Starting phenix.real_space_refine on Mon Mar 18 06:42:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xym_6789/03_2024/5xym_6789_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xym_6789/03_2024/5xym_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_6789/03_2024/5xym_6789.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xym_6789/03_2024/5xym_6789.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xym_6789/03_2024/5xym_6789_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xym_6789/03_2024/5xym_6789_neut.pdb" } resolution = 3.08 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= 0.001 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 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. 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-5265/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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 51} 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: {'rna2p_pur': 281, 'rna2p_pyr': 130, 'rna3p_pur': 1261, 'rna3p_pyr': 993} Link IDs: {'rna2p': 411, 'rna3p': 2253} 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: {'rna2p_pur': 6, 'rna2p_pyr': 10, 'rna3p_pur': 56, 'rna3p_pyr': 44} Link IDs: {'rna2p': 16, 'rna3p': 99} Chain: "C" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2097 Classifications: {'peptide': 273} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 252} Chain: "D" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1578 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 203} Chain: "E" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1560 Classifications: {'peptide': 208} Link IDs: {'CIS': 2, 'PTRANS': 11, '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: {'CIS': 1, 'PTRANS': 10, '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: {'CIS': 2, 'PTRANS': 6, 'TRANS': 135} Chain: "M" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1079 Classifications: {'peptide': 134} Link IDs: {'CIS': 1, 'PTRANS': 9, '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: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 120} 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: {'CIS': 1, 'PTRANS': 4, '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: {'PCIS': 1, 'TRANS': 59} 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: 33.72, per 1000 atoms: 0.40 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: 34.36 Conformation dependent library (CDL) restraints added in 3.7 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: 29.01 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: 153.31 Time building geometry restraints manager: 37.21 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: 51891 35.96 - 71.92: 5994 71.92 - 107.88: 808 107.88 - 143.84: 10 143.84 - 179.79: 27 Dihedral angle restraints: 58730 sinusoidal: 49935 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 58727 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 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: 1.370 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: 0.100 Extract box with map and model: 8.010 Check model and map are aligned: 0.900 Set scattering table: 0.610 Process input model: 311.740 Find NCS groups from input model: 1.460 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: 0.020 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 327.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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= 0.677 Chirality : 0.096 0.654 17616 Planarity : 0.004 0.056 7061 Dihedral : 23.421 179.795 53059 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 % Allowed : 6.26 % Favored : 91.18 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 29 HIS 0.006 0.001 HIS Z 52 PHE 0.012 0.001 PHE P 6 TYR 0.015 0.001 TYR F 15 ARG 0.006 0.000 ARG Q 50 *********************** 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 : 3.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 38 LYS cc_start: 0.7926 (ptpt) cc_final: 0.7256 (ptpp) REVERT: 1 20 TYR cc_start: 0.4727 (OUTLIER) cc_final: 0.4220 (m-80) REVERT: 2 25 MET cc_start: 0.7712 (mmm) cc_final: 0.7327 (mmm) REVERT: 3 8 SER cc_start: 0.8734 (m) cc_final: 0.8428 (t) REVERT: 3 15 ARG cc_start: 0.8496 (ttp-170) cc_final: 0.7963 (ttp80) REVERT: 4 22 ARG cc_start: 0.6400 (ttm170) cc_final: 0.6102 (ttp-170) REVERT: 4 24 MET cc_start: 0.7373 (mtt) cc_final: 0.7035 (mtt) REVERT: C 5 LYS cc_start: 0.7779 (mttt) cc_final: 0.7485 (ttmm) REVERT: C 23 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6554 (mt-10) REVERT: C 35 ARG cc_start: 0.7435 (mmt-90) cc_final: 0.7141 (mmp80) REVERT: C 83 GLU cc_start: 0.8279 (pt0) cc_final: 0.8077 (pt0) REVERT: C 112 LYS cc_start: 0.8266 (mptt) cc_final: 0.8061 (mppt) REVERT: C 119 SER cc_start: 0.8037 (m) cc_final: 0.7772 (t) REVERT: C 134 ARG cc_start: 0.8050 (ttm170) cc_final: 0.7820 (ttp80) REVERT: C 157 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7891 (mtm180) REVERT: C 169 GLU cc_start: 0.7782 (tt0) cc_final: 0.7532 (pm20) REVERT: C 190 ARG cc_start: 0.7578 (ttm-80) cc_final: 0.7339 (mmm160) REVERT: C 195 GLU cc_start: 0.7073 (pt0) cc_final: 0.6622 (tt0) REVERT: C 202 SER cc_start: 0.7872 (t) cc_final: 0.7672 (m) REVERT: C 217 LYS cc_start: 0.7881 (ttmm) cc_final: 0.7096 (tttm) REVERT: C 226 MET cc_start: 0.8462 (mtt) cc_final: 0.8186 (mtt) REVERT: C 259 LYS cc_start: 0.7809 (ttmm) cc_final: 0.7594 (mmmm) REVERT: D 16 VAL cc_start: 0.8686 (t) cc_final: 0.8406 (m) REVERT: D 20 ASN cc_start: 0.7877 (t0) cc_final: 0.7188 (t0) REVERT: D 22 LYS cc_start: 0.7790 (mtmm) cc_final: 0.7393 (mmtt) REVERT: D 166 MET cc_start: 0.8490 (mtt) cc_final: 0.8154 (mtp) REVERT: D 174 ARG cc_start: 0.7509 (ttt-90) cc_final: 0.7305 (ttt-90) REVERT: D 181 LYS cc_start: 0.7508 (tttm) cc_final: 0.6800 (tttt) REVERT: D 214 ARG cc_start: 0.6301 (ptt-90) cc_final: 0.5701 (mtm180) REVERT: E 67 ARG cc_start: 0.7491 (ptt180) cc_final: 0.7126 (ptt-90) REVERT: E 69 LYS cc_start: 0.7527 (ttpt) cc_final: 0.7319 (ttmm) REVERT: E 121 ASN cc_start: 0.7427 (m-40) cc_final: 0.7162 (m110) REVERT: E 151 ASN cc_start: 0.8534 (m-40) cc_final: 0.8202 (m110) REVERT: E 153 LYS cc_start: 0.7400 (mttp) cc_final: 0.7169 (mttt) REVERT: E 162 ASP cc_start: 0.7956 (t70) cc_final: 0.7587 (t0) REVERT: F 33 MET cc_start: 0.7417 (ptp) cc_final: 0.6984 (pmm) REVERT: F 73 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.5143 (tm-30) REVERT: F 90 MET cc_start: 0.7544 (mmm) cc_final: 0.7212 (mtp) REVERT: F 155 ARG cc_start: 0.6027 (mmm160) cc_final: 0.5790 (mmm160) REVERT: F 178 ARG cc_start: 0.8134 (ptp90) cc_final: 0.7354 (tpp80) REVERT: G 80 VAL cc_start: 0.6210 (t) cc_final: 0.5793 (t) REVERT: G 98 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.7203 (tm-30) REVERT: J 4 TYR cc_start: 0.8734 (t80) cc_final: 0.8087 (t80) REVERT: J 7 LYS cc_start: 0.7503 (mttp) cc_final: 0.7233 (mttt) REVERT: J 16 TYR cc_start: 0.8207 (m-80) cc_final: 0.7854 (m-80) REVERT: J 57 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7787 (pt) REVERT: J 120 LYS cc_start: 0.8589 (mttm) cc_final: 0.8265 (mttp) REVERT: K 7 ARG cc_start: 0.7363 (mtt-85) cc_final: 0.6959 (mmt180) REVERT: K 35 ILE cc_start: 0.7384 (mt) cc_final: 0.7118 (mt) REVERT: K 112 MET cc_start: 0.8193 (mmm) cc_final: 0.7718 (mmm) REVERT: L 128 LYS cc_start: 0.8070 (mmmt) cc_final: 0.7830 (mmmm) REVERT: M 1 MET cc_start: 0.6608 (mmm) cc_final: 0.6214 (mmt) REVERT: M 2 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6418 (pp) REVERT: M 45 ARG cc_start: 0.7804 (mmt90) cc_final: 0.7480 (mtp85) REVERT: M 56 ARG cc_start: 0.7399 (mmt-90) cc_final: 0.6863 (mmm-85) REVERT: M 66 ILE cc_start: 0.8512 (mt) cc_final: 0.8286 (mt) REVERT: M 76 LYS cc_start: 0.7853 (ttpp) cc_final: 0.7505 (tttp) REVERT: M 98 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7839 (mtmm) REVERT: M 112 LYS cc_start: 0.7730 (mptt) cc_final: 0.7317 (ttpp) REVERT: M 130 ARG cc_start: 0.8275 (ttm170) cc_final: 0.7991 (ttm170) REVERT: N 26 THR cc_start: 0.8931 (t) cc_final: 0.8464 (p) REVERT: N 101 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7718 (pt0) REVERT: O 108 THR cc_start: 0.8008 (t) cc_final: 0.7383 (p) REVERT: Q 75 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8320 (t) REVERT: R 86 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8321 (tttm) REVERT: R 87 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7605 (mtm180) REVERT: S 15 ARG cc_start: 0.7903 (ptm160) cc_final: 0.7697 (ptm-80) REVERT: S 18 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.8171 (mmm160) REVERT: S 66 GLN cc_start: 0.7978 (tp40) cc_final: 0.7632 (tp40) REVERT: S 106 ARG cc_start: 0.8821 (mtt-85) cc_final: 0.8564 (mtt-85) REVERT: T 48 LYS cc_start: 0.8444 (tptm) cc_final: 0.8090 (tppp) REVERT: T 68 ARG cc_start: 0.7410 (ttm170) cc_final: 0.7148 (ttm110) REVERT: T 75 LYS cc_start: 0.7520 (pttp) cc_final: 0.6916 (ptmm) REVERT: U 20 LYS cc_start: 0.8166 (ttmt) cc_final: 0.7242 (tptp) REVERT: U 39 ASN cc_start: 0.7746 (t0) cc_final: 0.7201 (t0) REVERT: U 68 VAL cc_start: 0.7921 (t) cc_final: 0.7609 (m) REVERT: V 19 THR cc_start: 0.8373 (p) cc_final: 0.8014 (m) REVERT: V 24 SER cc_start: 0.8436 (t) cc_final: 0.8088 (m) REVERT: V 26 GLN cc_start: 0.7409 (tp-100) cc_final: 0.6965 (tp-100) REVERT: V 48 GLU cc_start: 0.7972 (pt0) cc_final: 0.7746 (pt0) REVERT: V 76 GLN cc_start: 0.7677 (tp-100) cc_final: 0.7421 (mm-40) REVERT: V 93 GLN cc_start: 0.8010 (mt0) cc_final: 0.7779 (mt0) REVERT: V 122 THR cc_start: 0.7680 (p) cc_final: 0.7400 (t) REVERT: W 35 GLU cc_start: 0.7729 (tt0) cc_final: 0.7465 (tt0) REVERT: Y 48 ARG cc_start: 0.7907 (mtp-110) cc_final: 0.7681 (mtp-110) REVERT: Z 46 LEU cc_start: 0.8261 (tp) cc_final: 0.8059 (tp) REVERT: Z 55 GLU cc_start: 0.7255 (tt0) cc_final: 0.6865 (tt0) outliers start: 65 outliers final: 26 residues processed: 771 average time/residue: 0.9554 time to fit residues: 1168.8057 Evaluate side-chains 559 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 525 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 20 TYR Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 8 PRO Chi-restraints excluded: chain C residue 76 ASN Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain G residue 98 GLN Chi-restraints excluded: chain G residue 166 GLU Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 101 GLU Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 95 VAL Chi-restraints excluded: chain Y residue 43 ASN Chi-restraints excluded: chain Y residue 44 ASN 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: 0.7980 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: 0.0030 chunk 175 optimal weight: 8.9990 chunk 274 optimal weight: 9.9990 chunk 336 optimal weight: 5.9990 chunk 523 optimal weight: 5.9990 overall best weight: 3.3596 ------------------------------------------------------------------------------- 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 ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 143 HIS C 164 GLN D 34 ASN D 139 HIS E 121 ASN E 182 GLN E 190 ASN E 208 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 GLN ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 GLN J 117 GLN J 132 HIS J 144 GLN J 147 GLN M 35 GLN M 57 HIS 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 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: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 91402 Z= 0.303 Angle : 0.689 14.315 137258 Z= 0.354 Chirality : 0.041 0.392 17616 Planarity : 0.006 0.068 7061 Dihedral : 23.850 178.643 47103 Min Nonbonded Distance : 1.193 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 1.25 % Allowed : 7.09 % Favored : 91.66 % Rotamer: Outliers : 4.65 % Allowed : 11.19 % Favored : 84.17 % 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: -2.62 (0.14), residues: 3032 helix: -0.91 (0.17), residues: 778 sheet: -1.78 (0.19), residues: 620 loop : -2.16 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 214 HIS 0.007 0.001 HIS Q 41 PHE 0.025 0.002 PHE P 6 TYR 0.019 0.002 TYR Q 45 ARG 0.008 0.001 ARG E 112 *********************** 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 663 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 545 time to evaluate : 3.