Starting phenix.real_space_refine (version: dev) on Thu Apr 7 23:36:21 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xym_6789/04_2022/5xym_6789_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xym_6789/04_2022/5xym_6789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xym_6789/04_2022/5xym_6789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xym_6789/04_2022/5xym_6789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xym_6789/04_2022/5xym_6789_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xym_6789/04_2022/5xym_6789_neut.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "0 ARG 37": "NH1" <-> "NH2" Residue "1 ARG 7": "NH1" <-> "NH2" Residue "1 ARG 13": "NH1" <-> "NH2" Residue "1 TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 52": "OE1" <-> "OE2" Residue "2 ARG 15": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "3 ARG 30": "NH1" <-> "NH2" Residue "4 ARG 18": "NH1" <-> "NH2" Residue "4 ARG 19": "NH1" <-> "NH2" Residue "4 ARG 22": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 26": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 157": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "D TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 174": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "E PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 20": "NH1" <-> "NH2" Residue "F ARG 75": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 99": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F ARG 122": "NH1" <-> "NH2" Residue "F PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "K ARG 23": "NH1" <-> "NH2" Residue "K ARG 31": "NH1" <-> "NH2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 97": "NH1" <-> "NH2" Residue "K GLU 108": "OE1" <-> "OE2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 117": "NH1" <-> "NH2" Residue "O ARG 18": "NH1" <-> "NH2" Residue "O ARG 42": "NH1" <-> "NH2" Residue "O ARG 45": "NH1" <-> "NH2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "P ARG 48": "NH1" <-> "NH2" Residue "P ARG 49": "NH1" <-> "NH2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 103": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "R TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 87": "NH1" <-> "NH2" Residue "S ARG 102": "NH1" <-> "NH2" Residue "T ARG 8": "NH1" <-> "NH2" Residue "T ARG 66": "NH1" <-> "NH2" Residue "T ARG 68": "NH1" <-> "NH2" Residue "U TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 96": "NH1" <-> "NH2" Residue "V ARG 59": "NH1" <-> "NH2" Residue "W ARG 41": "NH1" <-> "NH2" Residue "W PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Y ARG 62": "NH1" <-> "NH2" Residue "a ARG 11": "NH1" <-> "NH2" Residue "a ARG 21": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 84069 Number of models: 1 Model: "" Number of chains: 32 Chain: "0" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 51, 'PCIS': 1} Chain: "1" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 384 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain breaks: 2 Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 502 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "4" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 298 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "A" Number of atoms: 57277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2665, 57277 Classifications: {'RNA': 2665} Modifications used: {'rna3p_pyr': 993, 'rna2p_pur': 281, 'rna3p_pur': 1261, 'rna2p_pyr': 130} Link IDs: {'rna3p': 2253, 'rna2p': 411} Chain breaks: 19 Chain: "B" Number of atoms: 2477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2477 Classifications: {'RNA': 116} Modifications used: {'rna3p_pyr': 44, 'rna2p_pur': 6, 'rna3p_pur': 56, 'rna2p_pyr': 10} Link IDs: {'rna3p': 99, 'rna2p': 16} Chain: "C" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2097 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 19, 'CIS': 1, 'TRANS': 252} Chain: "D" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1578 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 7, 'TRANS': 203, 'PCIS': 1} Chain: "E" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1560 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 11, 'CIS': 2, 'TRANS': 194} Chain: "F" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1372 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1074 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain breaks: 3 Chain: "H" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 255 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain breaks: 1 Chain: "J" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1130 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 10, 'CIS': 1, 'TRANS': 134} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1070 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'CIS': 2, 'TRANS': 135} Chain: "M" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1079 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'CIS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "N" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 910 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain: "O" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 103} Chain breaks: 2 Chain: "P" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "Q" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 120, 'PCIS': 1} Chain: "R" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "S" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 850 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "T" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'CIS': 1, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain breaks: 2 Chain: "V" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1264 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain breaks: 3 Chain: "W" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 563 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "X" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 465 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 4, 'TRANS': 57} Chain: "Y" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 516 Classifications: {'peptide': 61} Link IDs: {'TRANS': 59, 'PCIS': 1} Chain: "Z" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 470 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "a" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 189 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "A" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 146 Unusual residues: {' MG': 146} Classifications: {'undetermined': 146} Link IDs: {None: 145} Time building chain proxies: 34.86, per 1000 atoms: 0.41 Number of scatterers: 84069 At special positions: 0 Unit cell: (179.52, 234.96, 205.