Starting phenix.real_space_refine on Sat Mar 23 05:18:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn4_22401/03_2024/7jn4_22401_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn4_22401/03_2024/7jn4_22401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn4_22401/03_2024/7jn4_22401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn4_22401/03_2024/7jn4_22401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn4_22401/03_2024/7jn4_22401_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jn4_22401/03_2024/7jn4_22401_updated.pdb" } resolution = 2.68 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= 0.030 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: 4 Type Number sf(0) Gaussians S 280 5.16 5 C 22504 2.51 5 N 6240 2.21 5 O 6688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 187": "NH1" <-> "NH2" Residue "C PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "E PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 253": "NH1" <-> "NH2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "G ARG 21": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 79": "NH1" <-> "NH2" Residue "G ARG 187": "NH1" <-> "NH2" Residue "G PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 253": "NH1" <-> "NH2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "I ARG 21": "NH1" <-> "NH2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I ARG 79": "NH1" <-> "NH2" Residue "I ARG 187": "NH1" <-> "NH2" Residue "I PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 253": "NH1" <-> "NH2" Residue "I ARG 339": "NH1" <-> "NH2" Residue "I PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 32": "NH1" <-> "NH2" Residue "K ARG 79": "NH1" <-> "NH2" Residue "K ARG 187": "NH1" <-> "NH2" Residue "K PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 253": "NH1" <-> "NH2" Residue "K ARG 339": "NH1" <-> "NH2" Residue "K PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "M ARG 21": "NH1" <-> "NH2" Residue "M ARG 32": "NH1" <-> "NH2" Residue "M ARG 79": "NH1" <-> "NH2" Residue "M ARG 187": "NH1" <-> "NH2" Residue "M PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 253": "NH1" <-> "NH2" Residue "M ARG 339": "NH1" <-> "NH2" Residue "M PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 84": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 32": "NH1" <-> "NH2" Residue "O ARG 79": "NH1" <-> "NH2" Residue "O ARG 187": "NH1" <-> "NH2" Residue "O PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 253": "NH1" <-> "NH2" Residue "O ARG 339": "NH1" <-> "NH2" Residue "O PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 84": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35712 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'SMC:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "C" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'SMC:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "E" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'SMC:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "G" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'SMC:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "I" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'SMC:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "K" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'SMC:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "M" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'SMC:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "O" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3304 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 405} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'SMC:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "P" Number of atoms: 1131 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} Conformer: "B" Number of residues, atoms: 138, 1130 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 9, 'TRANS': 128} bond proxies already assigned to first conformer: 1162 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "F" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "G" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "K" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "L" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "M" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "P" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 21.37, per 1000 atoms: 0.60 Number of scatterers: 35712 At special positions: 0 Unit cell: (145.41, 145.41, 127.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 280 16.00 O 6688 8.00 N 6240 7.00 C 22504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS C 247 " distance=2.06 Simple disulfide: pdb=" SG CYS A 449 " - pdb=" SG CYS A 459 " distance=2.03 Simple disulfide: pdb=" SG CYS C 449 " - pdb=" SG CYS C 459 " distance=2.03 Simple disulfide: pdb=" SG CYS E 247 " - pdb=" SG CYS G 247 " distance=2.06 Simple disulfide: pdb=" SG CYS E 449 " - pdb=" SG CYS E 459 " distance=2.03 Simple disulfide: pdb=" SG CYS G 449 " - pdb=" SG CYS G 459 " distance=2.03 Simple disulfide: pdb=" SG CYS I 247 " - pdb=" SG CYS K 247 " distance=2.06 Simple disulfide: pdb=" SG CYS I 449 " - pdb=" SG CYS I 459 " distance=2.03 Simple disulfide: pdb=" SG CYS K 449 " - pdb=" SG CYS K 459 " distance=2.03 Simple disulfide: pdb=" SG CYS M 247 " - pdb=" SG CYS O 247 " distance=2.06 Simple disulfide: pdb=" SG CYS M 449 " - pdb=" SG CYS M 459 " distance=2.03 Simple disulfide: pdb=" SG CYS O 449 " - pdb=" SG CYS O 459 " distance=2.03 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: 14.04 Conformation dependent library (CDL) restraints added in 6.2 seconds 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 169 helices and 32 sheets defined 37.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.03 Creating SS restraints... Processing helix chain 'A' and resid 50 through 59 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 142 through 145 No H-bonds generated for 'chain 'A' and resid 142 through 145' Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 182 through 195 removed outlier: 3.515A pdb=" N GLY A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 232 removed outlier: 3.687A pdb=" N LEU A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 258 Processing helix chain 'A' and resid 269 through 272 No H-bonds generated for 'chain 'A' and resid 269 through 272' Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 298 through 302 Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'A' and resid 338 through 350 Processing helix chain 'A' and resid 384 through 394 Proline residue: A 388 - end of helix removed outlier: 4.003A pdb=" N VAL A 391 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 393 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 394 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 433 Processing helix chain 'A' and resid 441 through 451 removed outlier: 3.859A pdb=" N