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 38 LYS cc_start: 0.7606 (ptpt) cc_final: 0.7277 (ptpp) REVERT: 2 17 ARG cc_start: 0.7059 (mtp180) cc_final: 0.6669 (mtp-110) REVERT: 2 25 MET cc_start: 0.7558 (mmm) cc_final: 0.6759 (mmm) REVERT: 4 18 ARG cc_start: 0.7209 (ptm-80) cc_final: 0.6968 (ptm160) REVERT: C 5 LYS cc_start: 0.7722 (mttt) cc_final: 0.7351 (ttmm) REVERT: C 23 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6635 (mt-10) REVERT: C 35 ARG cc_start: 0.7193 (mmt-90) cc_final: 0.6753 (mmt180) REVERT: C 95 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7340 (pp) REVERT: C 101 GLU cc_start: 0.6673 (tt0) cc_final: 0.5949 (tp30) REVERT: C 126 LYS cc_start: 0.7173 (ttmm) cc_final: 0.6200 (ptpt) REVERT: C 134 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7864 (ttp80) REVERT: C 135 ASN cc_start: 0.7753 (t0) cc_final: 0.7474 (m110) REVERT: C 186 ASP cc_start: 0.7637 (t0) cc_final: 0.7298 (t0) REVERT: C 202 SER cc_start: 0.8105 (t) cc_final: 0.7719 (m) REVERT: C 217 LYS cc_start: 0.7752 (ttmm) cc_final: 0.6973 (tttm) REVERT: C 218 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7603 (ptm-80) REVERT: C 257 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.8208 (p) REVERT: C 266 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7890 (mtmm) REVERT: D 20 ASN cc_start: 0.8018 (t0) cc_final: 0.7630 (t0) REVERT: D 22 LYS cc_start: 0.7616 (mtmm) cc_final: 0.7279 (mptt) REVERT: D 166 MET cc_start: 0.8639 (mtt) cc_final: 0.8250 (mtp) REVERT: D 174 ARG cc_start: 0.7261 (ttt-90) cc_final: 0.6876 (ttt-90) REVERT: D 181 LYS cc_start: 0.7378 (tttm) cc_final: 0.6780 (ttmt) REVERT: D 214 ARG cc_start: 0.6567 (ptt-90) cc_final: 0.5788 (mtm180) REVERT: E 13 LYS cc_start: 0.7553 (ptpt) cc_final: 0.7341 (ptpt) REVERT: E 24 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7435 (tp) REVERT: E 67 ARG cc_start: 0.7539 (ptt180) cc_final: 0.7287 (ptt90) REVERT: E 75 ARG cc_start: 0.7515 (mtm180) cc_final: 0.7109 (mtm180) REVERT: E 117 ASP cc_start: 0.7900 (t0) cc_final: 0.7603 (t0) REVERT: E 121 ASN cc_start: 0.7202 (m110) cc_final: 0.6928 (m-40) REVERT: E 151 ASN cc_start: 0.8161 (m-40) cc_final: 0.7683 (m110) REVERT: E 153 LYS cc_start: 0.7661 (mttp) cc_final: 0.7300 (mttt) REVERT: F 31 ASN cc_start: 0.6517 (m-40) cc_final: 0.6214 (t0) REVERT: F 33 MET cc_start: 0.7383 (ptp) cc_final: 0.7052 (ppp) REVERT: F 49 ASP cc_start: 0.7237 (t0) cc_final: 0.6078 (m-30) REVERT: F 92 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7554 (mm) REVERT: F 178 ARG cc_start: 0.8267 (ptp90) cc_final: 0.7391 (tpp80) REVERT: G 24 LEU cc_start: 0.6328 (mt) cc_final: 0.6003 (tp) REVERT: G 69 SER cc_start: 0.8707 (m) cc_final: 0.8501 (m) REVERT: G 73 ILE cc_start: 0.6846 (mm) cc_final: 0.6643 (tp) REVERT: G 96 ARG cc_start: 0.7528 (mtm110) cc_final: 0.7277 (mtm110) REVERT: J 4 TYR cc_start: 0.8652 (t80) cc_final: 0.8012 (t80) REVERT: J 57 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7677 (pt) REVERT: J 71 LYS cc_start: 0.7741 (mttt) cc_final: 0.7323 (mmtm) REVERT: K 78 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7561 (tttp) REVERT: L 35 ARG cc_start: 0.8556 (mtt-85) cc_final: 0.8342 (mtt180) REVERT: L 50 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7213 (p90) REVERT: L 128 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7894 (mmmm) REVERT: M 45 ARG cc_start: 0.7909 (mmt90) cc_final: 0.7421 (mtt-85) REVERT: M 56 ARG cc_start: 0.7492 (mmt-90) cc_final: 0.7114 (mmm-85) REVERT: M 60 ARG cc_start: 0.8249 (ptt90) cc_final: 0.7057 (mmm160) REVERT: M 112 LYS cc_start: 0.7635 (mptt) cc_final: 0.7267 (ttpp) REVERT: N 13 SER cc_start: 0.8631 (t) cc_final: 0.8237 (m) REVERT: P 55 SER cc_start: 0.8266 (m) cc_final: 0.8017 (p) REVERT: P 79 ASN cc_start: 0.7834 (t0) cc_final: 0.7086 (t0) REVERT: P 88 ARG cc_start: 0.7044 (ttm110) cc_final: 0.6785 (mtm180) REVERT: P 111 GLU cc_start: 0.7662 (pt0) cc_final: 0.7367 (tt0) REVERT: Q 22 LYS cc_start: 0.7820 (mmmt) cc_final: 0.7519 (mtmt) REVERT: Q 30 ARG cc_start: 0.8280 (mtt90) cc_final: 0.8065 (mtm-85) REVERT: Q 47 TYR cc_start: 0.8733 (t80) cc_final: 0.8405 (t80) REVERT: Q 59 LYS cc_start: 0.7609 (mtpp) cc_final: 0.7397 (ttmt) REVERT: Q 84 LYS cc_start: 0.7400 (pttp) cc_final: 0.7163 (ttmt) REVERT: R 54 ASP cc_start: 0.7834 (m-30) cc_final: 0.7406 (m-30) REVERT: R 80 ASN cc_start: 0.8048 (m-40) cc_final: 0.7036 (p0) REVERT: R 87 ARG cc_start: 0.8405 (mtt180) cc_final: 0.8133 (mtm180) REVERT: R 88 GLN cc_start: 0.8365 (mt0) cc_final: 0.7435 (mt0) REVERT: R 93 GLN cc_start: 0.8357 (mt0) cc_final: 0.8043 (mt0) REVERT: S 15 ARG cc_start: 0.7850 (ptm160) cc_final: 0.7438 (mtm180) REVERT: S 18 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7944 (mmm160) REVERT: S 66 GLN cc_start: 0.8081 (tp40) cc_final: 0.7278 (tp40) REVERT: T 48 LYS cc_start: 0.8387 (tptm) cc_final: 0.7962 (tppt) REVERT: T 68 ARG cc_start: 0.7445 (ttm170) cc_final: 0.7131 (ttm110) REVERT: T 81 ARG cc_start: 0.7431 (mtt90) cc_final: 0.7108 (mtt90) REVERT: U 20 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7321 (tptp) REVERT: V 30 ASP cc_start: 0.6544 (m-30) cc_final: 0.6269 (m-30) REVERT: V 45 GLN cc_start: 0.7562 (tt0) cc_final: 0.6886 (mt0) REVERT: V 76 GLN cc_start: 0.7737 (tp-100) cc_final: 0.7157 (mm-40) REVERT: V 90 ARG cc_start: 0.8057 (mtm110) cc_final: 0.7071 (mmt-90) REVERT: V 109 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7534 (mt-10) REVERT: V 131 ILE cc_start: 0.6321 (tt) cc_final: 0.5983 (tp) REVERT: W 35 GLU cc_start: 0.7903 (tt0) cc_final: 0.7484 (tt0) REVERT: X 46 LYS cc_start: 0.7093 (mtpt) cc_final: 0.6713 (mtpt) REVERT: X 48 ARG cc_start: 0.8627 (tpp80) cc_final: 0.8427 (tpp-160) REVERT: Y 36 MET cc_start: 0.7860 (mmm) cc_final: 0.7498 (mmm) REVERT: Z 23 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7258 (mm) outliers start: 118 outliers final: 69 residues processed: 627 average time/residue: 0.9146 time to fit residues: 940.9015 Evaluate side-chains 567 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 490 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 54 LEU Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 2 residue 23 LEU Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 218 ARG Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 57 ILE Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 104 ARG Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 35 GLN Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 101 GLU Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 7 ILE Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 71 ILE Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain X residue 52 CYS Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 59 VAL 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: 4.9990 chunk 356 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 524 optimal weight: 0.6980 chunk 567 optimal weight: 3.9990 chunk 467 optimal weight: 7.9990 chunk 520 optimal weight: 0.9980 chunk 178 optimal weight: 8.9990 chunk 421 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 HIS ** 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 117 GLN M 35 GLN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN V 93 GLN V 129 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 91402 Z= 0.221 Angle : 0.591 14.551 137258 Z= 0.303 Chirality : 0.035 0.266 17616 Planarity : 0.005 0.070 7061 Dihedral : 23.704 179.720 47073 Min Nonbonded Distance : 1.122 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 1.22 % Allowed : 7.68 % Favored : 91.09 % Rotamer: Outliers : 4.45 % Allowed : 15.20 % Favored : 80.35 % 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: -2.14 (0.14), residues: 3032 helix: -0.17 (0.18), residues: 778 sheet: -1.57 (0.20), residues: 593 loop : -2.02 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 250 HIS 0.009 0.001 HIS D 139 PHE 0.024 0.002 PHE P 6 TYR 0.013 0.001 TYR S 82 ARG 0.008 0.001 ARG M 130 *********************** 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 634 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 521 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7029 (mpp80) REVERT: 0 38 LYS cc_start: 0.7625 (ptpt) cc_final: 0.7360 (ptpp) REVERT: 2 17 ARG cc_start: 0.7231 (mtp180) cc_final: 0.6739 (mtp-110) REVERT: 2 25 MET cc_start: 0.7504 (mmm) cc_final: 0.6694 (mmm) REVERT: 3 48 THR cc_start: 0.7603 (OUTLIER) cc_final: 0.7097 (p) REVERT: 4 18 ARG cc_start: 0.7353 (ptm-80) cc_final: 0.6983 (ptm160) REVERT: C 5 LYS cc_start: 0.7748 (mttt) cc_final: 0.7334 (ttmm) REVERT: C 23 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6716 (mt-10) REVERT: C 35 ARG cc_start: 0.7348 (mmt-90) cc_final: 0.7039 (mmt180) REVERT: C 95 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7335 (pp) REVERT: C 101 GLU cc_start: 0.6980 (tt0) cc_final: 0.6287 (tp30) REVERT: C 126 LYS cc_start: 0.7098 (ttmm) cc_final: 0.6228 (ptpt) REVERT: C 140 THR cc_start: 0.8263 (m) cc_final: 0.7970 (m) REVERT: C 200 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6499 (pm20) REVERT: C 202 SER cc_start: 0.8391 (t) cc_final: 0.8137 (m) REVERT: C 217 LYS cc_start: 0.7737 (ttmm) cc_final: 0.7016 (ttpp) REVERT: C 257 