Starting phenix.real_space_refine on Mon Mar 18 03:55:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqb_22432/03_2024/7jqb_22432.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqb_22432/03_2024/7jqb_22432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqb_22432/03_2024/7jqb_22432.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqb_22432/03_2024/7jqb_22432.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqb_22432/03_2024/7jqb_22432.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqb_22432/03_2024/7jqb_22432.pdb" } resolution = 2.7 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= 0.013 sd= 0.131 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8402 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1696 5.49 5 S 178 5.16 5 C 40659 2.51 5 N 13783 2.21 5 O 18660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 80": "NH1" <-> "NH2" Residue "a ARG 85": "NH1" <-> "NH2" Residue "a TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 87": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "b GLU 90": "OE1" <-> "OE2" Residue "b PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 271": "OD1" <-> "OD2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 66": "NH1" <-> "NH2" Residue "d ARG 67": "NH1" <-> "NH2" Residue "E ASP 14": "OD1" <-> "OD2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 81": "NH1" <-> "NH2" Residue "f ARG 101": "NH1" <-> "NH2" Residue "f ARG 104": "NH1" <-> "NH2" Residue "G TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 127": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G GLU 176": "OE1" <-> "OE2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "g TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H ARG 198": "NH1" <-> "NH2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "h ARG 47": "NH1" <-> "NH2" Residue "h ARG 60": "NH1" <-> "NH2" Residue "h PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 100": "NH1" <-> "NH2" Residue "h ASP 126": "OD1" <-> "OD2" Residue "h ASP 144": "OD1" <-> "OD2" Residue "h TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 18": "OE1" <-> "OE2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 81": "NH1" <-> "NH2" Residue "I ASP 132": "OD1" <-> "OD2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 41": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J ARG 141": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 83": "NH1" <-> "NH2" Residue "K ASP 95": "OD1" <-> "OD2" Residue "K ARG 138": "NH1" <-> "NH2" Residue "L ARG 65": "NH1" <-> "NH2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N GLU 66": "OE1" <-> "OE2" Residue "N GLU 87": "OE1" <-> "OE2" Residue "N ASP 113": "OD1" <-> "OD2" Residue "N TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q GLU 74": "OE1" <-> "OE2" Residue "Q PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "S ASP 82": "OD1" <-> "OD2" Residue "S ASP 101": "OD1" <-> "OD2" Residue "S ASP 110": "OD1" <-> "OD2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 14": "NH1" <-> "NH2" Residue "T ASP 21": "OD1" <-> "OD2" Residue "T ARG 39": "NH1" <-> "NH2" Residue "T ARG 55": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 121": "NH1" <-> "NH2" Residue "T ARG 142": "NH1" <-> "NH2" Residue "U ARG 16": "NH1" <-> "NH2" Residue "U ARG 62": "NH1" <-> "NH2" Residue "U ARG 84": "NH1" <-> "NH2" Residue "U ARG 102": "NH1" <-> "NH2" Residue "U ARG 121": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 87": "NH1" <-> "NH2" Residue "W ASP 4": "OD1" <-> "OD2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 20": "NH1" <-> "NH2" Residue "Z PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 61": "NH1" <-> "NH2" Residue "Z ARG 110": "NH1" <-> "NH2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 68": "NH1" <-> "NH2" Residue "M ARG 191": "NH1" <-> "NH2" Residue "M ARG 198": "NH1" <-> "NH2" Residue "M ASP 206": "OD1" <-> "OD2" Residue "M ARG 221": "NH1" <-> "NH2" Residue "M PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 252": "NH1" <-> "NH2" Residue "O ASP 3": "OD1" <-> "OD2" Residue "O PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 97": "NH1" <-> "NH2" Residue "O PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P ARG 121": "NH1" <-> "NH2" Residue "X PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X ASP 131": "OD1" <-> "OD2" Residue "X ARG 141": "NH1" <-> "NH2" Residue "X ARG 150": "NH1" <-> "NH2" Residue "Y PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 85": "OD1" <-> "OD2" Residue "Y PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 5": "NH1" <-> "NH2" Residue "c ARG 8": "NH1" <-> "NH2" Residue "c ARG 17": "NH1" <-> "NH2" Residue "c ARG 67": "NH1" <-> "NH2" Residue "c PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 107": "NH1" <-> "NH2" Residue "e ASP 6": "OD1" <-> "OD2" Residue "e PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 74976 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 36229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36229 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 146, 'rna2p_pyr': 111, 'rna3p_pur': 752, 'rna3p_pyr': 688} Link IDs: {'rna2p': 256, 'rna3p': 1440} Chain breaks: 11 Chain: "a" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "d" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 488 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "G" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1471 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain breaks: 1 Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1058 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "F" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 280 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "M" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2083 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain: "O" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1296 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 150} Chain: "P" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 141} Chain: "X" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Y" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "c" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1106 Classifications: {'peptide': 142} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 136} Chain: "e" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 659 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 77} Time building chain proxies: 29.51, per 1000 atoms: 0.39 Number of scatterers: 74976 At special positions: 0 Unit cell: (161.268, 216.804, 273.408, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 178 16.00 P 1696 15.00 O 18660 8.00 N 13783 7.00 C 40659 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 30.37 Conformation dependent library (CDL) restraints added in 5.3 seconds 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9004 Finding SS restraints... Secondary structure from input PDB file: 163 helices and 60 sheets defined 32.8% alpha, 16.6% beta 481 base pairs and 980 stacking pairs defined. Time for finding SS restraints: 26.18 Creating SS restraints... Processing helix chain 'a' and resid 54 through 59 removed outlier: 3.641A pdb=" N CYS a 59 " --> pdb=" O TYR a 55 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 65 Processing helix chain 'a' and resid 69 through 78 removed outlier: 3.868A pdb=" N GLU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 94 removed outlier: 3.893A pdb=" N GLN a 89 " --> pdb=" O ARG a 85 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU a 90 " --> pdb=" O ALA a 86 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU a 91 " --> pdb=" O ALA a 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 11 through 21 removed outlier: 3.644A pdb=" N LYS B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 36 removed outlier: 4.454A pdb=" N GLN B 36 " --> pdb=" O GLN B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 67 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.529A pdb=" N GLY B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 206 through 215 removed outlier: 4.381A pdb=" N GLU B 211 " --> pdb=" O PRO B 207 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 56 removed outlier: 4.556A pdb=" N ASP b 52 " --> pdb=" O ALA b 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER b 54 " --> pdb=" O VAL b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'C' and resid 23 through 26 removed outlier: 3.588A pdb=" N SER C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 26' Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.535A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 178 removed outlier: 3.598A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 187 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.585A pdb=" N GLU C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 78 through 85 removed outlier: 3.613A pdb=" N PHE D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 99 removed outlier: 3.598A pdb=" N PHE D 97 " --> pdb=" O ILE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.653A pdb=" N ILE D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 218 removed outlier: 3.626A pdb=" N LEU D 213 " --> pdb=" O VAL D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 246 removed outlier: 3.823A pdb=" N THR D 240 " --> pdb=" O PHE D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 3.506A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 269 through 274 Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 12 through 29 removed outlier: 3.506A pdb=" N ILE E 16 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 59 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.523A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE E 77 " --> pdb=" O VAL E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 112 Processing helix chain 'E' and resid 114 through 129 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'f' and resid 83 through 89 Processing helix chain 'f' and resid 103 through 116 removed outlier: 3.636A pdb=" N ARG f 114 " --> pdb=" O GLN f 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 36 Processing helix chain 'G' and resid 61 through 65 Processing helix chain 'G' and resid 67 through 75 removed outlier: 3.757A pdb=" N ARG G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 105 removed outlier: 3.677A pdb=" N ILE G 92 " --> pdb=" O MET G 88 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N