LYS A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.858A pdb=" N ILE B 58 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 removed outlier: 3.697A pdb=" N GLU B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 94 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 59 Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 124 through 126 No H-bonds generated for 'chain 'C' and resid 124 through 126' Processing helix chain 'C' and resid 142 through 145 No H-bonds generated for 'chain 'C' and resid 142 through 145' Processing helix chain 'C' and resid 155 through 162 Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.513A pdb=" N GLY C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 removed outlier: 3.684A pdb=" N LEU C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 220 " --> pdb=" O ASP C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 258 Processing helix chain 'C' and resid 269 through 272 No H-bonds generated for 'chain 'C' and resid 269 through 272' Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 298 through 302 Processing helix chain 'C' and resid 311 through 321 Processing helix chain 'C' and resid 338 through 350 Processing helix chain 'C' and resid 384 through 394 Proline residue: C 388 - end of helix removed outlier: 4.004A pdb=" N VAL C 391 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 392 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 393 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 394 " --> pdb=" O VAL C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 433 Processing helix chain 'C' and resid 441 through 451 removed outlier: 3.862A pdb=" N LYS C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 460 Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.858A pdb=" N ILE D 58 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 99 removed outlier: 3.699A pdb=" N GLU D 92 " --> pdb=" O GLN D 88 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 94 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 59 Processing helix chain 'E' and resid 105 through 107 No H-bonds generated for 'chain 'E' and resid 105 through 107' Processing helix chain 'E' and resid 113 through 120 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 142 through 145 No H-bonds generated for 'chain 'E' and resid 142 through 145' Processing helix chain 'E' and resid 155 through 162 Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.509A pdb=" N GLY E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 232 removed outlier: 3.685A pdb=" N LEU E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE E 220 " --> pdb=" O ASP E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 258 Processing helix chain 'E' and resid 269 through 272 No H-bonds generated for 'chain 'E' and resid 269 through 272' Processing helix chain 'E' and resid 274 through 287 Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'E' and resid 311 through 321 Processing helix chain 'E' and resid 338 through 350 Processing helix chain 'E' and resid 384 through 394 Proline residue: E 388 - end of helix removed outlier: 3.982A pdb=" N VAL E 391 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 392 " --> pdb=" O ALA E 389 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE E 393 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE E 394 " --> pdb=" O VAL E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 433 Processing helix chain 'E' and resid 441 through 451 removed outlier: 3.855A pdb=" N LYS E 450 " --> pdb=" O ARG E 446 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP E 451 " --> pdb=" O SER E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 460 Processing helix chain 'F' and resid 23 through 35 Processing helix chain 'F' and resid 55 through 59 removed outlier: 3.858A pdb=" N ILE F 58 " --> pdb=" O GLU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 99 removed outlier: 3.698A pdb=" N GLU F 92 " --> pdb=" O GLN F 88 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 59 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 113 through 120 Processing helix chain 'G' and resid 124 through 126 No H-bonds generated for 'chain 'G' and resid 124 through 126' Processing helix chain 'G' and resid 142 through 145 No H-bonds generated for 'chain 'G' and resid 142 through 145' Processing helix chain 'G' and resid 155 through 162 Processing helix chain 'G' and resid 182 through 195 removed outlier: 3.514A pdb=" N GLY G 195 " --> pdb=" O GLU G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 232 removed outlier: 3.684A pdb=" N LEU G 219 " --> pdb=" O ARG G 215 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE G 220 " --> pdb=" O ASP G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 258 Processing helix chain 'G' and resid 269 through 272 No H-bonds generated for 'chain 'G' and resid 269 through 272' Processing helix chain 'G' and resid 274 through 287 Processing helix chain 'G' and resid 298 through 302 Processing helix chain 'G' and resid 311 through 321 Processing helix chain 'G' and resid 338 through 350 Processing helix chain 'G' and resid 384 through 394 Proline residue: G 388 - end of helix removed outlier: 3.988A pdb=" N VAL G 391 " --> pdb=" O PRO G 388 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU G 392 " --> pdb=" O ALA G 389 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE G 393 " --> pdb=" O LEU G 390 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE G 394 " --> pdb=" O VAL G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 433 Processing helix chain 'G' and resid 441 through 451 removed outlier: 3.866A pdb=" N LYS G 450 " --> pdb=" O ARG G 446 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N TRP G 451 " --> pdb=" O SER G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 460 Processing helix chain 'H' and resid 23 through 35 Processing helix chain 'H' and resid 55 through 59 removed outlier: 3.857A pdb=" N ILE H 58 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 99 removed outlier: 3.686A pdb=" N GLU H 92 " --> pdb=" O GLN H 88 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 59 Processing helix chain 'I' and resid 105 through 107 No H-bonds generated for 'chain 'I' and resid 105 through 107' Processing helix chain 'I' and resid 113 through 120 Processing helix chain 'I' and resid 124 through 126 No H-bonds generated for 'chain 'I' and resid 124 through 126' Processing helix chain 'I' and resid 142 through 145 No H-bonds generated for 'chain 'I' and resid 142 through 145' Processing helix chain 'I' and resid 155 through 162 Processing helix chain 'I' and resid 182 through 195 removed outlier: 3.511A pdb=" N GLY I 195 " --> pdb=" O GLU I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 232 removed outlier: 3.686A pdb=" N LEU I 219 " --> pdb=" O ARG I 215 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE I 220 " --> pdb=" O ASP I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 258 Processing helix chain 'I' and resid 269 through 272 No H-bonds generated for 'chain 'I' and resid 269 through 272' Processing helix chain 'I' and resid 274 through 287 Processing helix chain 'I' and resid 298 through 302 Processing helix chain 'I' and resid 311 through 321 Processing helix chain 'I' and resid 338 through 350 Processing helix chain 'I' and resid 384 through 394 Proline residue: I 388 - end of helix removed outlier: 3.993A pdb=" N VAL I 391 " --> pdb=" O PRO I 388 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU I 392 " --> pdb=" O ALA I 389 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE I 393 " --> pdb=" O LEU I 390 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE I 394 " --> pdb=" O VAL I 391 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 433 Processing helix chain 'I' and resid 441 through 451 removed outlier: 3.858A pdb=" N LYS I 450 " --> pdb=" O ARG I 446 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TRP I 451 " --> pdb=" O SER I 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 453 through 460 Processing helix chain 'J' and resid 23 through 35 Processing helix chain 'J' and resid 55 through 59 removed outlier: 3.858A pdb=" N ILE J 58 " --> pdb=" O GLU J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 99 removed outlier: 3.684A pdb=" N GLU J 92 " --> pdb=" O GLN J 88 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL J 94 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 59 Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 120 Processing helix chain 'K' and resid 124 through 126 No H-bonds generated for 'chain 'K' and resid 124 through 126' Processing helix chain 'K' and resid 142 through 145 No H-bonds generated for 'chain 'K' and resid 142 through 145' Processing helix chain 'K' and resid 155 through 162 Processing helix chain 'K' and resid 182 through 195 removed outlier: 3.514A pdb=" N GLY K 195 " --> pdb=" O GLU K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 232 removed outlier: 3.684A pdb=" N LEU K 219 " --> pdb=" O ARG K 215 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE K 220 " --> pdb=" O ASP K 216 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 258 Processing helix chain 'K' and resid 269 through 272 No H-bonds generated for 'chain 'K' and resid 269 through 272' Processing helix chain 'K' and resid 274 through 287 Processing helix chain 'K' and resid 298 through 302 Processing helix chain 'K' and resid 311 through 321 Processing helix chain 'K' and resid 338 through 350 Processing helix chain 'K' and resid 358 through 360 No H-bonds generated for 'chain 'K' and resid 358 through 360' Processing helix chain 'K' and resid 384 through 394 Proline residue: K 388 - end of helix removed outlier: 3.991A pdb=" N VAL K 391 " --> pdb=" O PRO K 388 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU K 392 " --> pdb=" O ALA K 389 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE K 393 " --> pdb=" O LEU K 390 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE K 394 " --> pdb=" O VAL K 391 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 433 Processing helix chain 'K' and resid 441 through 451 removed outlier: 3.868A pdb=" N LYS K 450 " --> pdb=" O ARG K 446 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TRP K 451 " --> pdb=" O SER K 447 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 460 Processing helix chain 'L' and resid 23 through 35 Processing helix chain 'L' and resid 55 through 59 removed outlier: 3.856A pdb=" N ILE L 58 " --> pdb=" O GLU L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 99 removed outlier: 3.701A pdb=" N GLU L 92 " --> pdb=" O GLN L 88 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL L 94 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 59 Processing helix chain 'M' and resid 105 through 107 No H-bonds generated for 'chain 'M' and resid 105 through 107' Processing helix chain 'M' and resid 113 through 120 Processing helix chain 'M' and resid 124 through 126 No H-bonds generated for 'chain 'M' and resid 124 through 126' Processing helix chain 'M' and resid 142 through 145 No H-bonds generated for 'chain 'M' and resid 142 through 145' Processing helix chain 'M' and resid 155 through 162 Processing helix chain 'M' and resid 182 through 195 removed outlier: 3.515A pdb=" N GLY M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 214 through 232 removed outlier: 3.686A pdb=" N LEU M 219 " --> pdb=" O ARG M 215 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE M 220 " --> pdb=" O ASP M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 258 Processing helix chain 'M' and resid 269 through 272 No H-bonds generated for 'chain 'M' and resid 269 through 272' Processing helix chain 'M' and resid 274 through 287 Processing helix chain 'M' and resid 298 through 302 Processing helix chain 'M' and resid 311 through 321 Processing helix chain 'M' and resid 338 through 350 Processing helix chain 'M' and resid 384 through 394 Proline residue: M 388 - end of helix removed outlier: 4.007A pdb=" N VAL M 391 " --> pdb=" O PRO M 388 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU M 392 " --> pdb=" O ALA M 389 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE M 393 " --> pdb=" O LEU M 390 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE M 394 " --> pdb=" O VAL M 391 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 433 Processing helix chain 'M' and resid 441 through 451 removed outlier: 3.855A pdb=" N LYS M 450 " --> pdb=" O ARG M 446 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TRP M 451 " --> pdb=" O SER M 447 " (cutoff:3.500A) Processing helix chain 'M' and resid 453 through 460 Processing helix chain 'N' and resid 23 through 35 Processing helix chain 'N' and resid 55 through 59 removed outlier: 3.860A pdb=" N ILE N 58 " --> pdb=" O GLU N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 99 removed outlier: 3.694A pdb=" N GLU N 92 " --> pdb=" O GLN N 88 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL N 94 " --> pdb=" O LEU N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 59 Processing helix chain 'O' and resid 105 through 107 No H-bonds generated for 'chain 'O' and resid 105 through 107' Processing helix chain 'O' and resid 113 through 120 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 142 through 145 No H-bonds generated for 'chain 'O' and resid 142 through 145' Processing helix chain 'O' and resid 155 through 162 Processing helix chain 'O' and resid 182 through 195 removed outlier: 3.513A pdb=" N GLY O 195 " --> pdb=" O GLU O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 214 through 232 removed outlier: 3.684A pdb=" N LEU O 219 " --> pdb=" O ARG O 215 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE O 220 " --> pdb=" O ASP O 216 