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 2781 15.00 Mg 146 11.99 O 23625 8.00 N 15797 7.00 C 41676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 14 " distance=2.02 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 27 " distance=1.68 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=1.76 Simple disulfide: pdb=" SG CYS X 8 " - pdb=" SG CYS X 52 " distance=1.95 Simple disulfide: pdb=" SG CYS X 8 " - pdb=" SG CYS X 55 " distance=1.67 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: 36.31 Conformation dependent library (CDL) restraints added in 3.3 seconds 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5656 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 49 sheets defined 28.2% alpha, 15.8% beta 758 base pairs and 1584 stacking pairs defined. Time for finding SS restraints: 29.37 Creating SS restraints... Processing helix chain '0' and resid 9 through 18 removed outlier: 3.830A pdb=" N ARG 0 14 " --> pdb=" O ARG 0 10 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG 0 16 " --> pdb=" O ASN 0 12 " (cutoff:3.500A) Processing helix chain '0' and resid 40 through 42 No H-bonds generated for 'chain '0' and resid 40 through 42' Processing helix chain '0' and resid 43 through 50 removed outlier: 4.046A pdb=" N ARG 0 48 " --> pdb=" O LEU 0 44 " (cutoff:3.500A) Processing helix chain '2' and resid 11 through 20 Processing helix chain '2' and resid 20 through 26 removed outlier: 3.514A pdb=" N ARG 2 24 " --> pdb=" O GLY 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 27 through 41 Processing helix chain '3' and resid 7 through 14 removed outlier: 4.102A pdb=" N LYS 3 12 " --> pdb=" O SER 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 37 through 44 removed outlier: 3.519A pdb=" N ARG 3 43 " --> pdb=" O LYS 3 39 " (cutoff:3.500A) Processing helix chain '3' and resid 54 through 62 removed outlier: 3.623A pdb=" N ASN 3 59 " --> pdb=" O ASN 3 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 removed outlier: 3.523A pdb=" N ILE C 204 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 215 removed outlier: 3.802A pdb=" N MET C 212 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 62 Processing helix chain 'D' and resid 63 through 74 removed outlier: 3.731A pdb=" N GLN D 69 " --> pdb=" O PRO D 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE D 70 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 95 removed outlier: 3.693A pdb=" N VAL D 92 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 107 removed outlier: 3.966A pdb=" N ILE D 105 " --> pdb=" O THR D 102 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE D 106 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER D 107 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 102 through 107' Processing helix chain 'D' and resid 126 through 131 Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 30 through 46 removed outlier: 3.552A pdb=" N GLN E 36 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 121 removed outlier: 3.573A pdb=" N ARG E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 148 removed outlier: 3.618A pdb=" N THR E 147 " --> pdb=" O THR E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 169 removed outlier: 3.928A pdb=" N VAL E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 191 removed outlier: 3.841A pdb=" N ALA E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 209 Processing helix chain 'F' and resid 11 through 17 Processing helix chain 'F' and resid 17 through 27 removed outlier: 3.808A pdb=" N GLU F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 55 removed outlier: 3.596A pdb=" N ALA F 50 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ALA F 54 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS F 55 " --> pdb=" O ARG F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 68 removed outlier: 3.954A pdb=" N ALA F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN F 62 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 112 removed outlier: 3.724A pdb=" N ARG F 109 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 169 through 180 Processing helix chain 'G' and resid 60 through 82 removed outlier: 3.939A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU G 68 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE G 73 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL G 80 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU G 82 " --> pdb=" O THR G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.726A pdb=" N ARG G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 removed outlier: 3.656A pdb=" N GLY H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG H 27 " --> pdb=" O ASP H 23 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 removed outlier: 3.819A pdb=" N ARG H 33 " --> pdb=" O TYR H 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 38 removed outlier: 3.647A pdb=" N LEU J 35 " --> pdb=" O ALA J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 4.195A pdb=" N VAL J 100 " --> pdb=" O HIS J 96 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY J 107 " --> pdb=" O ASN J 103 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 109 " --> pdb=" O ILE J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 118 removed outlier: 3.852A pdb=" N GLN J 117 " --> pdb=" O LYS J 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 110 removed outlier: 4.407A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 117 removed outlier: 3.502A pdb=" N VAL K 115 " --> pdb=" O PHE K 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 9 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.585A pdb=" N LEU L 61 " --> pdb=" O ILE L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 87 Processing helix chain 'L' and resid 96 through 102 Processing helix chain 'L' and resid 130 through 141 removed outlier: 3.665A pdb=" N ALA L 140 " --> pdb=" O ALA L 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 59 removed outlier: 3.555A pdb=" N HIS M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 124 removed outlier: 3.567A pdb=" N ALA M 121 " --> pdb=" O ALA M 117 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS M 123 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS M 124 " --> pdb=" O ARG M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.513A pdb=" N GLU N 30 " --> pdb=" O THR N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.571A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Proline residue: N 46 - end of helix removed outlier: 3.608A pdb=" N LYS N 50 " --> pdb=" O PRO N 46 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU N 51 " --> pdb=" O TYR N 47 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS N 54 " --> pdb=" O LYS N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 68 Processing helix chain 'N' and resid 72 through 82 removed outlier: 3.570A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'O' and resid 10 through 26 removed outlier: 3.913A pdb=" N ARG O 14 " --> pdb=" O ILE O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 96 removed outlier: 3.513A pdb=" N GLY O 85 " --> pdb=" O SER O 81 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU O 87 " --> pdb=" O ARG O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 124 removed outlier: 3.558A pdb=" N ALA O 119 " --> pdb=" O ALA O 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 77 through 81 removed outlier: 3.673A pdb=" N ILE P 80 " --> pdb=" O SER P 77 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP P 81 " --> pdb=" O PRO P 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 77 through 81' Processing helix chain 'P' and resid 98 through 103 removed outlier: 3.829A pdb=" N LEU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG P 103 " --> pdb=" O LEU P 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 98 through 103' Processing helix chain 'Q' and resid 10 through 21 removed outlier: 4.149A pdb=" N ARG Q 14 " --> pdb=" O ALA Q 10 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.041A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 72 removed outlier: 3.633A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLY Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.614A pdb=" N VAL Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP Q 102 " --> pdb=" O LEU Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 116 removed outlier: 3.622A pdb=" N LEU Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP Q 111 " --> pdb=" O THR Q 107 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA Q 116 " --> pdb=" O VAL Q 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 56 Processing helix chain 'S' and resid 23 through 32 removed outlier: 4.429A pdb=" N VAL S 27 " --> pdb=" O LYS S 23 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE S 28 " --> pdb=" O ALA S 24 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU S 30 " --> pdb=" O ARG S 26 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL S 31 " --> pdb=" O VAL S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 35 through 45 removed outlier: 3.896A pdb=" N ASP S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU S 43 " --> pdb=" O ALA S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 50 through 68 removed outlier: 3.597A pdb=" N VAL S 54 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS S 56 " --> pdb=" O GLU S 52 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL S 57 " --> pdb=" O PRO S 53 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 12 removed outlier: 4.502A pdb=" N ILE T 11 " --> pdb=" O PRO T 7 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU T 12 " --> pdb=" O ARG T 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 7 through 12' Processing helix chain 'T' and resid 17 through 25 removed outlier: 4.207A pdb=" N GLU T 25 " --> pdb=" O TYR T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 51 removed outlier: 3.538A pdb=" N LYS T 43 " --> pdb=" O LYS T 39 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 21 through 31 removed outlier: 3.536A pdb=" N ARG V 25 " --> pdb=" O LYS V 21 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN V 26 " --> pdb=" O GLY V 22 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 62 removed outlier: 3.665A pdb=" N ALA V 56 " --> pdb=" O ARG V 52 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU V 58 " --> pdb=" O PHE V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 160 through 162 No H-bonds generated for 'chain 'V' and resid 160 through 162' Processing helix chain 'X' and resid 52 through 58 Processing helix chain 'Y' and resid 15 through 39 removed outlier: 3.655A pdb=" N PHE Y 34 " --> pdb=" O PHE Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 66 removed outlier: 3.970A pdb=" N ARG Y 48 " --> pdb=" O ASN Y 44 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR Y 49 " --> pdb=" O ARG Y 45 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL Y 50 " --> pdb=" O ARG Y 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR Y 58 " --> pdb=" O ILE Y 54 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR Y 59 " --> pdb=" O ALA Y 55 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG Y 64 " --> pdb=" O VAL Y 60 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.684A pdb=" N LEU Z 26 " --> pdb=" O SER Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.642A pdb=" N GLY Z 45 " --> pdb=" O ALA Z 41 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL Z 50 " --> pdb=" O LEU Z 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 3 through 10 removed outlier: 3.506A pdb=" N LYS a 8 " --> pdb=" O ARG a 4 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG a 9 " --> pdb=" O GLY a 5 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 14 removed outlier: 3.962A pdb=" N SER a 14 " --> pdb=" O ARG a 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 11 through 14' Processing sheet with id=AA1, first strand: chain '1' and resid 9 through 12 removed outlier: 4.199A pdb=" N TYR 1 22 " --> pdb=" O LEU 1 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '3' and resid 24 through 25 Processing sheet with id=AA3, first strand: chain '4' and resid 17 through 18 Processing sheet with id=AA4, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 37 removed outlier: 4.319A pdb=" N LEU C 37 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG C 60 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 76 through 77 Processing sheet with id=AA7, first strand: chain 'C' and resid 81 through 83 removed outlier: 3.602A pdb=" N ARG C 103 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 167 removed outlier: 5.601A pdb=" N LEU C 165 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG C 176 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY C 167 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 115 through 116 removed outlier: 5.896A pdb=" N VAL D 28 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N MET D 13 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL D 26 " --> pdb=" O MET D 13 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN D 15 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL D 24 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS D 195 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL D 182 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 78 through 85 removed outlier: 6.935A pdb=" N ARG D 78 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU D 56 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ALA D 49 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ILE D 39 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N GLN D 51 " --> pdb=" O THR D 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 124 through 125 removed outlier: 3.584A pdb=" N ALA D 124 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY D 168 " --> pdb=" O ALA D 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 7 through 8 removed outlier: 6.443A pdb=" N HIS E 125 " --> pdb=" O PHE E 196 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU E 155 " --> pdb=" O VAL E 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 73 through 76 removed outlier: 7.041A pdb=" N VAL F 164 " --> pdb=" O VAL F 39 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N VAL F 41 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR F 162 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL F 43 " --> pdb=" O ASP F 160 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASP F 160 " --> pdb=" O VAL F 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 17 through 19 removed outlier: 3.562A pdb=" N LEU G 35 " --> pdb=" O ASN G 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 123 through 128 removed outlier: 7.106A pdb=" N LYS G 131 " --> pdb=" O GLU G 127 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY G 136 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR G 84 " --> pdb=" O GLY G 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 95 through 96 removed outlier: 3.856A pdb=" N ARG G 96 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AC1, first strand: chain 'J' and resid 122 through 124 removed outlier: 3.925A pdb=" N ILE J 138 " --> pdb=" O TRP J 15 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 75 through 77 Processing sheet with id=AC3, first strand: chain 'K' and resid 5 through 8 removed outlier: 5.071A pdb=" N SER K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS K 21 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N CYS K 21 " --> pdb=" O THR K 42 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR K 42 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 77 through 79 removed outlier: 6.548A pdb=" N THR P 57 " --> pdb=" O ARG P 49 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ARG P 49 " --> pdb=" O THR P 57 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR P 24 " --> pdb=" O LEU P 86 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS P 82 " --> pdb=" O HIS P 28 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 102 through 103 removed outlier: 6.117A pdb=" N VAL K 102 " --> pdb=" O LEU K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'L' and resid 76 through 79 removed outlier: 6.167A pdb=" N GLN L 76 " --> pdb=" O LYS L 111 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU L 113 " --> pdb=" O GLN L 76 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL L 78 " --> pdb=" O LEU L 113 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL L 110 " --> pdb=" O LYS L 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'L' and resid 123 through 125 removed outlier: 6.109A pdb=" N VAL L 124 " --> pdb=" O THR L 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'M' and resid 102 through 106 removed outlier: 6.167A pdb=" N VAL M 102 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA M 36 " --> pdb=" O VAL M 102 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 40 through 43 Processing sheet with id=AD1, first strand: chain 'M' and resid 75 through 76 Processing sheet with id=AD2, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.367A pdb=" N MET N 110 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL N 100 " --> pdb=" O MET N 110 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 58 through 64 removed outlier: 5.905A pdb=" N THR O 59 " --> pdb=" O ASN O 53 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASN O 53 " --> pdb=" O THR O 59 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA O 61 " --> pdb=" O LEU O 51 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 13 through 17 removed outlier: 7.211A pdb=" N TYR R 4 " --> pdb=" O VAL R 42 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL R 42 " --> pdb=" O TYR R 4 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE R 6 " --> pdb=" O ALA R 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 22 through 25 removed outlier: 3.918A pdb=" N VAL R 96 " --> pdb=" O GLU R 66 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N GLU R 66 " --> pdb=" O VAL R 96 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 73 through 78 Processing sheet with id=AD7, first strand: chain 'S' and resid 9 through 17 removed outlier: 3.912A pdb=" N TYR S 16 " --> pdb=" O SER S 108 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER S 108 " --> pdb=" O TYR S 16 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLU S 115 " --> pdb=" O VAL S 78 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL S 78 " --> pdb=" O GLU S 115 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 93 through 94 Processing sheet with id=AD9, first strand: chain 'T' and resid 28 through 31 Processing sheet with id=AE1, first strand: chain 'T' and resid 66 through 67 Processing sheet with id=AE2, first strand: chain 'U' and resid 66 through 67 removed outlier: 6.787A pdb=" N LYS U 32 " --> pdb=" O ALA U 26 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ALA U 26 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU U 34 " --> pdb=" O LEU U 24 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.607A pdb=" N GLN U 62 " --> pdb=" O ILE U 41 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 83 through 