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.7974 (p) REVERT: C 262 LYS cc_start: 0.7520 (ttmm) cc_final: 0.7202 (ttmt) REVERT: C 266 LYS cc_start: 0.8184 (mtpp) cc_final: 0.7911 (mtmm) REVERT: D 20 ASN cc_start: 0.8015 (t0) cc_final: 0.7740 (t0) REVERT: D 22 LYS cc_start: 0.7300 (mtmm) cc_final: 0.6836 (mmtt) REVERT: D 83 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7945 (mt-10) REVERT: D 170 MET cc_start: 0.8378 (ttt) cc_final: 0.8080 (ttt) REVERT: D 174 ARG cc_start: 0.7268 (ttt-90) cc_final: 0.6875 (ttt-90) REVERT: D 181 LYS cc_start: 0.7602 (tttm) cc_final: 0.7029 (ttmt) REVERT: D 214 ARG cc_start: 0.6634 (ptt-90) cc_final: 0.6152 (mtp180) REVERT: E 3 LEU cc_start: 0.7121 (mt) cc_final: 0.6475 (tp) REVERT: E 24 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7222 (tp) REVERT: E 30 ASN cc_start: 0.7682 (p0) cc_final: 0.7413 (p0) REVERT: E 75 ARG cc_start: 0.7553 (mtm180) cc_final: 0.7225 (mtm180) REVERT: E 117 ASP cc_start: 0.8174 (t0) cc_final: 0.7491 (t0) REVERT: E 121 ASN cc_start: 0.7186 (m110) cc_final: 0.6896 (m110) REVERT: E 149 THR cc_start: 0.5933 (OUTLIER) cc_final: 0.5510 (t) REVERT: E 150 GLU cc_start: 0.8058 (tt0) cc_final: 0.7580 (mp0) REVERT: E 151 ASN cc_start: 0.8087 (m-40) cc_final: 0.7581 (m110) REVERT: E 153 LYS cc_start: 0.7636 (mttp) cc_final: 0.7213 (mttt) REVERT: F 31 ASN cc_start: 0.5912 (m-40) cc_final: 0.5601 (t0) REVERT: F 49 ASP cc_start: 0.7235 (t0) cc_final: 0.6475 (m-30) REVERT: F 103 MET cc_start: 0.7442 (ttp) cc_final: 0.6993 (ptt) REVERT: F 144 MET cc_start: 0.7440 (mtp) cc_final: 0.7240 (ptp) REVERT: F 146 HIS cc_start: 0.6072 (m-70) cc_final: 0.5795 (m-70) REVERT: F 178 ARG cc_start: 0.8052 (ptp90) cc_final: 0.7523 (tpp80) REVERT: G 24 LEU cc_start: 0.6561 (mt) cc_final: 0.6127 (tt) REVERT: G 103 ASN cc_start: 0.6930 (m110) cc_final: 0.6680 (m-40) REVERT: G 153 ARG cc_start: 0.8666 (tpt170) cc_final: 0.8339 (tpt170) REVERT: J 4 TYR cc_start: 0.8828 (t80) cc_final: 0.8240 (t80) REVERT: J 71 LYS cc_start: 0.7916 (mttt) cc_final: 0.7477 (mmtm) REVERT: K 78 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7552 (tttt) REVERT: L 50 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7349 (p90) REVERT: L 72 ARG cc_start: 0.8099 (ttt90) cc_final: 0.7838 (ttt90) REVERT: L 85 LYS cc_start: 0.7642 (mmtp) cc_final: 0.7414 (mmmm) REVERT: L 128 LYS cc_start: 0.7917 (mmmt) cc_final: 0.7556 (mmmm) REVERT: M 6 LYS cc_start: 0.8328 (ttpp) cc_final: 0.7856 (ttpt) REVERT: M 56 ARG cc_start: 0.7492 (mmt-90) cc_final: 0.7250 (mmm-85) REVERT: M 58 ILE cc_start: 0.7651 (tt) cc_final: 0.7363 (tt) REVERT: M 60 ARG cc_start: 0.8289 (ptt90) cc_final: 0.7086 (mmm160) REVERT: M 66 ILE cc_start: 0.8691 (mt) cc_final: 0.8418 (mt) REVERT: M 112 LYS cc_start: 0.7649 (mptt) cc_final: 0.7264 (ttpp) REVERT: N 6 LYS cc_start: 0.8337 (mtpp) cc_final: 0.7968 (ttpp) REVERT: N 13 SER cc_start: 0.8346 (t) cc_final: 0.8016 (m) REVERT: O 32 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7550 (p) REVERT: P 55 SER cc_start: 0.8352 (m) cc_final: 0.8097 (p) REVERT: P 79 ASN cc_start: 0.7707 (t0) cc_final: 0.6989 (t0) REVERT: P 88 ARG cc_start: 0.7079 (ttm110) cc_final: 0.6831 (mtm180) REVERT: P 111 GLU cc_start: 0.7644 (pt0) cc_final: 0.7359 (tt0) REVERT: Q 6 ARG cc_start: 0.6363 (OUTLIER) cc_final: 0.5215 (ptm160) REVERT: Q 22 LYS cc_start: 0.7802 (mmmt) cc_final: 0.7534 (mtmt) REVERT: Q 59 LYS cc_start: 0.7415 (mtpp) cc_final: 0.7186 (ttmt) REVERT: R 26 LYS cc_start: 0.7629 (tttt) cc_final: 0.7384 (ttpt) REVERT: R 54 ASP cc_start: 0.7855 (m-30) cc_final: 0.7451 (m-30) REVERT: R 80 ASN cc_start: 0.7743 (m-40) cc_final: 0.7058 (p0) REVERT: R 88 GLN cc_start: 0.8229 (mt0) cc_final: 0.7392 (mt0) REVERT: R 93 GLN cc_start: 0.8180 (mt0) cc_final: 0.7964 (mt0) REVERT: S 15 ARG cc_start: 0.7750 (ptm160) cc_final: 0.7435 (mtm180) REVERT: S 18 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7732 (mmm160) REVERT: T 68 ARG cc_start: 0.7441 (ttm170) cc_final: 0.7116 (ttm110) REVERT: U 20 LYS cc_start: 0.8093 (ttmt) cc_final: 0.7277 (tttp) REVERT: U 103 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7709 (ttpp) REVERT: V 45 GLN cc_start: 0.7723 (tt0) cc_final: 0.6985 (mt0) REVERT: V 76 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7311 (mm-40) REVERT: V 90 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7147 (mmt-90) REVERT: W 36 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7672 (tt) REVERT: W 50 ASN cc_start: 0.8189 (m-40) cc_final: 0.7958 (m-40) REVERT: X 50 ASN cc_start: 0.8158 (m-40) cc_final: 0.7783 (m-40) REVERT: Y 46 ARG cc_start: 0.7421 (tpt90) cc_final: 0.7089 (mtp85) REVERT: Z 3 GLU cc_start: 0.7617 (mp0) cc_final: 0.7202 (pt0) REVERT: Z 23 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7570 (mt) outliers start: 113 outliers final: 75 residues processed: 594 average time/residue: 0.8948 time to fit residues: 874.4198 Evaluate side-chains 585 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 498 time to evaluate : 3.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 37 ARG Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 2 residue 23 LEU Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain N residue 101 GLU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 56 ASN Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 7 ILE Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 71 ILE Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain X residue 17 SER Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 518 optimal weight: 5.9990 chunk 394 optimal weight: 8.9990 chunk 272 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 250 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 chunk 526 optimal weight: 0.0570 chunk 557 optimal weight: 7.9990 chunk 275 optimal weight: 9.9990 chunk 499 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 overall best weight: 6.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 63 ASN ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 ASN ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 HIS H 28 ASN J 96 HIS J 117 GLN N 102 ASN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN S 48 GLN V 26 GLN V 93 GLN W 44 HIS X 45 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 91402 Z= 0.505 Angle : 0.812 14.279 137258 Z= 0.406 Chirality : 0.047 0.323 17616 Planarity : 0.007 0.093 7061 Dihedral : 23.896 178.242 47067 Min Nonbonded Distance : 1.006 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 1.19 % Allowed : 8.28 % Favored : 90.53 % Rotamer: Outliers : 5.91 % Allowed : 16.19 % Favored : 77.90 % 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: -2.34 (0.14), residues: 3032 helix: -0.42 (0.18), residues: 786 sheet: -1.65 (0.20), residues: 585 loop : -2.12 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 214 HIS 0.017 0.002 HIS D 139 PHE 0.021 0.002 PHE P 6 TYR 0.018 0.002 TYR 1 20 ARG 0.010 0.001 ARG 2 22 *********************** 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 662 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 512 time to evaluate : 4.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 17 ARG cc_start: 0.7459 (mtp180) cc_final: 0.6795 (mtp-110) REVERT: 2 25 MET cc_start: 0.7361 (mmm) cc_final: 0.6823 (mmm) REVERT: 4 8 LYS cc_start: 0.8247 (mttm) cc_final: 0.7908 (mttm) REVERT: 4 18 ARG cc_start: 0.7526 (ptm-80) cc_final: 0.7245 (ptm160) REVERT: C 6 TYR cc_start: 0.8117 (m-80) cc_final: 0.7559 (m-80) REVERT: C 23 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6839 (mt-10) REVERT: C 35 ARG cc_start: 0.7410 (mmt-90) cc_final: 0.7007 (mmt180) REVERT: C 85 ASP cc_start: 0.7904 (t0) cc_final: 0.7610 (t0) REVERT: C 95 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7349 (pp) REVERT: C 101 GLU cc_start: 0.6956 (tt0) cc_final: 0.6411 (tp30) REVERT: C 113 GLN cc_start: 0.8453 (pt0) cc_final: 0.8214 (pt0) REVERT: C 126 LYS cc_start: 0.7456 (ttmm) cc_final: 0.6420 (ptpt) REVERT: C 135 ASN cc_start: 0.7928 (t0) cc_final: 0.7624 (m110) REVERT: C 177 MET cc_start: 0.8350 (mmt) cc_final: 0.8062 (mmt) REVERT: C 200 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6685 (pm20) REVERT: C 202 SER cc_start: 0.8599 (t) cc_final: 0.8345 (m) REVERT: C 217 LYS cc_start: 0.7956 (ttmm) cc_final: 0.7206 (tttm) REVERT: C 252 LYS cc_start: 0.8678 (mttt) cc_final: 0.8438 (mttm) REVERT: C 262 LYS cc_start: 0.7403 (ttmm) cc_final: 0.6901 (ttmt) REVERT: C 266 LYS cc_start: 0.8236 (mtpp) cc_final: 0.7949 (mtmm) REVERT: D 83 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7631 (mt-10) REVERT: D 104 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7260 (tm-30) REVERT: D 127 MET cc_start: 0.7988 (mmm) cc_final: 0.7553 (mmm) REVERT: D 174 ARG cc_start: 0.7327 (ttt-90) cc_final: 0.7015 (ttt-90) REVERT: D 181 LYS cc_start: 0.7511 (tttm) cc_final: 0.6948 (ttmt) REVERT: D 214 ARG cc_start: 0.6603 (ptt-90) cc_final: 0.6268 (mtp180) REVERT: E 24 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7478 (tp) REVERT: E 46 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6427 (ttt-90) REVERT: E 117 ASP cc_start: 0.8105 (t0) cc_final: 0.7390 (t0) REVERT: E 121 ASN cc_start: 0.7203 (m110) cc_final: 0.6959 (m110) REVERT: E 150 GLU cc_start: 0.8046 (tt0) cc_final: 0.7605 (mp0) REVERT: F 90 MET cc_start: 0.7158 (mtp) cc_final: 0.6365 (mtp) REVERT: F 178 ARG cc_start: 0.8121 (ptp90) cc_final: 0.7355 (tpp80) REVERT: G 24 LEU cc_start: 0.6472 (mt) cc_final: 0.6121 (tt) REVERT: G 153 ARG cc_start: 0.8691 (tpt170) cc_final: 0.8386 (tpt170) REVERT: J 4 TYR cc_start: 0.8667 (t80) cc_final: 0.8148 (t80) REVERT: J 71 LYS cc_start: 0.8000 (mttt) cc_final: 0.7411 (mttm) REVERT: K 9 LYS cc_start: 0.8879 (pttp) cc_final: 0.8623 (pttp) REVERT: K 54 ARG cc_start: 0.7370 (ttt-90) cc_final: 0.7022 (ttp-170) REVERT: K 78 LYS cc_start: 0.8213 (ttpt) cc_final: 0.7552 (tttt) REVERT: L 35 ARG cc_start: 0.8802 (mtp85) cc_final: 0.8383 (mtt-85) REVERT: L 50 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.6938 (p90) REVERT: L 128 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7657 (mmmm) REVERT: M 6 LYS cc_start: 0.8214 (ttpp) cc_final: 0.7757 (ttpt) REVERT: M 56 ARG cc_start: 0.7525 (mmt-90) cc_final: 0.7268 (mmm-85) REVERT: M 58 ILE cc_start: 0.7652 (tt) cc_final: 0.7364 (tt) REVERT: M 60 ARG cc_start: 0.8373 (ptt90) cc_final: 0.7099 (mmm160) REVERT: M 75 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7925 (p) REVERT: M 91 GLU cc_start: 0.7846 (tp30) cc_final: 0.7527 (tp30) REVERT: M 112 LYS cc_start: 0.7700 (mptt) cc_final: 0.7338 (ttpp) REVERT: N 6 LYS cc_start: 0.8385 (mtpp) cc_final: 0.8031 (ttpp) REVERT: N 13 SER cc_start: 0.8596 (t) cc_final: 0.8348 (m) REVERT: O 12 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: O 32 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7531 (p) REVERT: O 90 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: P 55 SER cc_start: 0.8514 (m) cc_final: 0.8231 (p) REVERT: P 61 ARG cc_start: 0.7922 (ttt90) cc_final: 0.7491 (ttt-90) REVERT: P 79 ASN cc_start: 0.8019 (t0) cc_final: 0.7645 (t0) REVERT: Q 22 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7813 (mtmt) REVERT: Q 47 TYR cc_start: 0.8730 (t80) cc_final: 0.8364 (t80) REVERT: Q 59 LYS cc_start: 0.7444 (mtpp) cc_final: 0.7180 (ttmt) REVERT: R 54 ASP cc_start: 0.7850 (m-30) cc_final: 0.7511 (m-30) REVERT: R 88 GLN cc_start: 0.8455 (mt0) cc_final: 0.7477 (mt0) REVERT: R 93 GLN cc_start: 0.8523 (mt0) cc_final: 0.8242 (mt0) REVERT: S 15 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7647 (mtm180) REVERT: S 85 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7740 (mt-10) REVERT: T 48 LYS cc_start: 0.8323 (tptm) cc_final: 0.7880 (tppt) REVERT: T 68 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7414 (ttm110) REVERT: T 76 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.7497 (mtt180) REVERT: T 81 ARG cc_start: 0.7484 (mtt90) cc_final: 0.7160 (mtt90) REVERT: U 20 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7305 (tptp) REVERT: V 24 SER cc_start: 0.8033 (t) cc_final: 0.7822 (m) REVERT: V 26 GLN cc_start: 0.7497 (tp40) cc_final: 0.7248 (tp40) REVERT: V 48 GLU cc_start: 0.7984 (pt0) cc_final: 0.7775 (pt0) REVERT: V 76 GLN cc_start: 0.7709 (tp-100) cc_final: 0.7275 (mm-40) REVERT: V 90 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7079 (mmt-90) REVERT: V 131 ILE cc_start: 0.6454 (tt) cc_final: 0.6068 (tp) REVERT: V 132 GLU cc_start: 0.6073 (mt-10) cc_final: 0.5677 (mt-10) REVERT: W 21 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8036 (tp) REVERT: W 36 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7602 (tt) REVERT: W 37 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6774 (pp) REVERT: X 6 ASP cc_start: 0.7874 (m-30) cc_final: 0.7634 (m-30) REVERT: X 28 ARG cc_start: 0.8494 (ptt180) cc_final: 0.8285 (ptt180) REVERT: X 46 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6816 (mtmt) REVERT: Y 46 ARG cc_start: 0.7408 (tpt90) cc_final: 0.6946 (mtp85) REVERT: Z 3 GLU cc_start: 0.7443 (mp0) cc_final: 0.7127 (pt0) REVERT: Z 23 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7610 (mt) REVERT: Z 51 HIS cc_start: 0.6695 (t-90) cc_final: 0.6392 (t70) outliers start: 150 outliers final: 107 residues processed: 610 average time/residue: 0.8921 time to fit residues: 894.5943 Evaluate side-chains 621 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 499 time to evaluate : 4.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 37 ARG Chi-restraints excluded: chain 0 residue 51 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 3 residue 59 ASN Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 104 GLU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 7 ILE Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 71 ILE Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 37 LEU Chi-restraints excluded: chain X residue 17 SER Chi-restraints excluded: chain X residue 46 LYS Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 49 THR Chi-restraints excluded: chain Z residue 59 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 464 optimal weight: 6.9990 chunk 316 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 415 optimal weight: 8.9990 chunk 230 optimal weight: 20.0000 chunk 475 optimal weight: 4.9990 chunk 385 optimal weight: 20.0000 chunk 0 optimal weight: 0.9990 chunk 284 optimal weight: 7.9990 chunk 500 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN J 96 HIS J 117 GLN O 56 ASN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 91402 Z= 0.314 Angle : 0.659 14.212 137258 Z= 0.335 Chirality : 0.039 0.288 17616 Planarity : 0.005 0.073 7061 Dihedral : 23.775 178.648 47063 Min Nonbonded Distance : 1.058 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 1.22 % Allowed : 8.15 % Favored : 90.63 % Rotamer: Outliers : 6.66 % Allowed : 16.74 % Favored : 76.60 % 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: -0.09 (0.19), residues: 776 sheet: -1.46 (0.21), residues: 578 loop : -2.06 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 250 HIS 0.013 0.001 HIS D 139 PHE 0.018 0.002 PHE P 6 TYR 0.013 0.002 TYR C 104 ARG 0.008 0.001 ARG X 37 *********************** 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 670 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 501 time to evaluate : 3.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 7 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8045 (p) REVERT: 2 17 ARG cc_start: 0.7426 (mtp180) cc_final: 0.7014 (mmm-85) REVERT: 2 25 MET cc_start: 0.7378 (mmm) cc_final: 0.6884 (mmm) REVERT: 3 48 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7113 (p) REVERT: 4 8 LYS cc_start: 0.7963 (mttm) cc_final: 0.7616 (mttm) REVERT: 4 18 ARG cc_start: 0.7645 (ptm-80) cc_final: 0.7346 (ptm160) REVERT: C 23 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6942 (mt-10) REVERT: C 35 ARG cc_start: 0.7422 (mmt-90) cc_final: 0.6977 (mmt180) REVERT: C 85 ASP cc_start: 0.7911 (t0) cc_final: 0.7608 (t0) REVERT: C 95 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7513 (pp) REVERT: C 126 LYS cc_start: 0.7307 (ttmm) cc_final: 0.6263 (ptpt) REVERT: C 135 ASN cc_start: 0.7869 (t0) cc_final: 0.7643 (m110) REVERT: C 200 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6603 (pm20) REVERT: C 202 SER cc_start: 0.8591 (t) cc_final: 0.8369 (m) REVERT: C 217 LYS cc_start: 0.7922 (ttmm) cc_final: 0.7179 (tttm) REVERT: C 229 VAL cc_start: 0.7814 (OUTLIER) cc_final: 0.7600 (p) REVERT: C 252 LYS cc_start: 0.8628 (mttt) cc_final: 0.8408 (mttm) REVERT: C 266 LYS cc_start: 0.8216 (mtpp) cc_final: 0.7955 (mtmm) REVERT: D 20 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7700 (t0) REVERT: D 22 LYS cc_start: 0.7647 (mtpp) cc_final: 0.6884 (mmtt) REVERT: D 83 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7752 (mt-10) REVERT: D 170 MET cc_start: 0.8685 (ttt) cc_final: 0.8403 (ttt) REVERT: D 181 LYS cc_start: 0.7519 (tttm) cc_final: 0.6974 (ttmt) REVERT: D 214 ARG cc_start: 0.6554 (ptt-90) cc_final: 0.6278 (mtp180) REVERT: E 3 LEU cc_start: 0.7650 (mm) cc_final: 0.6473 (tp) REVERT: E 24 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7665 (tp) REVERT: E 46 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6145 (ttt-90) REVERT: E 117 ASP cc_start: 0.8085 (t0) cc_final: 0.7409 (t0) REVERT: E 121 ASN cc_start: 0.7153 (m110) cc_final: 0.6873 (m110) REVERT: E 151 ASN cc_start: 0.8020 (m-40) cc_final: 0.7566 (m110) REVERT: E 184 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7696 (p0) REVERT: F 13 GLN cc_start: 0.6507 (OUTLIER) cc_final: 0.5458 (mm-40) REVERT: F 90 MET cc_start: 0.7153 (mtp) cc_final: 0.6318 (mtp) REVERT: F 98 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6295 (mm) REVERT: F 128 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.5801 (mt0) REVERT: F 147 GLU cc_start: 0.8106 (mp0) cc_final: 0.7574 (tp30) REVERT: F 178 ARG cc_start: 0.8065 (ptp90) cc_final: 0.7356 (tpp80) REVERT: G 24 LEU cc_start: 0.6501 (mt) cc_final: 0.6138 (tt) REVERT: G 153 ARG cc_start: 0.8673 (tpt170) cc_final: 0.8291 (tpt170) REVERT: J 4 TYR cc_start: 0.8648 (t80) cc_final: 0.8129 (t80) REVERT: J 19 ASP cc_start: 0.8130 (p0) cc_final: 0.7881 (p0) REVERT: J 71 LYS cc_start: 0.7977 (mttt) cc_final: 0.7442 (mttm) REVERT: J 108 MET cc_start: 0.8500 (mtt) cc_final: 0.8104 (mtt) REVERT: K 9 LYS cc_start: 0.8868 (pttp) cc_final: 0.8539 (pttp) REVERT: K 54 ARG cc_start: 0.7362 (ttt-90) cc_final: 0.6954 (ttp-170) REVERT: K 78 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7537 (tttt) REVERT: L 128 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7600 (mmmm) REVERT: M 6 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7889 (ttpt) REVERT: M 56 ARG cc_start: 0.7568 (mmt-90) cc_final: 0.7224 (mmm-85) REVERT: M 60 ARG cc_start: 0.8351 (ptt90) cc_final: 0.7040 (mmm160) REVERT: M 112 LYS cc_start: 0.7659 (mptt) cc_final: 0.7285 (ttpp) REVERT: N 6 LYS cc_start: 0.8372 (mtpp) cc_final: 0.8001 (ttpp) REVERT: N 13 SER cc_start: 0.8471 (t) cc_final: 0.8214 (m) REVERT: O 32 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7513 (p) REVERT: O 90 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.6471 (mp0) REVERT: P 55 SER cc_start: 0.8463 (m) cc_final: 0.8170 (p) REVERT: P 79 ASN cc_start: 0.7972 (t0) cc_final: 0.7346 (t0) REVERT: Q 6 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5359 (ptm160) REVERT: Q 13 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6834 (mtpp) REVERT: Q 22 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7633 (mtmt) REVERT: Q 59 LYS cc_start: 0.7406 (mtpp) cc_final: 0.7159 (ttmt) REVERT: R 54 ASP cc_start: 0.7851 (m-30) cc_final: 0.7528 (m-30) REVERT: R 88 GLN cc_start: 0.8243 (mt0) cc_final: 0.7374 (mt0) REVERT: S 15 ARG cc_start: 0.7936 (ptm160) cc_final: 0.7577 (mtm180) REVERT: T 48 LYS cc_start: 0.8368 (tptm) cc_final: 0.7919 (tppt) REVERT: T 68 ARG cc_start: 0.7710 (ttm170) cc_final: 0.7431 (ttm110) REVERT: U 20 LYS cc_start: 0.8340 (ttmt) cc_final: 0.7295 (tptp) REVERT: V 24 SER cc_start: 0.8019 (t) cc_final: 0.7817 (m) REVERT: V 26 GLN cc_start: 0.7409 (tp40) cc_final: 0.6874 (tp-100) REVERT: V 45 GLN cc_start: 0.7713 (tt0) cc_final: 0.6908 (mt0) REVERT: V 76 GLN cc_start: 0.7702 (tp-100) cc_final: 0.7483 (tp40) REVERT: V 90 ARG cc_start: 0.8309 (mtm110) cc_final: 0.7479 (mmt-90) REVERT: V 131 ILE cc_start: 0.6343 (tt) cc_final: 0.6054 (tp) REVERT: V 142 GLU cc_start: 0.5623 (pm20) cc_final: 0.5307 (pm20) REVERT: V 170 LEU cc_start: 0.7375 (tp) cc_final: 0.7171 (tt) REVERT: W 21 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8016 (tp) REVERT: W 36 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7773 (tt) REVERT: X 6 ASP cc_start: 0.7870 (m-30) cc_final: 0.7616 (m-30) REVERT: Y 46 ARG cc_start: 0.7422 (tpt90) cc_final: 0.6972 (mtp85) REVERT: Z 3 GLU cc_start: 0.7478 (mp0) cc_final: 0.7068 (pt0) REVERT: Z 23 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7592 (mt) outliers start: 169 outliers final: 118 residues processed: 614 average time/residue: 0.8988 time to fit residues: 914.3731 Evaluate side-chains 619 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 482 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 37 ARG Chi-restraints excluded: chain 0 residue 51 LEU Chi-restraints excluded: chain 0 residue 54 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 3 residue 34 GLU Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 3 residue 