HIS G 101 " --> pdb=" O PHE G 97 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU G 102 " --> pdb=" O GLU G 98 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 103 " --> pdb=" O ILE G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 4.126A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY G 120 " --> pdb=" O ILE G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 156 removed outlier: 4.082A pdb=" N TRP G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS G 155 " --> pdb=" O ILE G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 182 removed outlier: 4.385A pdb=" N ALA G 174 " --> pdb=" O ALA G 170 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU G 176 " --> pdb=" O CYS G 172 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU G 177 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN G 179 " --> pdb=" O ASP G 175 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.922A pdb=" N LYS G 192 " --> pdb=" O TYR G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 200 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 26 through 28 No H-bonds generated for 'chain 'H' and resid 26 through 28' Processing helix chain 'H' and resid 39 through 42 removed outlier: 3.763A pdb=" N GLY H 42 " --> pdb=" O ASP H 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 39 through 42' Processing helix chain 'H' and resid 137 through 146 Processing helix chain 'H' and resid 152 through 157 removed outlier: 3.834A pdb=" N VAL H 157 " --> pdb=" O ARG H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 236 removed outlier: 3.930A pdb=" N LYS H 195 " --> pdb=" O ARG H 191 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS H 215 " --> pdb=" O LYS H 211 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS H 223 " --> pdb=" O GLU H 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 29 removed outlier: 3.833A pdb=" N LEU I 28 " --> pdb=" O SER I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 74 removed outlier: 4.449A pdb=" N LYS I 70 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS I 74 " --> pdb=" O LYS I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 87 removed outlier: 4.292A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS I 85 " --> pdb=" O ARG I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.728A pdb=" N LEU I 130 " --> pdb=" O HIS I 126 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU I 131 " --> pdb=" O ASP I 127 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP I 132 " --> pdb=" O ALA I 128 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL I 134 " --> pdb=" O LEU I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 167 removed outlier: 3.962A pdb=" N VAL I 166 " --> pdb=" O GLN I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 181 removed outlier: 3.757A pdb=" N GLY I 175 " --> pdb=" O GLU I 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 27 No H-bonds generated for 'chain 'J' and resid 25 through 27' Processing helix chain 'J' and resid 88 through 93 removed outlier: 4.290A pdb=" N ARG J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR J 93 " --> pdb=" O GLU J 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 88 through 93' Processing helix chain 'J' and resid 106 through 117 removed outlier: 3.662A pdb=" N SER J 115 " --> pdb=" O GLN J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 137 Processing helix chain 'J' and resid 143 through 152 removed outlier: 3.853A pdb=" N ARG J 152 " --> pdb=" O LYS J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 169 removed outlier: 4.183A pdb=" N GLN J 165 " --> pdb=" O LEU J 161 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN J 167 " --> pdb=" O GLU J 163 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN J 168 " --> pdb=" O GLU J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 183 Processing helix chain 'J' and resid 191 through 206 removed outlier: 3.684A pdb=" N ARG J 200 " --> pdb=" O GLU J 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 36 removed outlier: 3.545A pdb=" N ASP K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN K 27 " --> pdb=" O SER K 23 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU K 31 " --> pdb=" O GLN K 27 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 61 removed outlier: 3.707A pdb=" N VAL K 46 " --> pdb=" O GLU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 removed outlier: 3.768A pdb=" N ASN K 75 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 92 Processing helix chain 'K' and resid 93 through 97 removed outlier: 3.687A pdb=" N ILE K 97 " --> pdb=" O LEU K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 107 Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 131 removed outlier: 3.782A pdb=" N VAL K 128 " --> pdb=" O HIS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 155 No H-bonds generated for 'chain 'K' and resid 153 through 155' Processing helix chain 'K' and resid 173 through 183 removed outlier: 3.601A pdb=" N LYS K 179 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 186 No H-bonds generated for 'chain 'K' and resid 184 through 186' Processing helix chain 'L' and resid 4 through 16 removed outlier: 