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 258 Processing helix chain 'O' and resid 269 through 272 No H-bonds generated for 'chain 'O' and resid 269 through 272' Processing helix chain 'O' and resid 274 through 287 Processing helix chain 'O' and resid 298 through 302 Processing helix chain 'O' and resid 311 through 321 Processing helix chain 'O' and resid 338 through 350 Processing helix chain 'O' and resid 384 through 394 Proline residue: O 388 - end of helix removed outlier: 3.997A pdb=" N VAL O 391 " --> pdb=" O PRO O 388 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU O 392 " --> pdb=" O ALA O 389 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE O 393 " --> pdb=" O LEU O 390 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE O 394 " --> pdb=" O VAL O 391 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 433 Processing helix chain 'O' and resid 441 through 451 removed outlier: 3.866A pdb=" N LYS O 450 " --> pdb=" O ARG O 446 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRP O 451 " --> pdb=" O SER O 447 " (cutoff:3.500A) Processing helix chain 'O' and resid 453 through 460 Processing helix chain 'P' and resid 23 through 35 Processing helix chain 'P' and resid 55 through 59 removed outlier: 3.856A pdb=" N ILE P 58 " --> pdb=" O GLU P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 99 removed outlier: 3.709A pdb=" N GLU P 92 " --> pdb=" O GLN P 88 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL P 94 " --> pdb=" O LEU P 90 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 132 through 139 removed outlier: 6.808A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 237 through 239 removed outlier: 7.604A pdb=" N GLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA A 378 " --> pdb=" O GLN A 401 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 264 through 268 removed outlier: 6.166A pdb=" N LEU A 290 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS A 267 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS A 292 " --> pdb=" O HIS A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 74 through 76 removed outlier: 4.496A pdb=" N LEU B 42 " --> pdb=" O TRP B 76 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU B 107 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU B 122 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA B 109 " --> pdb=" O GLY B 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY B 120 " --> pdb=" O ALA B 109 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 132 through 139 removed outlier: 6.804A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 237 through 239 removed outlier: 7.602A pdb=" N GLN C 401 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA C 378 " --> pdb=" O GLN C 401 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 264 through 268 removed outlier: 6.166A pdb=" N LEU C 290 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS C 267 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS C 292 " --> pdb=" O HIS C 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 74 through 76 removed outlier: 4.499A pdb=" N LEU D 42 " --> pdb=" O TRP D 76 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU D 107 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU D 122 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA D 109 " --> pdb=" O GLY D 120 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLY D 120 " --> pdb=" O ALA D 109 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 132 through 139 removed outlier: 6.805A pdb=" N ALA E 39 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU E 138 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU E 37 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP E 86 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA E 102 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N CYS E 84 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 237 through 239 removed outlier: 7.600A pdb=" N GLN E 401 " --> pdb=" O PRO E 376 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA E 378 " --> pdb=" O GLN E 401 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 264 through 268 removed outlier: 6.166A pdb=" N LEU E 290 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS E 267 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N HIS E 292 " --> pdb=" O HIS E 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 74 through 76 removed outlier: 4.503A pdb=" N LEU F 42 " --> pdb=" O TRP F 76 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU F 107 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LEU F 122 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA F 109 " --> pdb=" O GLY F 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLY F 120 " --> pdb=" O ALA F 109 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 132 through 139 removed outlier: 6.804A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU G 37 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP G 86 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 237 through 239 removed outlier: 7.594A pdb=" N GLN G 401 " --> pdb=" O PRO G 376 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA G 378 " --> pdb=" O GLN G 401 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 264 through 268 removed outlier: 6.166A pdb=" N LEU G 290 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS G 267 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS G 292 " --> pdb=" O HIS G 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 74 through 76 removed outlier: 4.503A pdb=" N LEU H 42 " --> pdb=" O TRP H 76 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU H 107 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LEU H 122 " --> pdb=" O LEU H 107 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ALA H 109 " --> pdb=" O GLY H 120 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY H 120 " --> pdb=" O ALA H 109 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 132 through 139 removed outlier: 6.808A pdb=" N ALA I 39 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU I 138 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU I 37 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP I 86 " --> pdb=" O TYR I 100 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA I 102 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N CYS I 84 " --> pdb=" O ALA I 102 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 237 through 239 removed outlier: 7.599A pdb=" N GLN I 401 " --> pdb=" O PRO I 376 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA I 378 " --> pdb=" O GLN I 401 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 264 through 268 removed outlier: 6.166A pdb=" N LEU I 290 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N HIS I 267 " --> pdb=" O LEU I 290 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS I 292 " --> pdb=" O HIS I 