residues: 1412 sheet: -2.27 (0.15), residues: 896 loop : -2.26 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP J 227 HIS 0.011 0.003 HIS B 295 PHE 0.022 0.003 PHE D 9 TYR 0.027 0.003 TYR D 315 ARG 0.009 0.002 ARG G 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1006 time to evaluate : 3.937 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: 0.4678 time to fit residues: 755.4957 Evaluate side-chains 531 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 527 time to evaluate : 3.860 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2970 time to fit residues: 7.4042 ------------------------------------------------------------------------------- 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 45 HIS 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN G 90 ASN G 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: 0.7522 moved from start: 0.2603 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= 0.222 Angle : 0.607 7.910 46328 Z= 0.315 Chirality : 0.046 0.162 5220 Planarity : 0.005 0.055 5980 Dihedral : 7.348 59.617 5080 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.05 % Allowed : 11.60 % Favored : 85.36 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 20 HIS 0.010 0.001 HIS G 46 PHE 0.020 0.002 PHE J 127 TYR 0.020 0.002 TYR F 321 ARG 0.007 0.001 ARG E 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 660 time to evaluate : 3.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 72 residues processed: 721 average time/residue: 0.4151 time to fit residues: 502.0495 Evaluate side-chains 586 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 514 time to evaluate : 3.559 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.2998 time to fit residues: 45.6437 ------------------------------------------------------------------------------- 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: 0.9990 chunk 117 optimal weight: 9.9990 chunk 314 optimal weight: 8.9990 chunk 257 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 378 optimal weight: 20.0000 chunk 408 optimal weight: 3.9990 chunk 337 optimal weight: 5.9990 chunk 375 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 303 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 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 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 ** J 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 34096 Z= 0.282 Angle : 0.621 7.757 46328 Z= 0.319 Chirality : 0.047 0.235 5220 Planarity : 0.005 0.057 5980 Dihedral : 7.176 59.107 5080 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.82 % Allowed : 14.16 % Favored : 83.01 % 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 (0.12), residues: 4240 helix: -0.21 (0.14), residues: 1408 sheet: -1.65 (0.16), residues: 936 loop : -1.43 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP P 33 HIS 0.011 0.001 HIS B 46 PHE 0.018 0.002 PHE B 127 TYR 0.020 0.002 TYR F 321 ARG 0.005 0.001 ARG F 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 550 time to evaluate : 3.930 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: 100 outliers final: 56 residues processed: 623 average time/residue: 0.4172 time to fit residues: 436.8450 Evaluate side-chains 527 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 471 time to evaluate : 3.777 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.3172 time to fit residues: 38.7020 ------------------------------------------------------------------------------- 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: 0.4980 chunk 284 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 254 optimal weight: 0.9980 chunk 379 optimal weight: 0.0370 chunk 402 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 359 optimal weight: 4.9990 chunk 108 optimal weight: 0.0670 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 249 GLN ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 260 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 GLN N 45 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 ASN ** 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 284 HIS B 309 GLN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34096 Z= 0.151 Angle : 0.570 12.804 46328 Z= 0.286 Chirality : 0.045 0.222 5220 Planarity : 0.004 0.055 5980 Dihedral : 6.461 59.581 5080 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.61 % Allowed : 16.37 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 4240 helix: 0.09 (0.14), residues: 1444 sheet: -1.25 (0.16), residues: 912 loop : -1.25 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP F 20 HIS 0.008 0.001 HIS B 46 PHE 0.025 0.001 PHE L 68 TYR 0.018 0.001 TYR F 49 ARG 0.004 0.000 ARG L 164 *********************** 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 668 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 611 time to evaluate : 3.875 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 outliers start: 57 outliers final: 28 residues processed: 634 average time/residue: 0.4238 time to fit residues: 447.7600 Evaluate side-chains 519 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 491 time to evaluate : 3.747 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.3261 time to fit residues: 21.4028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 334 optimal weight: 0.8980 chunk 228 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 299 optimal weight: 0.5980 chunk 165 optimal weight: 4.9990 chunk 343 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 205 optimal weight: 4.9990 chunk 360 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 HIS P 46 GLN D 45 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 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** E 240 ASN F 15 ASN ** 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** ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN O 240 ASN ** O 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN B 67 ASN B 90 ASN B 184 GLN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS G 67 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34096 Z= 0.281 Angle : 0.624 9.799 46328 Z= 0.318 Chirality : 0.047 0.262 5220 Planarity : 0.004 0.054 5980 Dihedral : 6.753 59.939 5080 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.40 % Allowed : 17.44 % Favored : 80.16 % 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: -1.12 (0.13), residues: 4240 helix: 0.11 (0.14), residues: 1448 sheet: -1.08 (0.17), residues: 912 loop : -1.13 (0.14), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP K 20 HIS 0.008 0.001 HIS B 284 PHE 0.023 0.002 PHE O 246 TYR 0.017 0.002 TYR K 49 ARG 0.005 0.001 ARG M 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8480 Ramachandran restraints generated. 4240 Oldfield, 0 Emsley, 4240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 514 time to evaluate : 3.869 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: 85 outliers final: 50 residues processed: 571 average time/residue: 0.4209 time to fit residues: 405.6362 Evaluate side-chains 506 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 456 time to evaluate : 3.950 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.3100 time to fit residues: 34.5714 ------------------------------------------------------------------------------- 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: 10.0000 chunk 362 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 402 optimal weight: 0.5980 chunk 334 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** ** A 174 GLN ** 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** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 173 GLN ** O 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN J 284 HIS B 279 ASN G 67 ASN ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34096 Z= 0.184 Angle : 0.591 10.948 46328 Z= 0.297 Chirality : 0.046 0.272 5220 Planarity : 0.004 0.052 5980 Dihedral : 6.508 59.557 5080 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.55 % Allowed : 18.79 % Favored : 79.66 % 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: -0.96 (0.13), residues: 4240 helix: 0.17 (0.14), residues: 1448 sheet: -1.01 (0.17), residues: 920 loop : -0.97 (0.15), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP K 20 HIS 0.010 0.001 HIS J 284 PHE 0.022 0.001 PHE J 127 TYR 0.015 0.001 TYR N 142 ARG 0.004 0.000 ARG G 53 *********************** 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 590 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 535 time to evaluate : 4.130 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: 55 outliers final: 31 residues processed: 567 average time/residue: 0.4088 time to fit residues: 392.8366 Evaluate side-chains 517 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 486 time to evaluate : 3.733 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2954 time to fit residues: 22.5311 ------------------------------------------------------------------------------- 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: 5.9990 chunk 45 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 293 optimal weight: 0.4980 chunk 227 optimal weight: 4.9990 chunk 338 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 400 optimal weight: 0.9990 chunk 250 optimal weight: 5.9990 chunk 244 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 GLN ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 10 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 34096 Z= 0.198 Angle : 0.599 12.998 46328 Z= 0.300 Chirality : 0.046 0.316 5220 Planarity : 0.004 0.053 5980 Dihedral : 6.384 59.430 5080 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.24 % Allowed : 19.86 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 4240 helix: 0.21 (0.14), residues: 1456 sheet: -1.02 (0.17), residues: 928 loop : -0.84 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP F 20 HIS 0.007 0.001 HIS P 16 PHE 0.026 0.001 PHE B 127 TYR 0.025 0.001 TYR D 142 ARG 0.004 0.000 ARG C 47 *********************** 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 559 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 515 time to evaluate : 4.834 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: 27 residues processed: 540 average time/residue: 0.4375 time to fit residues: 396.4920 Evaluate side-chains 499 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 472 time to evaluate : 3.910 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3043 time to fit residues: 20.7305 ------------------------------------------------------------------------------- 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: 3.9990 chunk 160 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 254 optimal weight: 0.9980 chunk 273 optimal weight: 9.9990 chunk 198 optimal weight: 2.9990 chunk 37 optimal weight: 0.4980 chunk 315 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** A 249 GLN ** 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 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 335 HIS ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN ** O 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN J 279 ASN ** B 206 GLN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34096 Z= 0.197 Angle : 0.612 14.945 46328 Z= 0.304 Chirality : 0.046 0.323 5220 Planarity : 0.004 0.056 5980 Dihedral : 6.330 59.381 5080 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.82 % Allowed : 20.49 % Favored : 78.70 % 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: -0.80 (0.13), residues: 4240 helix: 0.22 (0.14), residues: 1456 sheet: -0.96 (0.17), residues: 928 