59 ASN Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 24 LEU Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 13 GLN Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 69 SER Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 56 ASN Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 13 LYS Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 12 LYS Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 7 ILE Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 71 ILE Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 182 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain X residue 17 SER Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 12 THR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 49 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 59 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 187 optimal weight: 6.9990 chunk 502 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 327 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 558 optimal weight: 0.1980 chunk 463 optimal weight: 0.5980 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: 3.1384 ------------------------------------------------------------------------------- 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 D 21 ASN E 76 GLN E 208 ASN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN G 103 ASN H 28 ASN J 96 HIS J 117 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN V 93 GLN V 169 ASN W 19 GLN X 45 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 91402 Z= 0.278 Angle : 0.626 14.032 137258 Z= 0.318 Chirality : 0.037 0.282 17616 Planarity : 0.005 0.071 7061 Dihedral : 23.693 179.505 47062 Min Nonbonded Distance : 1.066 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 1.15 % Allowed : 8.21 % Favored : 90.63 % Rotamer: Outliers : 6.42 % Allowed : 18.51 % Favored : 75.07 % 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: -1.98 (0.14), residues: 3032 helix: 0.03 (0.19), residues: 780 sheet: -1.48 (0.21), residues: 580 loop : -1.96 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 250 HIS 0.011 0.001 HIS D 139 PHE 0.020 0.002 PHE F 27 TYR 0.012 0.002 TYR S 82 ARG 0.007 0.001 ARG X 37 *********************** 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 663 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 500 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 37 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7060 (mtp85) REVERT: 2 7 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8078 (p) REVERT: 2 17 ARG cc_start: 0.7162 (mtp180) cc_final: 0.6831 (mmm-85) REVERT: 2 25 MET cc_start: 0.7366 (mmm) cc_final: 0.6879 (mmm) REVERT: 3 48 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7123 (p) REVERT: 4 18 ARG cc_start: 0.7628 (ptm-80) cc_final: 0.7393 (ptm160) REVERT: C 23 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6891 (mt-10) REVERT: C 35 ARG cc_start: 0.7527 (mmt-90) cc_final: 0.7267 (mmt180) REVERT: C 85 ASP cc_start: 0.7921 (t0) cc_final: 0.7637 (t0) REVERT: C 95 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7519 (pp) REVERT: C 103 ARG cc_start: 0.7579 (mtt-85) cc_final: 0.7187 (mmt90) REVERT: C 126 LYS cc_start: 0.7407 (ttmm) cc_final: 0.6310 (ptpt) REVERT: C 135 ASN cc_start: 0.7880 (t0) cc_final: 0.7666 (m110) REVERT: C 200 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6639 (pm20) REVERT: C 202 SER cc_start: 0.8650 (t) cc_final: 0.8449 (m) REVERT: C 217 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7155 (tttm) REVERT: C 252 LYS cc_start: 0.8646 (mttt) cc_final: 0.8434 (mttm) REVERT: C 266 LYS cc_start: 0.8295 (mtpp) cc_final: 0.7991 (mtmm) REVERT: D 20 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7383 (t0) REVERT: D 22 LYS cc_start: 0.7615 (mtpp) cc_final: 0.6772 (mmtt) REVERT: D 83 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7730 (mt-10) REVERT: D 174 ARG cc_start: 0.7392 (ttt-90) cc_final: 0.6991 (ttt-90) REVERT: D 181 LYS cc_start: 0.7506 (tttm) cc_final: 0.6953 (ttmt) REVERT: E 30 ASN cc_start: 0.7508 (p0) cc_final: 0.7135 (p0) REVERT: E 46 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6077 (ttt-90) REVERT: E 117 ASP cc_start: 0.8036 (t0) cc_final: 0.7418 (t0) REVERT: E 121 ASN cc_start: 0.6942 (m110) cc_final: 0.6606 (m110) REVERT: E 151 ASN cc_start: 0.7988 (m-40) cc_final: 0.7533 (m110) REVERT: E 160 ARG cc_start: 0.6758 (ptm-80) cc_final: 0.6538 (ttp80) REVERT: E 184 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7564 (p0) REVERT: F 90 MET cc_start: 0.7199 (mtp) cc_final: 0.6394 (mtp) REVERT: F 98 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6304 (mm) REVERT: F 144 MET cc_start: 0.7258 (ptp) cc_final: 0.6983 (ptp) REVERT: F 147 GLU cc_start: 0.8145 (mp0) cc_final: 0.7605 (tp30) REVERT: F 159 MET cc_start: 0.7353 (pmm) cc_final: 0.6855 (pmm) REVERT: F 178 ARG cc_start: 0.8021 (ptp90) cc_final: 0.7511 (tpp80) REVERT: G 24 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6209 (tt) REVERT: G 153 ARG cc_start: 0.8657 (tpt170) cc_final: 0.8333 (tpt170) REVERT: J 4 TYR cc_start: 0.8669 (t80) cc_final: 0.8150 (t80) REVERT: J 19 ASP cc_start: 0.8096 (p0) cc_final: 0.7826 (p0) REVERT: J 71 LYS cc_start: 0.8045 (mttt) cc_final: 0.7516 (mttm) REVERT: J 108 MET cc_start: 0.8513 (mtt) cc_final: 0.8168 (mtt) REVERT: K 9 LYS cc_start: 0.8877 (pttp) cc_final: 0.8557 (pttp) REVERT: K 78 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7516 (tttt) REVERT: L 85 LYS cc_start: 0.7728 (mmtp) cc_final: 0.7484 (mmmm) REVERT: L 128 LYS cc_start: 0.7856 (mmmt) cc_final: 0.7439 (mmmm) REVERT: M 6 LYS cc_start: 0.8384 (ttpp) cc_final: 0.7986 (ttpt) REVERT: M 56 ARG cc_start: 0.7607 (mmt-90) cc_final: 0.7294 (mmm-85) REVERT: M 60 ARG cc_start: 0.8404 (ptt90) cc_final: 0.6995 (mmm160) REVERT: M 112 LYS cc_start: 0.7701 (mptt) cc_final: 0.7357 (ttpp) REVERT: N 6 LYS cc_start: 0.8361 (mtpp) cc_final: 0.7999 (ttpp) REVERT: N 13 SER cc_start: 0.8367 (t) cc_final: 0.8118 (m) REVERT: O 12 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: O 32 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7536 (p) REVERT: O 90 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6468 (mp0) REVERT: P 43 LYS cc_start: 0.7868 (tptt) cc_final: 0.7593 (tptt) REVERT: P 55 SER cc_start: 0.8391 (m) cc_final: 0.8128 (p) REVERT: P 79 ASN cc_start: 0.8021 (t0) cc_final: 0.7424 (t0) REVERT: P 86 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7522 (mt) REVERT: Q 6 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.5354 (ptm160) REVERT: Q 22 LYS cc_start: 0.7953 (mmmt) cc_final: 0.7671 (mtmt) REVERT: Q 59 LYS cc_start: 0.7388 (mtpp) cc_final: 0.7152 (ttmt) REVERT: Q 84 LYS cc_start: 0.7675 (ttpt) cc_final: 0.7002 (ttmt) REVERT: R 54 ASP cc_start: 0.7848 (m-30) cc_final: 0.7524 (m-30) REVERT: R 80 ASN cc_start: 0.8065 (m-40) cc_final: 0.7140 (p0) REVERT: R 88 GLN cc_start: 0.8224 (mt0) cc_final: 0.7827 (mt0) REVERT: S 15 ARG cc_start: 0.7786 (ptm160) cc_final: 0.7441 (mtm180) REVERT: T 48 LYS cc_start: 0.8399 (tptm) cc_final: 0.7960 (tppt) REVERT: T 68 ARG cc_start: 0.7673 (ttm170) cc_final: 0.7434 (ttm110) REVERT: U 20 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7184 (tptp) REVERT: V 26 GLN cc_start: 0.7424 (tp40) cc_final: 0.6876 (tp-100) REVERT: V 45 GLN cc_start: 0.7684 (tt0) cc_final: 0.6751 (mt0) REVERT: V 90 ARG cc_start: 0.8291 (mtm110) cc_final: 0.7487 (mmt-90) REVERT: V 113 LEU cc_start: 0.7395 (tp) cc_final: 0.7143 (tp) REVERT: V 131 ILE cc_start: 0.6348 (tt) cc_final: 0.6097 (tp) REVERT: V 170 LEU cc_start: 0.7279 (tp) cc_final: 0.6980 (tt) REVERT: W 21 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7999 (tp) REVERT: W 36 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7750 (tt) REVERT: X 6 ASP cc_start: 0.7885 (m-30) cc_final: 0.7608 (m-30) REVERT: Y 46 ARG cc_start: 0.7402 (tpt90) cc_final: 0.6987 (mtp85) REVERT: Z 3 GLU cc_start: 0.7381 (mp0) cc_final: 0.6860 (pt0) REVERT: Z 23 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7596 (mt) outliers start: 163 outliers final: 129 residues processed: 605 average time/residue: 0.9017 time to fit residues: 906.1439 Evaluate side-chains 639 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 492 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 37 ARG Chi-restraints excluded: chain 0 residue 51 LEU Chi-restraints excluded: chain 0 residue 54 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 3 residue 34 GLU Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 3 residue 59 ASN Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 3 residue 62 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 148 ILE Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 34 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 85 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 56 ASN Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 86 LEU Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 12 LYS Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 7 ILE Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 71 ILE Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 182 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain X residue 17 SER Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 38 THR Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 49 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 59 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 538 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 318 optimal weight: 2.9990 chunk 407 optimal weight: 0.9980 chunk 315 optimal weight: 3.9990 chunk 469 optimal weight: 0.5980 chunk 311 optimal weight: 2.9990 chunk 556 optimal weight: 0.9990 chunk 348 optimal weight: 0.0870 chunk 339 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 208 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN H 28 ASN J 96 HIS J 117 GLN ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 91402 Z= 0.148 Angle : 0.566 14.444 137258 Z= 0.289 Chirality : 0.033 0.278 17616 Planarity : 0.005 0.067 7061 Dihedral : 23.687 179.342 47062 Min Nonbonded Distance : 1.134 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 1.12 % Allowed : 7.39 % Favored : 91.49 % Rotamer: Outliers : 5.00 % Allowed : 20.20 % Favored : 74.79 % 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: -1.72 (0.15), residues: 3032 helix: 0.26 (0.19), residues: 780 sheet: -1.29 (0.22), residues: 564 loop : -1.81 (0.14), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 250 HIS 0.009 0.001 HIS T 34 PHE 0.020 0.001 PHE F 27 TYR 0.014 0.001 TYR S 82 ARG 0.008 0.000 ARG 3 30 *********************** 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 620 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 493 time to evaluate : 3.