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'J' and resid 74 through 76 removed outlier: 4.498A pdb=" N LEU J 42 " --> pdb=" O TRP J 76 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU J 107 " --> pdb=" O LEU J 122 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU J 122 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA J 109 " --> pdb=" O GLY J 120 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLY J 120 " --> pdb=" O ALA J 109 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 132 through 139 removed outlier: 6.805A pdb=" N ALA K 39 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU K 138 " --> pdb=" O LEU K 37 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU K 37 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP K 86 " --> pdb=" O TYR K 100 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA K 102 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N CYS K 84 " --> pdb=" O ALA K 102 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 237 through 239 removed outlier: 7.598A pdb=" N GLN K 401 " --> pdb=" O PRO K 376 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA K 378 " --> pdb=" O GLN K 401 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 264 through 268 removed outlier: 6.167A pdb=" N LEU K 290 " --> pdb=" O ILE K 265 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N HIS K 267 " --> pdb=" O LEU K 290 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N HIS K 292 " --> pdb=" O HIS K 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 74 through 76 removed outlier: 4.501A pdb=" N LEU L 42 " --> pdb=" O TRP L 76 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU L 107 " --> pdb=" O LEU L 122 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU L 122 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA L 109 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N GLY L 120 " --> pdb=" O ALA L 109 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 132 through 139 removed outlier: 6.810A pdb=" N ALA M 39 " --> pdb=" O GLU M 136 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU M 138 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU M 37 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP M 86 " --> pdb=" O TYR M 100 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA M 102 " --> pdb=" O CYS M 84 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N CYS M 84 " --> pdb=" O ALA M 102 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 237 through 239 removed outlier: 7.604A pdb=" N GLN M 401 " --> pdb=" O PRO M 376 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA M 378 " --> pdb=" O GLN M 401 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 264 through 268 removed outlier: 6.167A pdb=" N LEU M 290 " --> pdb=" O ILE M 265 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS M 267 " --> pdb=" O LEU M 290 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS M 292 " --> pdb=" O HIS M 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'N' and resid 74 through 76 removed outlier: 4.505A pdb=" N LEU N 42 " --> pdb=" O TRP N 76 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU N 107 " --> pdb=" O LEU N 122 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N LEU N 122 " --> pdb=" O LEU N 107 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ALA N 109 " --> pdb=" O GLY N 120 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLY N 120 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'O' and resid 132 through 139 removed outlier: 6.808A pdb=" N ALA O 39 " --> pdb=" O GLU O 136 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU O 138 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU O 37 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP O 86 " --> pdb=" O TYR O 100 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ALA O 102 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N CYS O 84 " --> pdb=" O ALA O 102 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 237 through 239 removed outlier: 7.596A pdb=" N GLN O 401 " --> pdb=" O PRO O 376 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA O 378 " --> pdb=" O GLN O 401 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'O' and resid 264 through 268 removed outlier: 6.165A pdb=" N LEU O 290 " --> pdb=" O ILE O 265 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N HIS O 267 " --> pdb=" O LEU O 290 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS O 292 " --> pdb=" O HIS O 267 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'P' and resid 74 through 76 removed outlier: 4.495A pdb=" N LEU P 42 " --> pdb=" O TRP P 76 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU P 107 " --> pdb=" O LEU P 122 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU P 122 " --> pdb=" O LEU P 107 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ALA P 109 " --> pdb=" O GLY P 120 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLY P 120 " --> pdb=" O ALA P 109 " (cutoff:3.500A) 1232 hydrogen bonds defined for protein. 3492 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: 12.19 Time building geometry restraints manager: 15.31 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: 11163 1.33 - 1.46: 9348 1.46 - 1.59: 15401 1.59 - 1.72: 0 1.72 - 1.84: 440 Bond restraints: 36352 Sorted by residual: bond pdb=" CB ARG O 194 " pdb=" CG ARG O 194 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.37e+01 bond pdb=" CB ARG I 194 " pdb=" CG ARG I 194 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.37e+01 bond pdb=" CB ARG K 194 " pdb=" CG ARG K 194 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.36e+01 bond pdb=" CB ARG E 194 " pdb=" CG ARG E 194 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.36e+01 bond pdb=" CB ARG A 194 " pdb=" CG ARG A 194 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.36e+01 ... (remaining 36347 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.42: 1010 105.42 - 112.60: 17369 112.60 - 119.79: 13363 119.79 - 126.98: 16940 126.98 - 134.16: 574 Bond angle restraints: 49256 Sorted by residual: angle pdb=" N GLU H 13 " pdb=" CA GLU H 13 " pdb=" C GLU H 13 " ideal model delta sigma weight residual 111.07 121.15 -10.08 1.07e+00 8.73e-01 8.88e+01 angle pdb=" N GLU L 13 " pdb=" CA GLU L 13 " pdb=" C GLU L 13 " ideal model delta sigma weight residual 111.07 121.12 -10.05 1.07e+00 8.73e-01 8.82e+01 angle pdb=" N GLU B 13 " pdb=" CA GLU B 13 " pdb=" C GLU B 13 " ideal model delta sigma weight residual 111.07 121.11 -10.04 1.07e+00 8.73e-01 8.81e+01 angle pdb=" N GLU N 13 " pdb=" CA GLU N 13 " pdb=" C GLU N 13 " ideal model delta sigma weight residual 111.07 121.11 -10.04 1.07e+00 8.73e-01 8.81e+01 angle pdb=" N GLU J 13 " pdb=" CA GLU J 13 " pdb=" C GLU J 13 " ideal model delta sigma weight residual 111.07 121.08 -10.01 1.07e+00 8.73e-01 8.76e+01 ... (remaining 49251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 