84 Processing sheet with id=AE5, first strand: chain 'V' and resid 45 through 50 removed outlier: 3.618A pdb=" N GLN V 45 " --> pdb=" O LEU V 37 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N LYS V 32 " --> pdb=" O GLN V 93 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N ALA V 95 " --> pdb=" O LYS V 32 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU V 97 " --> pdb=" O PRO V 34 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL V 36 " --> pdb=" O LEU V 97 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL V 99 " --> pdb=" O VAL V 36 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR V 38 " --> pdb=" O VAL V 99 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP V 84 " --> pdb=" O GLN V 93 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA V 95 " --> pdb=" O ALA V 82 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA V 82 " --> pdb=" O ALA V 95 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU V 97 " --> pdb=" O THR V 80 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR V 80 " --> pdb=" O LEU V 97 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL V 99 " --> pdb=" O ALA V 78 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA V 78 " --> pdb=" O VAL V 99 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 129 through 132 removed outlier: 3.691A pdb=" N LEU V 144 " --> pdb=" O THR V 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 122 through 125 removed outlier: 3.804A pdb=" N VAL V 182 " --> pdb=" O THR V 122 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL V 179 " --> pdb=" O ILE V 157 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE V 157 " --> pdb=" O VAL V 179 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 46 through 47 Processing sheet with id=AE9, first strand: chain 'W' and resid 51 through 53 Processing sheet with id=AF1, first strand: chain 'W' and resid 66 through 67 Processing sheet with id=AF2, first strand: chain 'X' and resid 13 through 16 Processing sheet with id=AF3, first strand: chain 'X' and resid 34 through 38 Processing sheet with id=AF4, first strand: chain 'Z' and resid 35 through 38 711 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1856 hydrogen bonds 2984 hydrogen bond angles 0 basepair planarities 758 basepair parallelities 1584 stacking parallelities Total time for adding SS restraints: 154.92 Time building geometry restraints manager: 39.67 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: 12361 1.33 - 1.46: 39311 1.46 - 1.58: 34111 1.58 - 1.70: 5541 1.70 - 1.82: 78 Bond restraints: 91402 Sorted by residual: bond pdb=" C1' A A1705 " pdb=" N9 A A1705 " ideal model delta sigma weight residual 1.475 1.396 0.079 1.50e-02 4.44e+03 2.79e+01 bond pdb=" C THR C 10 " pdb=" N PRO C 11 " ideal model delta sigma weight residual 1.329 1.388 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C SER G 128 " pdb=" N PRO G 129 " ideal model delta sigma weight residual 1.332 1.391 -0.059 1.30e-02 5.92e+03 2.08e+01 bond pdb=" N PRO Q 124 " pdb=" CD PRO Q 124 " ideal model delta sigma weight residual 1.474 1.536 -0.062 1.40e-02 5.10e+03 1.98e+01 bond pdb=" C ARG C 218 " pdb=" N PRO C 219 " ideal model delta sigma weight residual 1.332 1.389 -0.057 1.30e-02 5.92e+03 1.92e+01 ... (remaining 91397 not shown) Histogram of bond angle deviations from ideal: 99.47 - 107.33: 18672 107.33 - 115.19: 58156 115.19 - 123.05: 43715 123.05 - 130.90: 15938 130.90 - 138.76: 777 Bond angle restraints: 137258 Sorted by residual: angle pdb=" N VAL K 10 " pdb=" CA VAL K 10 " pdb=" C VAL K 10 " ideal model delta sigma weight residual 109.37 121.29 -11.92 1.35e+00 5.49e-01 7.80e+01 angle pdb=" N ASN E 171 " pdb=" CA ASN E 171 " pdb=" C ASN E 171 " ideal model delta sigma weight residual 111.28 120.37 -9.09 1.09e+00 8.42e-01 6.95e+01 angle pdb=" N ALA W 18 " pdb=" CA ALA W 18 " pdb=" C ALA W 18 " ideal model delta sigma weight residual 111.28 119.85 -8.57 1.09e+00 8.42e-01 6.17e+01 angle pdb=" C4' C A2429 " pdb=" C3' C A2429 " pdb=" O3' C A2429 " ideal model delta sigma weight residual 109.40 121.02 -11.62 1.50e+00 4.44e-01 6.00e+01 angle pdb=" O3' A A 119 " pdb=" C3' A A 119 " pdb=" C2' A A 119 " ideal model delta sigma weight residual 109.50 119.99 -10.49 1.50e+00 4.44e-01 4.89e+01 ... (remaining 137253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 46430 35.96 - 71.92: 1862 71.92 - 107.88: 137 107.88 - 143.84: 10 143.84 - 179.79: 27 Dihedral angle restraints: 48466 sinusoidal: 39671 harmonic: 8795 Sorted by residual: dihedral pdb=" O4' U A 386 " pdb=" C1' U A 386 " pdb=" N1 U A 386 " pdb=" C2 U A 386 " ideal model delta sinusoidal sigma weight residual -160.00 18.47 -178.47 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A3049 " pdb=" C1' C A3049 " pdb=" N1 C A3049 " pdb=" C2 C A3049 " ideal model delta sinusoidal sigma weight residual 200.00 23.02 176.98 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 142 " pdb=" C1' U A 142 " pdb=" N1 U A 142 " pdb=" C2 U A 142 " ideal model delta sinusoidal sigma weight residual 200.00 41.87 158.13 1 1.50e+01 4.44e-03 8.23e+01 ... (remaining 48463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 14091 0.131 - 0.262: 3495 0.262 - 0.392: 18 0.392 - 0.523: 8 0.523 - 0.654: 4 Chirality restraints: 17616 Sorted by residual: chirality pdb=" C3' A A 119 " pdb=" C4' A A 119 " pdb=" O3' A A 119 " pdb=" C2' A A 119 " both_signs ideal model delta sigma weight residual False -2.74 -2.09 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" C3' G A 762 " pdb=" C4' G A 762 " pdb=" O3' G A 762 " pdb=" C2' G A 762 " both_signs ideal model delta sigma weight residual False -2.74 -2.21 -0.54 2.00e-01 2.50e+01 7.19e+00 chirality pdb=" C3' C A2429 " pdb=" C4' C A2429 " pdb=" O3' C A2429 " pdb=" C2' C A2429 " both_signs ideal model delta sigma weight residual False -2.74 -2.21 -0.53 2.00e-01 2.50e+01 7.07e+00 ... (remaining 17613 not shown) Planarity restraints: 7061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY Y 39 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C GLY Y 39 " 0.049 2.00e-02 2.50e+03 pdb=" O GLY Y 39 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN Y 40 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 9 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C LYS K 9 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS K 9 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL K 10 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU N 30 