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 37 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7037 (mtp85) REVERT: 2 17 ARG cc_start: 0.7142 (mtp180) cc_final: 0.6857 (mmm-85) REVERT: 2 25 MET cc_start: 0.7350 (mmm) cc_final: 0.6613 (mmm) REVERT: 3 48 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7101 (p) REVERT: 4 18 ARG cc_start: 0.7591 (ptm-80) cc_final: 0.7383 (ptm160) REVERT: C 23 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6811 (mt-10) REVERT: C 35 ARG cc_start: 0.7497 (mmt-90) cc_final: 0.7211 (mmt180) REVERT: C 66 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8096 (t70) REVERT: C 85 ASP cc_start: 0.8004 (t0) cc_final: 0.7694 (t0) REVERT: C 95 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7457 (pp) REVERT: C 200 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6577 (pm20) REVERT: C 217 LYS cc_start: 0.7760 (ttmm) cc_final: 0.6899 (tttm) REVERT: C 226 MET cc_start: 0.7628 (mtt) cc_final: 0.7232 (mtt) REVERT: C 266 LYS cc_start: 0.8270 (mtpp) cc_final: 0.7954 (mtmm) REVERT: D 20 ASN cc_start: 0.7725 (t0) cc_final: 0.7455 (t0) REVERT: D 22 LYS cc_start: 0.7751 (mtpp) cc_final: 0.7131 (mmtp) REVERT: D 154 CYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7694 (t) REVERT: D 170 MET cc_start: 0.8497 (ttt) cc_final: 0.8003 (ttt) REVERT: D 181 LYS cc_start: 0.7514 (tttm) cc_final: 0.6969 (ttmt) REVERT: E 46 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.5935 (ttt-90) REVERT: E 117 ASP cc_start: 0.8031 (t70) cc_final: 0.7370 (t0) REVERT: E 121 ASN cc_start: 0.6962 (m110) cc_final: 0.6716 (m110) REVERT: E 151 ASN cc_start: 0.7955 (m-40) cc_final: 0.7487 (m110) REVERT: E 184 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7728 (p0) REVERT: F 90 MET cc_start: 0.7171 (mtp) cc_final: 0.6381 (mtp) REVERT: F 128 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.5854 (mt0) REVERT: F 147 GLU cc_start: 0.8144 (mp0) cc_final: 0.7544 (tp30) REVERT: F 172 GLU cc_start: 0.6252 (mp0) cc_final: 0.6050 (mp0) REVERT: F 178 ARG cc_start: 0.7968 (ptp90) cc_final: 0.7569 (tpp80) REVERT: G 24 LEU cc_start: 0.6537 (OUTLIER) cc_final: 0.6210 (tt) REVERT: G 153 ARG cc_start: 0.8585 (tpt170) cc_final: 0.8243 (tpt170) REVERT: J 4 TYR cc_start: 0.8651 (t80) cc_final: 0.8135 (t80) REVERT: J 19 ASP cc_start: 0.8007 (p0) cc_final: 0.7705 (p0) REVERT: J 71 LYS cc_start: 0.7971 (mttt) cc_final: 0.7574 (mttm) REVERT: J 108 MET cc_start: 0.8467 (mtt) cc_final: 0.8006 (mtt) REVERT: K 9 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8649 (pttp) REVERT: K 78 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7531 (tttt) REVERT: K 104 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7208 (ttp-110) REVERT: L 85 LYS cc_start: 0.7727 (mmtp) cc_final: 0.7482 (mmmm) REVERT: L 128 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7353 (mmmm) REVERT: M 6 LYS cc_start: 0.8409 (ttpp) cc_final: 0.8037 (ttpt) REVERT: M 45 ARG cc_start: 0.7721 (mmt90) cc_final: 0.7321 (mtt-85) REVERT: M 60 ARG cc_start: 0.8375 (ptt90) cc_final: 0.6980 (mmm160) REVERT: M 112 LYS cc_start: 0.7625 (mptt) cc_final: 0.7260 (ttpp) REVERT: N 6 LYS cc_start: 0.8322 (mtpp) cc_final: 0.8017 (ttpp) REVERT: N 13 SER cc_start: 0.8230 (t) cc_final: 0.7938 (m) REVERT: O 90 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: P 43 LYS cc_start: 0.7693 (tptt) cc_final: 0.7441 (tptt) REVERT: P 55 SER cc_start: 0.8342 (m) cc_final: 0.8053 (p) REVERT: P 79 ASN cc_start: 0.7936 (t0) cc_final: 0.7288 (t0) REVERT: Q 6 ARG cc_start: 0.6260 (OUTLIER) cc_final: 0.5228 (ptm160) REVERT: Q 22 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7559 (mtmt) REVERT: Q 59 LYS cc_start: 0.7375 (mtpp) cc_final: 0.7152 (ttmt) REVERT: Q 84 LYS cc_start: 0.7650 (ttpt) cc_final: 0.7034 (ttmt) REVERT: Q 98 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7624 (pt) REVERT: R 54 ASP cc_start: 0.7838 (m-30) cc_final: 0.7499 (m-30) REVERT: R 57 LYS cc_start: 0.7633 (mmmt) cc_final: 0.7138 (mttp) REVERT: R 80 ASN cc_start: 0.7928 (m-40) cc_final: 0.7061 (p0) REVERT: R 88 GLN cc_start: 0.8103 (mt0) cc_final: 0.7360 (mt0) REVERT: T 68 ARG cc_start: 0.7692 (ttm170) cc_final: 0.7492 (ttm110) REVERT: U 20 LYS cc_start: 0.8266 (ttmt) cc_final: 0.7166 (tptp) REVERT: V 26 GLN cc_start: 0.7397 (tp40) cc_final: 0.6827 (tp-100) REVERT: V 45 GLN cc_start: 0.7634 (tt0) cc_final: 0.6708 (mt0) REVERT: V 90 ARG cc_start: 0.8111 (mtm110) cc_final: 0.7289 (mmt-90) REVERT: V 113 LEU cc_start: 0.7660 (tp) cc_final: 0.7399 (tp) REVERT: V 131 ILE cc_start: 0.6213 (tt) cc_final: 0.5933 (tp) REVERT: V 142 GLU cc_start: 0.5800 (pm20) cc_final: 0.5554 (pm20) REVERT: W 36 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7674 (tt) REVERT: X 6 ASP cc_start: 0.7887 (m-30) cc_final: 0.7629 (m-30) REVERT: Y 46 ARG cc_start: 0.7394 (tpt90) cc_final: 0.6916 (mtp85) REVERT: Z 23 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7519 (mt) outliers start: 127 outliers final: 96 residues processed: 572 average time/residue: 0.9221 time to fit residues: 871.8149 Evaluate side-chains 585 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 472 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 37 ARG Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 3 residue 34 GLU Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 3 residue 59 ASN Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 9 LYS Chi-restraints excluded: chain K residue 104 ARG Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 12 LYS Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 7 ILE Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 71 ILE Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 182 VAL Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 59 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 344 optimal weight: 7.9990 chunk 222 optimal weight: 10.0000 chunk 332 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 353 optimal weight: 0.1980 chunk 378 optimal weight: 0.6980 chunk 274 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 437 optimal weight: 3.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN E 47 GLN E 76 GLN E 208 ASN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN H 28 ASN J 96 HIS J 117 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 91402 Z= 0.265 Angle : 0.610 13.645 137258 Z= 0.310 Chirality : 0.036 0.279 17616 Planarity : 0.005 0.065 7061 Dihedral : 23.641 179.835 47062 Min Nonbonded Distance : 1.071 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 1.15 % Allowed : 8.34 % Favored : 90.50 % Rotamer: Outliers : 5.47 % Allowed : 20.13 % Favored : 74.40 % 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: -1.74 (0.15), residues: 3032 helix: 0.22 (0.19), residues: 785 sheet: -1.27 (0.22), residues: 576 loop : -1.83 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 104 HIS 0.009 0.001 HIS D 139 PHE 0.019 0.002 PHE F 27 TYR 0.012 0.001 TYR S 82 ARG 0.009 0.001 ARG X 37 *********************** 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 637 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 498 time to evaluate : 3.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 37 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6972 (mtp85) REVERT: 2 7 THR cc_start: 0.8504 (OUTLIER) cc_final: 0.8087 (p) REVERT: 2 17 ARG cc_start: 0.7263 (mtp180) cc_final: 0.6918 (mmm-85) REVERT: 2 25 MET cc_start: 0.7360 (mmm) cc_final: 0.6873 (mmm) REVERT: 3 48 THR cc_start: 0.7601 (OUTLIER) cc_final: 0.7113 (p) REVERT: 4 8 LYS cc_start: 0.7963 (mttm) cc_final: 0.7724 (mttm) REVERT: C 23 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7093 (mt-10) REVERT: C 35 ARG cc_start: 0.7519 (mmt-90) cc_final: 0.7235 (mmt180) REVERT: C 52 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7424 (ptt180) REVERT: C 85 ASP cc_start: 0.8013 (t0) cc_final: 0.7740 (t0) REVERT: C 95 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7564 (pp) REVERT: C 200 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: C 217 LYS cc_start: 0.7773 (ttmm) cc_final: 0.6883 (tttm) REVERT: C 226 MET cc_start: 0.7760 (mtt) cc_final: 0.7451 (mtt) REVERT: C 266 LYS cc_start: 0.8323 (mtpp) cc_final: 0.7991 (mtmm) REVERT: D 22 LYS cc_start: 0.7559 (mtpp) cc_final: 0.6949 (mptt) REVERT: D 83 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7939 (mt-10) REVERT: D 170 MET cc_start: 0.8709 (ttt) cc_final: 0.8211 (ttt) REVERT: D 181 LYS cc_start: 0.7573 (tttm) cc_final: 0.6977 (ttmt) REVERT: E 30 ASN cc_start: 0.7533 (p0) cc_final: 0.7177 (p0) REVERT: E 46 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6045 (ttt-90) REVERT: E 117 ASP cc_start: 0.8216 (t70) cc_final: 0.7588 (t0) REVERT: E 121 ASN cc_start: 0.6885 (m110) cc_final: 0.6590 (m110) REVERT: E 150 GLU cc_start: 0.8125 (tt0) cc_final: 0.7640 (mp0) REVERT: E 151 ASN cc_start: 0.7980 (m-40) cc_final: 0.7484 (m110) REVERT: E 184 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7684 (p0) REVERT: F 90 MET cc_start: 0.7147 (mtp) cc_final: 0.6315 (mtp) REVERT: F 128 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.5898 (mt0) REVERT: F 147 GLU cc_start: 0.8182 (mp0) cc_final: 0.7564 (tp30) REVERT: F 154 ASP cc_start: 0.6698 (OUTLIER) cc_final: 0.6477 (m-30) REVERT: F 178 ARG cc_start: 0.8007 (ptp90) cc_final: 0.7602 (tpp80) REVERT: G 24 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6208 (tt) REVERT: G 153 ARG cc_start: 0.8664 (tpt170) cc_final: 0.8297 (tpt170) REVERT: J 4 TYR cc_start: 0.8679 (t80) cc_final: 0.8115 (t80) REVERT: J 19 ASP cc_start: 0.8202 (p0) cc_final: 0.7872 (p0) REVERT: J 71 LYS cc_start: 0.8006 (mttt) cc_final: 0.7508 (mttm) REVERT: J 108 MET cc_start: 0.8501 (mtt) cc_final: 0.8193 (mtt) REVERT: K 9 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8510 (pttp) REVERT: K 54 ARG cc_start: 0.7318 (ttt-90) cc_final: 0.6881 (ttp-170) REVERT: K 78 LYS cc_start: 0.8248 (ttpt) cc_final: 0.7506 (tttt) REVERT: L 85 LYS cc_start: 0.7736 (mmtp) cc_final: 0.7476 (mmmm) REVERT: L 128 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7488 (mmmm) REVERT: M 6 LYS cc_start: 0.8378 (ttpp) cc_final: 0.8024 (ttpt) REVERT: M 60 ARG cc_start: 0.8453 (ptt90) cc_final: 0.7116 (mmm160) REVERT: M 87 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7491 (mtpt) REVERT: M 112 LYS cc_start: 0.7669 (mptt) cc_final: 0.7316 (ttpp) REVERT: N 6 LYS cc_start: 0.8361 (mtpp) cc_final: 0.8012 (ttpp) REVERT: N 13 SER cc_start: 0.8351 (t) cc_final: 0.8112 (m) REVERT: O 12 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: O 90 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: P 43 LYS cc_start: 0.7701 (tptt) cc_final: 0.7383 (tptt) REVERT: P 55 SER cc_start: 0.8386 (m) cc_final: 