20001 14.26 - 28.53: 1312 28.53 - 42.79: 194 42.79 - 57.05: 73 57.05 - 71.32: 48 Dihedral angle restraints: 21628 sinusoidal: 8660 harmonic: 12968 Sorted by residual: dihedral pdb=" N LYS M 175 " pdb=" C LYS M 175 " pdb=" CA LYS M 175 " pdb=" CB LYS M 175 " ideal model delta harmonic sigma weight residual 122.80 138.27 -15.47 0 2.50e+00 1.60e-01 3.83e+01 dihedral pdb=" N LYS K 175 " pdb=" C LYS K 175 " pdb=" CA LYS K 175 " pdb=" CB LYS K 175 " ideal model delta harmonic sigma weight residual 122.80 138.20 -15.40 0 2.50e+00 1.60e-01 3.80e+01 dihedral pdb=" N LYS A 175 " pdb=" C LYS A 175 " pdb=" CA LYS A 175 " pdb=" CB LYS A 175 " ideal model delta harmonic sigma weight residual 122.80 138.20 -15.40 0 2.50e+00 1.60e-01 3.80e+01 ... (remaining 21625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 5049 0.154 - 0.309: 142 0.309 - 0.463: 9 0.463 - 0.618: 0 0.618 - 0.772: 8 Chirality restraints: 5208 Sorted by residual: chirality pdb=" CA LYS M 175 " pdb=" N LYS M 175 " pdb=" C LYS M 175 " pdb=" CB LYS M 175 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" CA LYS A 175 " pdb=" N LYS A 175 " pdb=" C LYS A 175 " pdb=" CB LYS A 175 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA LYS K 175 " pdb=" N LYS K 175 " pdb=" C LYS K 175 " pdb=" CB LYS K 175 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 ... (remaining 5205 not shown) Planarity restraints: 6464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE O 148 " 0.021 2.00e-02 2.50e+03 2.59e-02 1.18e+01 pdb=" CG PHE O 148 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE O 148 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE O 148 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE O 148 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE O 148 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE O 148 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 148 " 0.021 2.00e-02 2.50e+03 2.59e-02 1.17e+01 pdb=" CG PHE A 148 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 148 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE A 148 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 148 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 148 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 148 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 148 " -0.020 2.00e-02 2.50e+03 2.58e-02 1.17e+01 pdb=" CG PHE K 148 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE K 148 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE K 148 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE K 148 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE K 148 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE K 148 " -0.003 2.00e-02 2.50e+03 ... (remaining 6461 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 7296 2.76 - 3.30: 31377 3.30 - 3.83: 63203 3.83 - 4.37: 82433 4.37 - 4.90: 133195 Nonbonded interactions: 317504 Sorted by model distance: nonbonded pdb=" OD2 ASP M 216 " pdb=" O HOH M 501 " model vdw 2.229 2.440 nonbonded pdb=" OD2 ASP C 216 " pdb=" O HOH C 501 " model vdw 2.229 2.440 nonbonded pdb=" OD2 ASP A 216 " pdb=" O HOH A 501 " model vdw 2.229 2.440 nonbonded pdb=" OD2 ASP G 216 " pdb=" O HOH G 501 " model vdw 2.229 2.440 nonbonded pdb=" OD2 ASP O 216 " pdb=" O HOH O 501 " model vdw 2.229 2.440 ... (remaining 317499 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = (chain 'B' and (resid 1 through 63 or resid 65 through 138)) selection = (chain 'D' and (resid 1 through 63 or resid 65 through 138)) selection = (chain 'F' and (resid 1 through 63 or resid 65 through 138)) selection = (chain 'H' and (resid 1 through 63 or resid 65 through 138)) selection = (chain 'J' and (resid 1 through 63 or resid 65 through 138)) selection = (chain 'L' and (resid 1 through 63 or resid 65 through 138)) selection = (chain 'N' and (resid 1 through 63 or resid 65 through 138)) selection = (chain 'P' and (resid 1 through 63 or resid 65 through 138)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.800 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 94.950 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.230 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:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 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 : 0.013 0.111 36352 Z= 0.828 Angle : 1.221 11.559 49256 Z= 0.695 Chirality : 0.076 0.772 5208 Planarity : 0.009 0.063 6464 Dihedral : 10.930 71.315 13320 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.33 % Allowed : 3.19 % Favored : 95.48 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % 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: -3.84 (0.09), residues: 4448 helix: -3.73 (0.07), residues: 1656 sheet: -1.59 (0.17), residues: 760 loop : -1.69 (0.11), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP P 73 HIS 0.019 0.005 HIS C 292 PHE 0.057 0.007 PHE O 148 TYR 0.042 0.006 TYR J 17 ARG 0.020 0.002 ARG K 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 759 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 718 time to evaluate : 4.422 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: A 81 LYS cc_start: 0.8575 (pttt) cc_final: 0.8337 (pttt) REVERT: A 340 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7242 (tp30) REVERT: B 77 LYS cc_start: 0.8924 (mttt) cc_final: 0.8684 (mttt) REVERT: B 92 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8024 (mm-30) REVERT: B 114 LYS cc_start: 0.6297 (ttmt) cc_final: 0.5865 (ttpt) REVERT: B 133 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8125 (mm110) REVERT: C 81 LYS cc_start: 0.8639 (pttt) cc_final: 0.8424 (pttt) REVERT: C 340 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7244 (tp30) REVERT: C 349 MET cc_start: 0.8776 (mtp) cc_final: 0.8573 (mtm) REVERT: D 92 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8009 (mm-30) REVERT: D 114 LYS cc_start: 0.6073 (ttmt) cc_final: 0.5726 (ttpt) REVERT: D 133 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8073 (mm110) REVERT: E 81 LYS cc_start: 0.8619 (pttt) cc_final: 0.8411 (pttt) REVERT: E 340 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7259 (tp30) REVERT: E 349 MET cc_start: 0.8773 (mtp) cc_final: 0.8568 (mtm) REVERT: F 92 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8027 (mm-30) REVERT: F 114 LYS cc_start: 0.6108 (ttmt) cc_final: 0.5785 (ttpt) REVERT: F 133 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8078 (mm110) REVERT: G 340 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7234 (tp30) REVERT: G 349 MET cc_start: 0.8777 (mtp) cc_final: 0.8571 (mtm) REVERT: H 92 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8002 (mm-30) REVERT: H 114 LYS cc_start: 0.6148 (ttmt) cc_final: 0.5804 (ttpt) REVERT: I 81 LYS cc_start: 0.8639 (pttt) cc_final: 0.8428 (pttt) REVERT: I 340 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7213 (tp30) REVERT: J 92 