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C GLU N 30 " -0.039 2.00e-02 2.50e+03 pdb=" O GLU N 30 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS N 31 " 0.013 2.00e-02 2.50e+03 ... (remaining 7058 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 32 2.02 - 2.74: 8733 2.74 - 3.46: 100405 3.46 - 4.18: 268303 4.18 - 4.90: 367890 Nonbonded interactions: 745363 Sorted by model distance: nonbonded pdb=" O PHE E 25 " pdb=" OG SER E 116 " model vdw 1.297 2.440 nonbonded pdb=" O2' A A2145 " pdb=" N4 C A2147 " model vdw 1.566 2.520 nonbonded pdb=" O ALA C 121 " pdb=" ND2 ASN C 135 " model vdw 1.775 2.520 nonbonded pdb=" O2' A A3017 " pdb=" O4' C A3018 " model vdw 1.776 2.440 nonbonded pdb=" N1 A A1705 " pdb=" O2 C A1736 " model vdw 1.823 3.120 ... (remaining 745358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2781 5.49 5 Mg 146 5.21 5 S 44 5.16 5 C 41676 2.51 5 N 15797 2.21 5 O 23625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.950 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: 0.080 Extract box with map and model: 10.470 Check model and map are aligned: 0.980 Convert atoms to be neutral: 0.580 Process input model: 316.850 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 334.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.006 0.079 91402 Z= 0.383 Angle : 1.010 15.381 137258 Z= 0.676 Chirality : 0.096 0.654 17616 Planarity : 0.004 0.056 7061 Dihedral : 16.018 179.795 42795 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 2.51 % Allowed : 7.85 % Favored : 89.64 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.34 % 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: -3.59 (0.12), residues: 3032 helix: -2.45 (0.14), residues: 730 sheet: -2.24 (0.19), residues: 549 loop : -2.44 (0.12), residues: 1753 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 726 time to evaluate : 3.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 25 residues processed: 771 average time/residue: 0.9248 time to fit residues: 1133.0875 Evaluate side-chains 514 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 489 time to evaluate : 3.613 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.6184 time to fit residues: 32.4845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 487 optimal weight: 3.9990 chunk 437 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 295 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 452 optimal weight: 0.0020 chunk 175 optimal weight: 8.9990 chunk 274 optimal weight: 9.9990 chunk 336 optimal weight: 1.9990 chunk 523 optimal weight: 5.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 12 ASN 1 47 HIS 2 19 HIS 3 7 HIS 3 63 ASN C 53 HIS C 58 HIS ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 ASN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 ASN C 143 HIS C 164 GLN D 20 ASN D 21 ASN D 34 ASN D 139 HIS E 151 ASN E 182 GLN E 190 ASN E 208 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 GLN G 98 GLN ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN J 117 GLN ** J 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 144 GLN ** J 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 GLN N 102 ASN O 22 HIS O 56 ASN Q 41 HIS ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN R 67 HIS S 64 ASN S 109 HIS T 58 ASN V 26 GLN V 46 HIS ** V 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 64 ASN X 45 ASN a 17 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 91402 Z= 0.251 Angle : 0.654 14.710 137258 Z= 0.339 Chirality : 0.039 0.379 17616 Planarity : 0.006 0.082 7061 Dihedral : 15.068 177.971 36773 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 1.25 % Allowed : 6.89 % Favored : 91.85 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.34 % 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: -2.58 (0.14), residues: 3032 helix: -0.87 (0.17), residues: 779 sheet: -1.73 (0.20), residues: 592 loop : -2.16 (0.13), residues: 1661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 520 time to evaluate : 3.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 48 residues processed: 583 average time/residue: 0.8680 time to fit residues: 834.1137 Evaluate side-chains 517 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 469 time to evaluate : 3.601 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.6261 time to fit residues: 60.7635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 291 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 436 optimal weight: 9.9990 chunk 356 optimal weight: 0.0020 chunk 144 optimal weight: 8.9990 chunk 524 optimal weight: 1.9990 chunk 567 optimal weight: 7.9990 chunk 467 optimal weight: 6.9990 chunk 520 optimal weight: 0.6980 chunk 178 optimal weight: 8.9990 chunk 421 optimal weight: 8.9990 overall best weight: 3.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 63 ASN C 70 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN E 91 HIS E 208 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 GLN ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 HIS J 132 HIS J 147 GLN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN V 129 ASN W 44 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 91402 Z= 0.314 Angle : 0.663 14.773 137258 Z= 0.339 Chirality : 0.039 0.303 17616 Planarity : 0.006 0.099 7061 Dihedral : 15.053 179.371 36773 Min Nonbonded Distance : 1.153 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 1.19 % Allowed : 8.08 % Favored : 90.73 % Rotamer Outliers : 3.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.34 % 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: -2.24 (0.14), residues: 3032 helix: -0.29 (0.18), residues: 775 sheet: -1.60 (0.20), residues: 573 loop : -2.07 (0.13), residues: 1684 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 524 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 45 residues processed: 582 average time/residue: 0.9229 time to fit residues: 891.6143 Evaluate side-chains 528 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 483 time to evaluate : 3.639 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.6683 time to fit residues: 60.1431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 518 optimal weight: 2.9990 chunk 394 optimal weight: 0.9980 chunk 272 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 250 optimal weight: 7.9990 chunk 352 optimal weight: 6.9990 chunk 526 optimal weight: 20.0000 chunk 557 optimal weight: 1.9990 chunk 275 optimal weight: 10.0000 chunk 499 optimal weight: 0.6980 chunk 150 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 63 ASN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN E 208 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 GLN G 98 GLN J 58 ASN J 96 HIS J 117 GLN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 26 GLN V 93 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.086 91402 Z= 0.250 Angle : 0.607 15.195 137258 Z= 0.310 Chirality : 0.036 0.274 17616 Planarity : 0.005 0.078 7061 Dihedral : 14.870 179.895 36773 Min Nonbonded Distance : 1.073 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 1.19 % Allowed : 7.65 % Favored : 91.16 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.34 % 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: -2.00 (0.14), residues: 3032 helix: 0.05 (0.19), residues: 777 sheet: -1.40 (0.21), residues: 576 loop : -2.03 (0.14), residues: 1679 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 497 time to evaluate : 3.