3.700A pdb=" N ARG L 8 " --> pdb=" O PRO L 4 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU L 14 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU L 15 " --> pdb=" O ILE L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 54 removed outlier: 3.782A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER L 54 " --> pdb=" O GLN L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 removed outlier: 3.839A pdb=" N GLN L 77 " --> pdb=" O ASN L 73 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR L 78 " --> pdb=" O GLU L 74 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG L 80 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP L 81 " --> pdb=" O GLN L 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 19 removed outlier: 3.686A pdb=" N GLN N 19 " --> pdb=" O THR N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 43 removed outlier: 4.073A pdb=" N LYS N 40 " --> pdb=" O ARG N 36 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP N 43 " --> pdb=" O ALA N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 65 removed outlier: 3.547A pdb=" N LEU N 64 " --> pdb=" O MET N 60 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL N 65 " --> pdb=" O TYR N 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 60 through 65' Processing helix chain 'N' and resid 66 through 68 No H-bonds generated for 'chain 'N' and resid 66 through 68' Processing helix chain 'N' and resid 122 through 129 removed outlier: 4.130A pdb=" N GLU N 126 " --> pdb=" O ASP N 122 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 26 Processing helix chain 'Q' and resid 29 through 34 Processing helix chain 'Q' and resid 38 through 48 removed outlier: 3.551A pdb=" N LEU Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 62 removed outlier: 3.514A pdb=" N LEU Q 56 " --> pdb=" O LYS Q 52 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG Q 59 " --> pdb=" O SER Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 90 Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'R' and resid 47 through 58 removed outlier: 3.786A pdb=" N LEU R 51 " --> pdb=" O LEU R 47 " (cutoff:3.500A) Proline residue: R 54 - end of helix removed outlier: 3.771A pdb=" N LEU R 58 " --> pdb=" O PRO R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 100 removed outlier: 4.065A pdb=" N VAL R 93 " --> pdb=" O SER R 89 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS R 98 " --> pdb=" O ALA R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 112 removed outlier: 3.731A pdb=" N GLU R 107 " --> pdb=" O ALA R 103 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE R 108 " --> pdb=" O SER R 104 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU R 112 " --> pdb=" O ILE R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 120 removed outlier: 3.738A pdb=" N LEU R 119 " --> pdb=" O ASP R 116 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU R 120 " --> pdb=" O ARG R 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 116 through 120' Processing helix chain 'S' and resid 6 through 17 removed outlier: 3.602A pdb=" N ALA S 12 " --> pdb=" O THR S 8 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL S 15 " --> pdb=" O LYS S 11 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 24 removed outlier: 3.863A pdb=" N ARG S 23 " --> pdb=" O TYR S 20 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU S 24 " --> pdb=" O TYR S 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 20 through 24' Processing helix chain 'S' and resid 29 through 36 Processing helix chain 'S' and resid 45 through 62 removed outlier: 3.641A pdb=" N LYS S 49 " --> pdb=" O LYS S 45 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY S 52 " --> pdb=" O ASN S 48 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N HIS S 56 " --> pdb=" O GLY S 52 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG S 60 " --> pdb=" O HIS S 56 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN S 62 " --> pdb=" O MET S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 83 removed outlier: 3.768A pdb=" N ASN S 83 " --> pdb=" O GLU S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 109 removed outlier: 3.689A pdb=" N LYS S 103 " --> pdb=" O ASP S 99 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU S 109 " --> pdb=" O MET S 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 4.283A pdb=" N ILE T 30 " --> pdb=" O ILE T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 42 removed outlier: 3.782A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 removed outlier: 3.817A pdb=" N VAL T 64 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU T 65 " --> pdb=" O GLU T 61 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG T 66 " --> pdb=" O ASP T 62 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR T 69 " --> pdb=" O GLU T 65 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE T 70 " --> pdb=" O ARG T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 77 Processing helix chain 'T' and resid 80 through 84 removed outlier: 3.666A pdb=" N PHE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU T 84 " --> pdb=" O ASP T 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 80 through 84' Processing helix