loop : -0.77 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP F 20 HIS 0.009 0.001 HIS P 16 PHE 0.022 0.001 PHE G 68 TYR 0.024 0.001 TYR D 142 ARG 0.006 0.000 ARG B 164 *********************** 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 531 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 502 time to evaluate : 3.754 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: 29 outliers final: 16 residues processed: 516 average time/residue: 0.4262 time to fit residues: 372.3424 Evaluate side-chains 488 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 472 time to evaluate : 3.754 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3135 time to fit residues: 14.5646 ------------------------------------------------------------------------------- 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: 3.9990 chunk 384 optimal weight: 5.9990 chunk 350 optimal weight: 3.9990 chunk 373 optimal weight: 1.9990 chunk 224 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 337 optimal weight: 10.0000 chunk 353 optimal weight: 0.7980 chunk 372 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 GLN ** 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** ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 GLN ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 ASN G 67 ASN M 10 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 34096 Z= 0.234 Angle : 0.640 15.383 46328 Z= 0.318 Chirality : 0.047 0.308 5220 Planarity : 0.004 0.057 5980 Dihedral : 6.463 59.178 5080 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.87 % Allowed : 20.63 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4240 helix: 0.20 (0.14), residues: 1456 sheet: -0.98 (0.17), residues: 928 loop : -0.75 (0.15), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP K 20 HIS 0.008 0.001 HIS P 16 PHE 0.024 0.001 PHE O 246 TYR 0.021 0.002 TYR D 142 ARG 0.006 0.000 ARG B 164 *********************** 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: 31 poor density : 488 time to evaluate : 4.319 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 outliers start: 31 outliers final: 18 residues processed: 501 average time/residue: 0.4469 time to fit residues: 378.5070 Evaluate side-chains 478 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 460 time to evaluate : 3.723 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3434 time to fit residues: 16.3132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 245 optimal weight: 4.9990 chunk 395 optimal weight: 10.0000 chunk 241 optimal weight: 5.9990 chunk 187 optimal weight: 0.7980 chunk 274 optimal weight: 3.9990 chunk 414 optimal weight: 3.9990 chunk 381 optimal weight: 2.9990 chunk 330 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 ASN ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN ** 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 249 GLN ** K 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 HIS ** L 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 295 HIS M 10 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34096 Z= 0.239 Angle : 0.660 15.492 46328 Z= 0.328 Chirality : 0.047 0.319 5220 Planarity : 0.004 0.057 5980 Dihedral : 6.538 59.329 5080 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.59 % Allowed : 21.30 % Favored : 78.10 % 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: -0.83 (0.13), residues: 4240 helix: 0.19 (0.14), residues: 1452 sheet: -0.99 (0.17), residues: 928 loop : -0.76 (0.15), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.002 TRP F 20 HIS 0.011 0.001 HIS B 46 PHE 0.025 0.001 PHE G 68 TYR 0.025 0.002 TYR D 133 ARG 0.006 0.000 ARG B 164 ********************** 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 509 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 488 time to evaluate : 3.618 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 outliers start: 21 outliers final: 12 residues processed: 499 average time/residue: 0.4267 time to fit residues: 358.0659 Evaluate side-chains 473 residues out of total 3576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 461 time to evaluate : 4.101 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3227 time to fit residues: 12.5141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 262 optimal weight: 0.4980 chunk 351 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 304 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 330 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 339 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** A 173 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 240 ASN ** 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 240 ASN O 15 ASN ** O 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS C 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.103191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.080214 restraints weight = 87205.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.082692 restraints weight = 46652.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.084227 restraints weight = 31645.771| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 34096 Z= 0.340 Angle : 0.720 15.153 46328 Z= 0.360 Chirality : 0.049 0.333 5220 Planarity : 0.004 0.060 5980 Dihedral : 6.970 59.993 5080 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.79 % Allowed : 21.47 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 4240 helix: 0.10 (0.14), residues: 1436 sheet: -1.12 (0.17), residues: 936 loop : -0.92 (0.15), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.003 TRP K 20 HIS 0.010 0.001 HIS B 46 PHE 0.037 0.002 PHE K 246 TYR 0.032 0.002 TYR D 142 ARG 0.006 0.001 ARG B 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8006.43 seconds wall clock time: 146 minutes 23.02 seconds (8783.02 seconds total)