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8004 (mm-30) REVERT: J 114 LYS cc_start: 0.6125 (ttmt) cc_final: 0.5809 (ttpt) REVERT: J 133 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8054 (mm110) REVERT: K 340 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7262 (tp30) REVERT: K 349 MET cc_start: 0.8777 (mtp) cc_final: 0.8572 (mtm) REVERT: L 77 LYS cc_start: 0.8877 (mttt) cc_final: 0.8630 (mttt) REVERT: L 92 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8014 (mm-30) REVERT: L 114 LYS cc_start: 0.6104 (ttmt) cc_final: 0.5799 (ttpt) REVERT: M 340 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7245 (tp30) REVERT: M 349 MET cc_start: 0.8772 (mtp) cc_final: 0.8572 (mtm) REVERT: N 92 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8042 (mm-30) REVERT: N 114 LYS cc_start: 0.6073 (ttmt) cc_final: 0.5710 (ttpt) REVERT: N 133 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8067 (mm110) REVERT: O 81 LYS cc_start: 0.8580 (pttt) cc_final: 0.8334 (pttt) REVERT: O 340 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7188 (tp30) REVERT: P 92 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8005 (mm-30) REVERT: P 114 LYS cc_start: 0.6414 (ttmt) cc_final: 0.5990 (ttpt) outliers start: 41 outliers final: 16 residues processed: 750 average time/residue: 1.7509 time to fit residues: 1536.1543 Evaluate side-chains 653 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 637 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 1.9990 chunk 333 optimal weight: 6.9990 chunk 185 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 344 optimal weight: 8.9990 chunk 133 optimal weight: 0.9980 chunk 209 optimal weight: 8.9990 chunk 256 optimal weight: 2.9990 chunk 399 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN A 207 ASN A 229 GLN A 238 HIS A 241 ASN A 277 ASN A 304 GLN B 9 ASN C 96 GLN C 115 ASN C 163 ASN C 207 ASN C 229 GLN C 238 HIS C 241 ASN C 277 ASN C 287 ASN C 304 GLN ** D 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 207 ASN E 229 GLN E 238 HIS E 241 ASN E 277 ASN E 287 ASN E 304 GLN F 9 ASN G 115 ASN G 163 ASN G 207 ASN G 229 GLN G 238 HIS G 241 ASN G 277 ASN G 304 GLN H 9 ASN I 96 GLN I 163 ASN I 207 ASN I 229 GLN I 238 HIS I 241 ASN I 277 ASN I 287 ASN I 304 GLN J 9 ASN K 163 ASN K 207 ASN K 229 GLN K 238 HIS K 241 ASN K 277 ASN K 304 GLN L 9 ASN M 96 GLN M 163 ASN M 207 ASN M 229 GLN M 238 HIS M 241 ASN M 277 ASN M 304 GLN N 9 ASN O 96 GLN O 163 ASN O 207 ASN O 229 GLN O 238 HIS O 241 ASN O 277 ASN O 304 GLN P 9 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36352 Z= 0.199 Angle : 0.610 9.478 49256 Z= 0.314 Chirality : 0.043 0.166 5208 Planarity : 0.005 0.053 6464 Dihedral : 6.690 57.719 5048 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.12 % Allowed : 7.73 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.84 (0.11), residues: 4448 helix: -1.25 (0.11), residues: 1648 sheet: -0.84 (0.17), residues: 800 loop : -1.19 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 73 HIS 0.005 0.001 HIS I 238 PHE 0.039 0.002 PHE G 345 TYR 0.013 0.002 TYR H 67 ARG 0.006 0.001 ARG G 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 662 time to evaluate : 4.167 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: B 49 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.7241 (mtpt) REVERT: C 52 GLU cc_start: 0.7326 (tp30) cc_final: 0.7043 (tm-30) REVERT: C 205 ASN cc_start: 0.8368 (p0) cc_final: 0.8146 (p0) REVERT: C 349 MET cc_start: 0.8644 (mtp) cc_final: 0.8332 (mtm) REVERT: D 49 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.7279 (mtpt) REVERT: E 52 GLU cc_start: 0.7336 (tp30) cc_final: 0.7104 (tm-30) REVERT: E 203 ASP cc_start: 0.8080 (t70) cc_final: 0.7854 (t0) REVERT: E 349 MET cc_start: 0.8650 (mtp) cc_final: 0.8334 (mtm) REVERT: F 49 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.7243 (mtpt) REVERT: G 349 MET cc_start: 0.8646 (mtp) cc_final: 0.8331 (mtm) REVERT: H 49 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.7270 (mtpt) REVERT: H 87 MET cc_start: 0.7299 (pmm) cc_final: 0.6852 (pmm) REVERT: I 52 GLU cc_start: 0.7341 (tp30) cc_final: 0.7118 (tm-30) REVERT: I 83 ARG cc_start: 0.8407 (ptp-170) cc_final: 0.8202 (ptp-170) REVERT: I 205 ASN cc_start: 0.8346 (p0) cc_final: 0.8130 (p0) REVERT: I 305 ARG cc_start: 0.7679 (ttt-90) cc_final: 0.7384 (ttt180) REVERT: J 49 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.7245 (mtpt) REVERT: J 77 LYS cc_start: 0.8754 (mttt) cc_final: 0.8540 (mttt) REVERT: K 349 MET cc_start: 0.8646 (mtp) cc_final: 0.8334 (mtm) REVERT: L 49 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.7274 (mtpt) REVERT: M 203 ASP cc_start: 0.8053 (t70) cc_final: 0.7849 (t0) REVERT: M 349 MET cc_start: 0.8647 (mtp) cc_final: 0.8339 (mtm) REVERT: N 49 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.7255 (mtpt) REVERT: O 203 ASP cc_start: 0.8058 (t70) cc_final: 0.7855 (t0) REVERT: P 49 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.7269 (mtpt) outliers start: 70 outliers final: 33 residues processed: 710 average time/residue: 1.7704 time to fit residues: 1466.3213 Evaluate side-chains 645 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 604 time to evaluate : 3.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain I residue 392 GLU Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain N residue 49 LYS Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 359 SER Chi-restraints excluded: chain O residue 392 GLU Chi-restraints excluded: chain P residue 49 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 332 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 400 optimal weight: 0.9990 chunk 432 optimal weight: 9.9990 chunk 356 optimal weight: 10.0000 chunk 396 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 321 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN A 207 ASN A 277 ASN A 287 ASN ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 207 ASN C 277 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 ASN ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 207 ASN E 277 ASN ** E 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN G 207 ASN G 277 ASN G 287 ASN ** G 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN I 96 GLN I 115 ASN I 207 ASN I 277 ASN ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 ASN K 207 ASN K 277 ASN K 287 ASN ** K 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 ASN M 207 ASN M 277 ASN M 287 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 115 ASN O 207 ASN O 277 ASN O 287 ASN ** O 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 36352 Z= 0.302 Angle : 0.632 8.858 49256 Z= 0.323 Chirality : 0.045 0.174 5208 Planarity : 0.005 0.045 6464 Dihedral : 6.467 57.300 5048 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.48 % Allowed : 10.35 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.11), residues: 4448 helix: 0.09 (0.12), residues: 1648 sheet: -0.46 (0.17), residues: 800 loop : -1.00 (0.12), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 73 HIS 0.007 0.002 HIS I 153 PHE 0.033 0.003 PHE G 345 TYR 0.014 0.002 TYR L 67 ARG 0.006 0.001 ARG N 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8896 Ramachandran restraints generated. 