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 45 residues processed: 547 average time/residue: 0.8551 time to fit residues: 769.1238 Evaluate side-chains 520 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 475 time to evaluate : 3.670 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.5932 time to fit residues: 54.9868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 464 optimal weight: 10.0000 chunk 316 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 415 optimal weight: 0.5980 chunk 230 optimal weight: 20.0000 chunk 475 optimal weight: 3.9990 chunk 385 optimal weight: 20.0000 chunk 0 optimal weight: 4.9990 chunk 284 optimal weight: 9.9990 chunk 500 optimal weight: 0.9990 chunk 140 optimal weight: 8.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 63 ASN ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 208 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 GLN G 98 GLN ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 HIS J 117 GLN P 40 GLN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 93 GLN ** W 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 91402 Z= 0.218 Angle : 0.581 13.974 137258 Z= 0.296 Chirality : 0.035 0.268 17616 Planarity : 0.005 0.073 7061 Dihedral : 14.752 179.854 36773 Min Nonbonded Distance : 1.087 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 1.12 % Allowed : 7.68 % Favored : 91.19 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.34 % 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 (0.15), residues: 3032 helix: 0.18 (0.19), residues: 785 sheet: -1.39 (0.21), residues: 580 loop : -1.89 (0.14), residues: 1667 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 498 time to evaluate : 3.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 35 residues processed: 543 average time/residue: 0.8631 time to fit residues: 769.0664 Evaluate side-chains 507 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 472 time to evaluate : 3.634 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.6068 time to fit residues: 44.1054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 187 optimal weight: 7.9990 chunk 502 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 558 optimal weight: 0.7980 chunk 463 optimal weight: 4.9990 chunk 258 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 GLN E 76 GLN E 208 ASN F 34 GLN F 44 ASN G 98 GLN ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 HIS J 96 HIS J 117 GLN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN S 48 GLN V 26 GLN V 93 GLN V 169 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.088 91402 Z= 0.482 Angle : 0.790 14.722 137258 Z= 0.396 Chirality : 0.045 0.314 17616 Planarity : 0.007 0.083 7061 Dihedral : 15.221 178.271 36773 Min Nonbonded Distance : 1.027 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.87 % Favored : 89.87 % Rotamer Outliers : 3.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.10 (0.14), residues: 3032 helix: -0.18 (0.18), residues: 781 sheet: -1.41 (0.21), residues: 585 loop : -2.03 (0.14), residues: 1666 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 482 time to evaluate : 3.836 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 44 residues processed: 526 average time/residue: 0.8961 time to fit residues: 776.1859 Evaluate side-chains 516 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 472 time to evaluate : 3.655 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.6718 time to fit residues: 57.5045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 538 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 318 optimal weight: 0.9990 chunk 407 optimal weight: 0.9990 chunk 315 optimal weight: 0.8980 chunk 469 optimal weight: 8.9990 chunk 311 optimal weight: 3.9990 chunk 556 optimal weight: 1.9990 chunk 348 optimal weight: 1.9990 chunk 339 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 151 ASN E 208 ASN F 34 GLN F 44 ASN G 98 GLN G 103 ASN J 96 HIS J 117 GLN P 79 ASN Q 122 ASN ** V 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 93 GLN W 19 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.127 91402 Z= 0.185 Angle : 0.586 14.480 137258 Z= 0.299 Chirality : 0.034 0.259 17616 Planarity : 0.005 0.088 7061 Dihedral : 14.776 179.883 36773 Min Nonbonded Distance : 1.076 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 1.15 % Allowed : 7.88 % Favored : 90.96 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.34 % 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: -1.78 (0.15), residues: 3032 helix: 0.19 (0.19), residues: 785 sheet: -1.18 (0.22), residues: 552 loop : -1.90 (0.14), residues: 1695 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 483 time to evaluate : 3.703 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 500 average time/residue: 0.9301 time to fit residues: 761.9437 Evaluate side-chains 480 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 464 time to evaluate : 3.620 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.7670 time to fit residues: 24.8079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 344 optimal weight: 4.9990 chunk 222 optimal weight: 10.0000 chunk 332 optimal weight: 0.8980 chunk 167 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 353 optimal weight: 0.9980 chunk 378 optimal weight: 0.9980 chunk 274 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 437 optimal weight: 0.0870 overall best weight: 1.