0.8081 (p) REVERT: P 79 ASN cc_start: 0.7980 (t0) cc_final: 0.7210 (t0) REVERT: Q 6 ARG cc_start: 0.6396 (OUTLIER) cc_final: 0.6041 (ptt180) REVERT: Q 22 LYS cc_start: 0.7894 (mmmt) cc_final: 0.7654 (mtmt) REVERT: Q 30 ARG cc_start: 0.8336 (mtt90) cc_final: 0.8122 (mtt-85) REVERT: Q 59 LYS cc_start: 0.7376 (mtpp) cc_final: 0.7147 (ttmt) REVERT: Q 98 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7582 (pt) REVERT: R 54 ASP cc_start: 0.7837 (m-30) cc_final: 0.7507 (m-30) REVERT: R 57 LYS cc_start: 0.7585 (mmmt) cc_final: 0.7064 (mttp) REVERT: R 80 ASN cc_start: 0.7985 (m-40) cc_final: 0.7165 (p0) REVERT: R 88 GLN cc_start: 0.8090 (mt0) cc_final: 0.7807 (mt0) REVERT: T 48 LYS cc_start: 0.8407 (tptm) cc_final: 0.8092 (tppp) REVERT: T 68 ARG cc_start: 0.7738 (ttm170) cc_final: 0.7511 (ttm110) REVERT: U 20 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7179 (tptp) REVERT: V 26 GLN cc_start: 0.7429 (tp40) cc_final: 0.6862 (tp-100) REVERT: V 45 GLN cc_start: 0.7697 (tt0) cc_final: 0.6746 (mt0) REVERT: V 76 GLN cc_start: 0.7776 (tp-100) cc_final: 0.7392 (tp40) REVERT: V 90 ARG cc_start: 0.8263 (mtm110) cc_final: 0.7486 (mmt-90) REVERT: V 113 LEU cc_start: 0.7642 (tp) cc_final: 0.7402 (tp) REVERT: V 131 ILE cc_start: 0.6515 (tt) cc_final: 0.6248 (tp) REVERT: W 36 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7827 (tt) REVERT: Y 46 ARG cc_start: 0.7398 (tpt90) cc_final: 0.6999 (mtp85) REVERT: Z 23 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7580 (mt) outliers start: 139 outliers final: 109 residues processed: 585 average time/residue: 0.8902 time to fit residues: 856.2473 Evaluate side-chains 622 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 494 time to evaluate : 3.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 37 ARG Chi-restraints excluded: chain 0 residue 51 LEU Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 3 residue 34 GLU Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 3 residue 59 ASN Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 9 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 21 SER Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 12 LYS Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 7 ILE Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 71 ILE Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 182 VAL Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 59 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 505 optimal weight: 3.9990 chunk 532 optimal weight: 9.9990 chunk 486 optimal weight: 0.9990 chunk 518 optimal weight: 0.0970 chunk 311 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 406 optimal weight: 0.5980 chunk 159 optimal weight: 10.0000 chunk 468 optimal weight: 8.9990 chunk 490 optimal weight: 3.9990 chunk 516 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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** D 20 ASN E 76 GLN E 208 ASN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN H 28 ASN J 96 HIS J 117 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 91402 Z= 0.187 Angle : 0.584 13.896 137258 Z= 0.299 Chirality : 0.034 0.284 17616 Planarity : 0.005 0.094 7061 Dihedral : 23.655 179.957 47062 Min Nonbonded Distance : 1.086 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 1.12 % Allowed : 8.15 % Favored : 90.73 % Rotamer: Outliers : 5.47 % Allowed : 20.36 % Favored : 74.16 % 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: -1.69 (0.15), residues: 3032 helix: 0.27 (0.19), residues: 785 sheet: -1.22 (0.22), residues: 563 loop : -1.80 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 250 HIS 0.007 0.001 HIS T 34 PHE 0.019 0.001 PHE F 27 TYR 0.013 0.001 TYR S 82 ARG 0.010 0.000 ARG X 37 *********************** 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 626 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 487 time to evaluate : 3.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 37 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6956 (mtp85) REVERT: 2 7 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8081 (p) REVERT: 2 17 ARG cc_start: 0.7239 (mtp180) cc_final: 0.6904 (mmm-85) REVERT: 2 25 MET cc_start: 0.7348 (mmm) cc_final: 0.6865 (mmm) REVERT: 3 48 THR cc_start: 0.7586 (OUTLIER) cc_final: 0.7107 (p) REVERT: 4 8 LYS cc_start: 0.7956 (mttm) cc_final: 0.7699 (mttm) REVERT: C 23 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7071 (mt-10) REVERT: C 35 ARG cc_start: 0.7511 (mmt-90) cc_final: 0.7222 (mmt180) REVERT: C 85 ASP cc_start: 0.7994 (t0) cc_final: 0.7703 (t0) REVERT: C 95 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7545 (pp) REVERT: C 118 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: C 200 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6621 (pm20) REVERT: C 217 LYS cc_start: 0.7765 (ttmm) cc_final: 0.6894 (tttm) REVERT: C 226 MET cc_start: 0.7743 (mtt) cc_final: 0.7448 (mtt) REVERT: C 266 LYS cc_start: 0.8321 (mtpp) cc_final: 0.7991 (mtmm) REVERT: D 22 LYS cc_start: 0.7530 (mtpp) cc_final: 0.6932 (mptt) REVERT: D 83 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7900 (mt-10) REVERT: D 154 CYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7763 (t) REVERT: D 170 MET cc_start: 0.8691 (ttt) cc_final: 0.8194 (ttt) REVERT: D 174 ARG cc_start: 0.7296 (ttt-90) cc_final: 0.6897 (ttt-90) REVERT: D 181 LYS cc_start: 0.7584 (tttm) cc_final: 0.7018 (ttmt) REVERT: E 30 ASN cc_start: 0.7529 (p0) cc_final: 0.7156 (p0) REVERT: E 46 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.5950 (ttt-90) REVERT: E 117 ASP cc_start: 0.8206 (t70) cc_final: 0.7583 (t0) REVERT: E 121 ASN cc_start: 0.6873 (m110) cc_final: 0.6580 (m110) REVERT: E 150 GLU cc_start: 0.8107 (tt0) cc_final: 0.7621 (mp0) REVERT: E 151 ASN cc_start: 0.7973 (m-40) cc_final: 0.7475 (m110) REVERT: E 184 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7659 (p0) REVERT: F 90 MET cc_start: 0.7144 (mtp) cc_final: 0.6312 (mtp) REVERT: F 98 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6241 (mm) REVERT: F 128 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.5885 (mt0) REVERT: F 147 GLU cc_start: 0.8179 (mp0) cc_final: 0.7567 (tp30) REVERT: F 154 ASP cc_start: 0.6696 (OUTLIER) cc_final: 0.6474 (m-30) REVERT: F 178 ARG cc_start: 0.7951 (ptp90) cc_final: 0.7608 (tpp80) REVERT: G 24 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6208 (tt) REVERT: G 153 ARG cc_start: 0.8652 (tpt170) cc_final: 0.8313 (tpt170) REVERT: J 4 TYR cc_start: 0.8673 (t80) cc_final: 0.8107 (t80) REVERT: J 19 ASP cc_start: 0.8193 (p0) cc_final: 0.7849 (p0) REVERT: J 71 LYS cc_start: 0.8010 (mttt) cc_final: 0.7529 (mttm) REVERT: J 108 MET cc_start: 0.8479 (mtt) cc_final: 0.8180 (mtt) REVERT: K 9 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8507 (pttp) REVERT: K 78 LYS cc_start: 0.8254 (ttpt) cc_final: 0.7460 (tttt) REVERT: L 85 LYS cc_start: 0.7729 (mmtp) cc_final: 0.7469 (mmmm) REVERT: L 128 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7468 (mmmm) REVERT: M 6 LYS cc_start: 0.8385 (ttpp) cc_final: 0.8034 (ttpt) REVERT: M 60 ARG cc_start: 0.8444 (ptt90) cc_final: 0.7118 (mmm160) REVERT: M 87 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7456 (mtpt) REVERT: M 112 LYS cc_start: 0.7666 (mptt) cc_final: 0.7315 (ttpp) REVERT: N 6 LYS cc_start: 0.8351 (mtpp) cc_final: 0.8017 (ttpp) REVERT: N 13 SER cc_start: 0.8322 (t) cc_final: 0.8038 (m) REVERT: O 12 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.6775 (tm-30) REVERT: O 90 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6492 (mp0) REVERT: P 43 LYS cc_start: 0.7595 (tptt) cc_final: 0.7361 (tptt) REVERT: P 55 SER cc_start: 0.8368 (m) cc_final: 0.8063 (p) REVERT: P 79 ASN cc_start: 0.7945 (t0) cc_final: 0.7284 (t0) REVERT: Q 6 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5986 (ptt180) REVERT: Q 22 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7640 (mtmt) REVERT: Q 30 ARG cc_start: 0.8390 (mtt90) cc_final: 0.8172 (mtt-85) REVERT: Q 59 LYS cc_start: 0.7365 (mtpp) cc_final: 0.7140 (ttmt) REVERT: Q 98 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7580 (pt) REVERT: R 54 ASP cc_start: 0.7832 (m-30) cc_final: 0.7505 (m-30) REVERT: R 57 LYS cc_start: 0.7585 (mmmt) cc_final: 0.7106 (mttp) REVERT: R 80 ASN cc_start: 0.7943 (m-40) cc_final: 0.7080 (p0) REVERT: R 88 GLN cc_start: 0.8121 (mt0) cc_final: 0.7840 (mt0) REVERT: T 48 LYS cc_start: 0.8403 (tptm) cc_final: 0.8089 (tppp) REVERT: U 20 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7172 (tptp) REVERT: V 26 GLN cc_start: 0.7425 (tp40) cc_final: 0.6850 (tp-100) REVERT: V 45 GLN cc_start: 0.7677 (tt0) cc_final: 0.6737 (mt0) REVERT: V 76 GLN cc_start: 0.7775 (tp-100) cc_final: 0.7394 (tp40) REVERT: V 90 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7298 (mmt-90) REVERT: V 113 LEU cc_start: 0.7641 (tp) cc_final: 0.7391 (tp) REVERT: V 131 ILE cc_start: 0.6505 (tt) cc_final: 0.6241 (tp) REVERT: W 21 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7921 (tp) REVERT: W 36 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7794 (tt) REVERT: W 40 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6983 (pp30) REVERT: Y 46 ARG cc_start: 0.7424 (tpt90) cc_final: 0.6984 (mtp85) REVERT: Z 23 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7560 (mt) outliers start: 139 outliers final: 110 residues processed: 574 average time/residue: 0.8860 time to fit residues: 836.7448 Evaluate side-chains 614 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 481 time to evaluate : 3.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 37 ARG Chi-restraints excluded: chain 0 residue 51 LEU Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 3 residue 34 GLU Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 3 residue 59 ASN Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 13 LYS Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 9 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 133 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 12 LYS Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 7 ILE Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 71 ILE Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 182 VAL Chi-restraints excluded: chain W residue 21 LEU Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 40 GLN Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 340 optimal weight: 7.9990 chunk 548 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 259 optimal weight: 7.9990 chunk 380 optimal weight: 8.9990 chunk 574 optimal weight: 0.9990 chunk 529 optimal weight: 1.9990 chunk 457 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 353 optimal weight: 0.6980 chunk 280 optimal weight: 10.