4448 Oldfield, 0 Emsley, 4448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 613 time to evaluate : 3.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 ASN cc_start: 0.8234 (p0) cc_final: 0.8003 (p0) REVERT: A 339 ARG cc_start: 0.7635 (ttm170) cc_final: 0.7226 (ttm170) REVERT: B 49 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.7259 (mtpt) REVERT: B 80 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.6870 (mmt) REVERT: C 52 GLU cc_start: 0.7500 (tp30) cc_final: 0.7251 (tm-30) REVERT: C 205 ASN cc_start: 0.8298 (p0) cc_final: 0.8065 (p0) REVERT: C 339 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7495 (ttm170) REVERT: C 349 MET cc_start: 0.8703 (mtp) cc_final: 0.8434 (mtm) REVERT: D 49 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.7288 (mtpt) REVERT: D 80 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.6869 (mmt) REVERT: E 349 MET cc_start: 0.8703 (mtp) cc_final: 0.8445 (mtm) REVERT: F 49 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7256 (mtpt) REVERT: F 80 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.6841 (mmt) REVERT: G 205 ASN cc_start: 0.8301 (p0) cc_final: 0.8058 (p0) REVERT: G 349 MET cc_start: 0.8707 (mtp) cc_final: 0.8441 (mtm) REVERT: H 49 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7269 (mtpt) REVERT: H 77 LYS cc_start: 0.8667 (mttt) cc_final: 0.8462 (mttt) REVERT: H 80 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.6793 (mmt) REVERT: H 87 MET cc_start: 0.7343 (pmm) cc_final: 0.6928 (pmm) REVERT: H 133 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8004 (mm110) REVERT: I 83 ARG cc_start: 0.8375 (ptp-170) cc_final: 0.8129 (ptp-170) REVERT: I 205 ASN cc_start: 0.8281 (p0) cc_final: 0.8046 (p0) REVERT: I 305 ARG cc_start: 0.7674 (ttt-90) cc_final: 0.7383 (ttt180) REVERT: J 49 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.7253 (mtpt) REVERT: J 80 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.6845 (mmt) REVERT: K 339 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7530 (ttm170) REVERT: K 349 MET cc_start: 0.8707 (mtp) cc_final: 0.8445 (mtm) REVERT: L 49 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7274 (mtpt) REVERT: L 80 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.6786 (mmt) REVERT: L 92 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8005 (mm-30) REVERT: M 205 ASN cc_start: 0.8503 (p0) cc_final: 0.8090 (p0) REVERT: M 349 MET cc_start: 0.8707 (mtp) cc_final: 0.8433 (mtm) REVERT: N 49 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.7265 (mtpt) REVERT: N 80 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.6883 (mmt) REVERT: O 339 ARG cc_start: 0.7633 (ttm170) cc_final: 0.7281 (ttm170) REVERT: P 49 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7275 (mtpt) REVERT: P 80 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.6827 (mmt) outliers start: 83 outliers final: 51 residues processed: 668 average time/residue: 1.8551 time to fit residues: 1435.2934 Evaluate side-chains 658 residues out of total 3688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 591 time to evaluate : 3.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 253 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain B residue 49 LYS Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 175 LYS Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain G residue 253 ARG Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 175 LYS Chi-restraints excluded: chain I residue 253 ARG Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 331 VAL Chi-restraints excluded: chain J residue 49 LYS Chi-restraints excluded: chain J residue 80 MET Chi-restraints excluded: chain K residue 36 ILE Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 175 LYS Chi-restraints excluded: chain K residue 253 ARG Chi-restraints excluded: chain K residue 279 SER Chi-restraints excluded: chain K residue 359 SER Chi-restraints excluded: chain L residue 49 LYS Chi-restraints excluded: chain L residue 80 MET Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 124 VAL Chi-restraints excluded: chain M residue 175 LYS Chi-restraints excluded: chain M residue 253 ARG Chi-restraints excluded: chain M residue 279 SER Chi-restraints excluded: chain M residue 331 VAL Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain N residue 49 LYS Chi-restraints excluded: chain N residue 80 MET Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 175 LYS Chi-restraints excluded: chain O residue 253 ARG Chi-restraints excluded: chain O residue 279 SER Chi-restraints excluded: chain O residue 359 SER Chi-restraints excluded: chain P residue 49 LYS Chi-restraints excluded: chain P residue 80 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.0514 > 50: distance: 0 - 1: 22.719 distance: 1 - 2: 12.917 distance: 1 - 4: 23.739 distance: 2 - 3: 15.128 distance: 2 - 8: 31.438 distance: 4 - 5: 3.335 distance: 5 - 6: 58.260 distance: 6 - 7: 28.649 distance: 8 - 9: 46.798 distance: 9 - 10: 41.026 distance: 9 - 12: 48.341 distance: 10 - 16: 56.396 distance: 12 - 13: 58.377 distance: 13 - 14: 44.581 distance: 14 - 15: 46.241 distance: 17 - 18: 56.087 distance: 17 - 20: 56.348 distance: 18 - 19: 39.749 distance: 20 - 21: 35.279 distance: 20 - 22: 57.624 distance: 23 - 24: 56.120 distance: 24 - 25: 40.131 distance: 24 - 27: 40.846 distance: 25 - 26: 39.655 distance: 25 - 37: 40.501 distance: 27 - 28: 19.535 distance: 28 - 29: 13.163 distance: 28 - 30: 45.811 distance: 29 - 31: 41.914 distance: 30 - 32: 48.934 distance: 30 - 33: 38.271 distance: 31 - 32: 12.612 distance: 32 - 34: 19.942 distance: 33 - 35: 36.064 distance: 34 - 36: 31.866 distance: 35 - 36: 16.667 distance: 38 - 39: 55.633 distance: 38 - 41: 41.184 distance: 39 - 40: 41.146 distance: 41 - 42: 38.698 distance: 41 - 43: 56.564 distance: 44 - 45: 8.838 distance: 44 - 50: 57.972 distance: 45 - 46: 7.765 distance: 45 - 48: 57.348 distance: 46 - 47: 34.083 distance: 46 - 51: 12.750 distance: 48 - 49: 45.199 distance: 49 - 50: 48.721 distance: 51 - 52: 14.784 distance: 52 - 53: 10.028 distance: 52 - 55: 44.705 distance: 53 - 58: 55.538 distance: 55 - 56: 42.123 distance: 55 - 57: 10.130 distance: 58 - 59: 35.881 distance: 59 - 60: 40.938 distance: 59 - 62: 57.076 distance: 60 - 61: 39.310 distance: 60 - 66: 40.990 distance: 62 - 63: 55.300 distance: 63 - 64: 6.515 distance: 63 - 65: 39.160 distance: 66 - 67: 52.317 distance: 67 - 68: 33.256 distance: 67 - 70: 40.999 distance: 68 - 69: 42.832 distance: 68 - 74: 28.372 distance: 70 - 71: 3.030 distance: 71 - 72: 46.212 distance: 71 - 73: 22.235