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 GLN E 151 ASN E 208 ASN F 44 ASN G 98 GLN G 103 ASN J 96 HIS J 117 GLN J 130 HIS ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN R 88 GLN ** V 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 93 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.176 91402 Z= 0.182 Angle : 0.572 14.461 137258 Z= 0.293 Chirality : 0.033 0.286 17616 Planarity : 0.005 0.096 7061 Dihedral : 14.746 179.693 36773 Min Nonbonded Distance : 1.096 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 1.12 % Allowed : 7.82 % Favored : 91.06 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.65 (0.15), residues: 3032 helix: 0.30 (0.19), residues: 784 sheet: -1.07 (0.22), residues: 536 loop : -1.83 (0.14), residues: 1712 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 466 time to evaluate : 4.182 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 479 average time/residue: 0.9033 time to fit residues: 707.3300 Evaluate side-chains 475 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 457 time to evaluate : 3.652 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.6092 time to fit residues: 24.5977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 505 optimal weight: 0.8980 chunk 532 optimal weight: 6.9990 chunk 486 optimal weight: 7.9990 chunk 518 optimal weight: 0.5980 chunk 311 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 406 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 468 optimal weight: 0.9980 chunk 490 optimal weight: 5.9990 chunk 516 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 47 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 GLN E 76 GLN E 151 ASN E 208 ASN F 44 ASN G 98 GLN G 103 ASN J 96 HIS J 117 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 93 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.420 91402 Z= 0.222 Angle : 0.569 27.304 137258 Z= 0.291 Chirality : 0.032 0.276 17616 Planarity : 0.005 0.098 7061 Dihedral : 14.567 179.596 36773 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 1.02 % Allowed : 7.72 % Favored : 91.26 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.34 % 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: -1.60 (0.15), residues: 3032 helix: 0.33 (0.19), residues: 798 sheet: -1.07 (0.22), residues: 551 loop : -1.79 (0.14), residues: 1683 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 471 time to evaluate : 3.687 Fit side-chains outliers start: 35 outliers final: 21 residues processed: 487 average time/residue: 0.9145 time to fit residues: 737.6062 Evaluate side-chains 478 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 457 time to evaluate : 3.686 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.6206 time to fit residues: 28.7724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 340 optimal weight: 0.9990 chunk 548 optimal weight: 0.0000 chunk 334 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 380 optimal weight: 5.9990 chunk 574 optimal weight: 9.9990 chunk 529 optimal weight: 0.4980 chunk 457 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 353 optimal weight: 0.7980 chunk 280 optimal weight: 10.0000 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 47 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN E 76 GLN ** E 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN G 98 GLN G 103 ASN J 96 HIS J 117 GLN ** V 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 93 GLN Y 35 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.608 91402 Z= 0.287 Angle : 0.609 73.790 137258 Z= 0.305 Chirality : 0.032 0.270 17616 Planarity : 0.005 0.117 7061 Dihedral : 14.567 179.594 36773 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 1.06 % Allowed : 7.72 % Favored : 91.23 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.34 % 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: -1.59 (0.15), residues: 3032 helix: 0.34 (0.19), residues: 798 sheet: -1.07 (0.22), residues: 551 loop : -1.79 (0.14), residues: 1683 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6064 Ramachandran restraints generated. 3032 Oldfield, 0 Emsley, 3032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 460 time to evaluate : 3.646 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 464 average time/residue: 0.8761 time to fit residues: 670.0273 Evaluate side-chains 466 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 458 time to evaluate : 3.600 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.8626 time to fit residues: 15.0975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 363 optimal weight: 6.9990 chunk 487 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 422 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 458 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 470 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 47 HIS ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN E 76 GLN F 44 ASN G 98 GLN G 103 ASN J 96 HIS J 117 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 93 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.141619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.113013 restraints weight = 109196.342| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 0.59 r_work: 0.3197 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 0.68 restraints_weight: 0.2500 r_work: 0.3176 rms_B_bonded: 0.83 restraints_weight: 0.1250 r_work: 0.3162 rms_B_bonded: 1.03 restraints_weight: 0.0625 r_work: 0.3146 rms_B_bonded: 1.30 restraints_weight: 0.0312 r_work: 0.3127 rms_B_bonded: 1.64 restraints_weight: 0.0156 r_work: 0.3102 rms_B_bonded: 2.09 restraints_weight: 0.0078 r_work: 0.3071 rms_B_bonded: 2.67 restraints_weight: 0.0039 r_work: 0.3030 rms_B_bonded: 3.46 restraints_weight: 0.0020 r_work: 0.2973 rms_B_bonded: 4.57 restraints_weight: 0.0010 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.605 91402 Z= 0.286 Angle : 0.609 73.898 137258 Z= 0.305 Chirality : 0.032 0.269 17616 Planarity : 0.005 0.116 7061 Dihedral : 14.567 179.594 36773 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 1.06 % Allowed : 7.72 % Favored : 91.23 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.34 % 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: -1.59 (0.15), residues: 3032 helix: 0.34 (0.19), residues: 798 sheet: -1.07 (0.22), residues: 551 loop : -1.79 (0.14), residues: 1683 =============================================================================== Job complete usr+sys time: 13355.91 seconds wall clock time: 239 minutes 9.45 seconds (14349.45 seconds total)