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** D 20 ASN E 76 GLN E 208 ASN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN H 28 ASN J 96 HIS J 117 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 91402 Z= 0.206 Angle : 0.584 14.371 137258 Z= 0.297 Chirality : 0.034 0.291 17616 Planarity : 0.005 0.086 7061 Dihedral : 23.626 179.766 47062 Min Nonbonded Distance : 1.089 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 1.09 % Allowed : 8.44 % Favored : 90.47 % Rotamer: Outliers : 5.40 % Allowed : 20.68 % Favored : 73.93 % 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: -1.66 (0.15), residues: 3032 helix: 0.29 (0.19), residues: 785 sheet: -1.22 (0.22), residues: 565 loop : -1.79 (0.14), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 104 HIS 0.007 0.001 HIS D 139 PHE 0.019 0.001 PHE F 27 TYR 0.019 0.001 TYR E 204 ARG 0.010 0.001 ARG X 37 ********************** 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 633 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 496 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 37 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.6965 (mtp85) REVERT: 2 7 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8081 (p) REVERT: 2 17 ARG cc_start: 0.7244 (mtp180) cc_final: 0.6910 (mmm-85) REVERT: 2 25 MET cc_start: 0.7379 (mmm) cc_final: 0.6604 (mmm) REVERT: 3 48 THR cc_start: 0.7548 (OUTLIER) cc_final: 0.7102 (p) REVERT: 4 8 LYS cc_start: 0.7930 (mttm) cc_final: 0.7658 (mttm) REVERT: C 23 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7081 (mt-10) REVERT: C 35 ARG cc_start: 0.7516 (mmt-90) cc_final: 0.7221 (mmt180) REVERT: C 85 ASP cc_start: 0.7985 (t0) cc_final: 0.7703 (t0) REVERT: C 95 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7522 (pp) REVERT: C 200 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6610 (pm20) REVERT: C 217 LYS cc_start: 0.7756 (ttmm) cc_final: 0.6885 (tttm) REVERT: C 226 MET cc_start: 0.7777 (mtt) cc_final: 0.7494 (mtt) REVERT: C 266 LYS cc_start: 0.8323 (mtpp) cc_final: 0.7992 (mtmm) REVERT: D 22 LYS cc_start: 0.7528 (mtpp) cc_final: 0.6860 (mptt) REVERT: D 83 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7891 (mt-10) REVERT: D 154 CYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7750 (t) REVERT: D 170 MET cc_start: 0.8584 (ttt) cc_final: 0.8069 (ttt) REVERT: D 174 ARG cc_start: 0.7311 (ttt-90) cc_final: 0.6912 (ttt-90) REVERT: D 181 LYS cc_start: 0.7608 (tttm) cc_final: 0.7022 (ttmt) REVERT: E 30 ASN cc_start: 0.7500 (p0) cc_final: 0.7122 (p0) REVERT: E 46 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.5978 (ttt-90) REVERT: E 117 ASP cc_start: 0.8199 (t70) cc_final: 0.7552 (t0) REVERT: E 121 ASN cc_start: 0.6866 (m110) cc_final: 0.6546 (m110) REVERT: E 151 ASN cc_start: 0.7976 (m-40) cc_final: 0.7500 (m110) REVERT: E 184 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7630 (p0) REVERT: F 90 MET cc_start: 0.7152 (mtp) cc_final: 0.6318 (mtp) REVERT: F 98 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6244 (mm) REVERT: F 128 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.5867 (mt0) REVERT: F 144 MET cc_start: 0.7278 (ptp) cc_final: 0.6915 (ptp) REVERT: F 147 GLU cc_start: 0.8179 (mp0) cc_final: 0.7573 (tp30) REVERT: F 154 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6423 (m-30) REVERT: F 178 ARG cc_start: 0.7973 (ptp90) cc_final: 0.7645 (tpp80) REVERT: G 24 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6210 (tt) REVERT: G 153 ARG cc_start: 0.8647 (tpt170) cc_final: 0.8315 (tpt170) REVERT: J 4 TYR cc_start: 0.8682 (t80) cc_final: 0.8127 (t80) REVERT: J 19 ASP cc_start: 0.8171 (p0) cc_final: 0.7743 (p0) REVERT: J 71 LYS cc_start: 0.7997 (mttt) cc_final: 0.7583 (mttm) REVERT: J 108 MET cc_start: 0.8494 (mtt) cc_final: 0.8195 (mtt) REVERT: J 143 LYS cc_start: 0.8199 (ttpp) cc_final: 0.7350 (mttt) REVERT: K 9 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8473 (pttp) REVERT: K 54 ARG cc_start: 0.7271 (ttt-90) cc_final: 0.6934 (ttp-170) REVERT: K 78 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7505 (tttt) REVERT: K 94 ARG cc_start: 0.7561 (ptp-170) cc_final: 0.7145 (ptp-170) REVERT: K 104 ARG cc_start: 0.7768 (ttp-110) cc_final: 0.7270 (ttp-110) REVERT: L 85 LYS cc_start: 0.7740 (mmtp) cc_final: 0.7477 (mmmm) REVERT: L 128 LYS cc_start: 0.7946 (mmmt) cc_final: 0.7470 (mmmm) REVERT: M 6 LYS cc_start: 0.8383 (ttpp) cc_final: 0.8001 (ttpt) REVERT: M 60 ARG cc_start: 0.8404 (ptt90) cc_final: 0.7076 (mmm160) REVERT: M 87 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7441 (mtpt) REVERT: M 112 LYS cc_start: 0.7665 (mptt) cc_final: 0.7316 (ttpp) REVERT: N 6 LYS cc_start: 0.8328 (mtpp) cc_final: 0.7995 (ttpp) REVERT: N 13 SER cc_start: 0.8314 (t) cc_final: 0.8032 (m) REVERT: O 12 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: O 90 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: P 55 SER cc_start: 0.8364 (m) cc_final: 0.8050 (p) REVERT: P 79 ASN cc_start: 0.7917 (t0) cc_final: 0.7259 (t0) REVERT: Q 6 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.5989 (ptt180) REVERT: Q 22 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7637 (mtmt) REVERT: Q 30 ARG cc_start: 0.8398 (mtt90) cc_final: 0.8179 (mtt-85) REVERT: Q 59 LYS cc_start: 0.7374 (mtpp) cc_final: 0.7153 (ttmt) REVERT: Q 98 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7575 (pt) REVERT: R 54 ASP cc_start: 0.7824 (m-30) cc_final: 0.7487 (m-30) REVERT: R 57 LYS cc_start: 0.7626 (mmmt) cc_final: 0.7154 (mttp) REVERT: R 80 ASN cc_start: 0.7937 (m-40) cc_final: 0.7090 (p0) REVERT: R 88 GLN cc_start: 0.8133 (mt0) cc_final: 0.7851 (mt0) REVERT: T 48 LYS cc_start: 0.8415 (tptm) cc_final: 0.8097 (tppp) REVERT: U 20 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7171 (tptp) REVERT: V 45 GLN cc_start: 0.7676 (tt0) cc_final: 0.6728 (mt0) REVERT: V 76 GLN cc_start: 0.7784 (tp-100) cc_final: 0.7409 (tp40) REVERT: V 90 ARG cc_start: 0.8123 (mtm110) cc_final: 0.7301 (mmt-90) REVERT: V 113 LEU cc_start: 0.7630 (tp) cc_final: 0.7381 (tp) REVERT: V 131 ILE cc_start: 0.6519 (tt) cc_final: 0.6268 (tp) REVERT: W 36 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7814 (tt) REVERT: W 40 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6796 (pp30) REVERT: X 6 ASP cc_start: 0.8130 (m-30) cc_final: 0.7805 (m-30) REVERT: Y 46 ARG cc_start: 0.7425 (tpt90) cc_final: 0.6945 (mtp85) REVERT: Z 23 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7560 (mt) outliers start: 137 outliers final: 111 residues processed: 584 average time/residue: 0.9578 time to fit residues: 920.0445 Evaluate side-chains 617 residues out of total 2541 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 485 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 37 ARG Chi-restraints excluded: chain 0 residue 51 LEU Chi-restraints excluded: chain 1 residue 48 VAL Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 3 residue 34 GLU Chi-restraints excluded: chain 3 residue 48 THR Chi-restraints excluded: chain 3 residue 59 ASN Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 145 VAL Chi-restraints excluded: chain C residue 157 ARG Chi-restraints excluded: chain C residue 200 GLU Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 154 CYS Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 46 ARG Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 164 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 184 ASN Chi-restraints excluded: chain E residue 193 ASP Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 154 ASP Chi-restraints excluded: chain F residue 161 ILE Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 135 SER Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 43 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 9 LYS Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 49 MET Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 115 ASP Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 87 LYS Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 89 ASP Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 12 GLU Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 90 GLU Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 67 VAL Chi-restraints excluded: chain P residue 85 VAL Chi-restraints excluded: chain P residue 93 ARG Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 98 LEU Chi-restraints excluded: chain Q residue 125 SER Chi-restraints excluded: chain R residue 12 LYS Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 93 GLN Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 7 ILE Chi-restraints excluded: chain V residue 69 LEU Chi-restraints excluded: chain V residue 71 ILE Chi-restraints excluded: chain V residue 79 LEU Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 123 LEU Chi-restraints excluded: chain V residue 152 GLU Chi-restraints excluded: chain V residue 182 VAL Chi-restraints excluded: chain W residue 36 ILE Chi-restraints excluded: chain W residue 40 GLN Chi-restraints excluded: chain Y residue 10 LEU Chi-restraints excluded: chain Y residue 41 LEU Chi-restraints excluded: chain Y residue 44 ASN Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain Z residue 9 VAL Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 577 random chunks: chunk 363 optimal weight: 9.9990 chunk 487 optimal weight: 5.9990 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: 0.6980 chunk 191 optimal weight: 7.9990 chunk 470 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN E 76 GLN E 208 ASN ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN H 28 ASN J 96 HIS J 117 GLN ** P 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN V 93 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.141737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.109190 restraints weight = 110399.924| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 0.86 r_work: 0.3142 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 91402 Z= 0.369 Angle : 0.689 14.578 137258 Z= 0.348 Chirality : 0.041 0.295 17616 Planarity : 0.006 0.066 7061 Dihedral : 23.696 179.048 47062 Min Nonbonded Distance : 1.052 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 1.19 % Allowed : 8.97 % Favored : 89.84 % Rotamer: Outliers : 5.59 % Allowed : 20.52 % Favored : 73.89 % 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: -1.82 (0.15), residues: 3032 helix: 0.05 (0.19), residues: 785 sheet: -1.26 (0.22), residues: 577 loop : -1.85 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 104 HIS 0.015 0.002 HIS D 139 PHE 0.020 0.002 PHE F 27 TYR 0.015 0.002 TYR 1 20 ARG 0.009 0.001 ARG X 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16262.48 seconds wall clock time: 288 minutes 40.72 seconds (17320.72 seconds total)