chain 'T' and resid 99 through 113 removed outlier: 4.310A pdb=" N ASP T 104 " --> pdb=" O ALA T 100 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN T 105 " --> pdb=" O ASN T 101 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU T 111 " --> pdb=" O LEU T 107 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 128 removed outlier: 3.545A pdb=" N LEU T 123 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 140 through 144 Processing helix chain 'U' and resid 13 through 21 removed outlier: 3.930A pdb=" N ALA U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 36 removed outlier: 4.408A pdb=" N ASP U 35 " --> pdb=" O GLU U 32 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR U 36 " --> pdb=" O TRP U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 3.584A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA U 61 " --> pdb=" O ALA U 57 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR U 65 " --> pdb=" O ALA U 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU U 66 " --> pdb=" O ARG U 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 removed outlier: 3.581A pdb=" N THR U 76 " --> pdb=" O VAL U 72 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS U 77 " --> pdb=" O GLY U 73 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE U 78 " --> pdb=" O SER U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 105 removed outlier: 3.517A pdb=" N ARG U 102 " --> pdb=" O SER U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 110 removed outlier: 3.515A pdb=" N LEU U 110 " --> pdb=" O ALA U 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 139 removed outlier: 4.116A pdb=" N ASP U 132 " --> pdb=" O GLN U 128 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN U 137 " --> pdb=" O ARG U 133 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 46 removed outlier: 3.539A pdb=" N GLU V 33 " --> pdb=" O VAL V 29 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL V 35 " --> pdb=" O SER V 31 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP V 38 " --> pdb=" O LYS V 34 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU V 39 " --> pdb=" O VAL V 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS V 44 " --> pdb=" O ILE V 40 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS V 46 " --> pdb=" O GLY V 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 Processing helix chain 'W' and resid 64 through 76 Processing helix chain 'Z' and resid 36 through 49 removed outlier: 3.713A pdb=" N GLU Z 42 " --> pdb=" O THR Z 38 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS Z 43 " --> pdb=" O GLU Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 55 removed outlier: 3.676A pdb=" N VAL Z 54 " --> pdb=" O THR Z 51 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE Z 55 " --> pdb=" O PRO Z 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 51 through 55' Processing helix chain 'Z' and resid 78 through 83 Processing helix chain 'Z' and resid 87 through 93 Processing helix chain 'Z' and resid 103 through 115 Processing helix chain 'Z' and resid 121 through 126 Processing helix chain 'F' and resid 152 through 161 Processing helix chain 'F' and resid 165 through 178 Processing helix chain 'M' and resid 10 through 14 removed outlier: 3.548A pdb=" N ALA M 14 " --> pdb=" O ARG M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 19 Processing helix chain 'M' and resid 37 through 41 removed outlier: 4.209A pdb=" N CYS M 41 " --> pdb=" O LEU M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 50 Processing helix chain 'M' and resid 57 through 66 removed outlier: 3.742A pdb=" N VAL M 61 " --> pdb=" O THR M 57 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 135 No H-bonds generated for 'chain 'M' and resid 133 through 135' Processing helix chain 'M' and resid 223 through 225 No H-bonds generated for 'chain 'M' and resid 223 through 225' Processing helix chain 'M' and resid 247 through 259 removed outlier: 3.513A pdb=" N ASP M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 52 removed outlier: 3.513A pdb=" N ILE O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 42 Processing helix chain 'P' and resid 46 through 57 removed outlier: 3.543A pdb=" N VAL P 52 " --> pdb=" O SER P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 67 removed outlier: 3.560A pdb=" N VAL P 66 " --> pdb=" O GLN P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 78 removed outlier: 3.552A pdb=" N SER P 77 " --> pdb=" O ARG P 73 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS P 78 " --> pdb=" O ILE P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 105 removed outlier: 3.932A pdb=" N ARG P 104 " --> pdb=" O LYS P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 131 removed outlier: 3.575A pdb=" N ILE P 116 " --> pdb=" O LYS P 112 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR P 131 " --> pdb=" O ARG P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 151 removed outlier: 3.557A pdb=" N VAL P 150 " --> pdb=" O ALA P 146 " (cutoff:3.500A) Processing helix chain 'X' and resid 70 through 88 removed outlier: 3.538A pdb=" N ALA X 74 " --> pdb=" O SER X 70 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS X 86 " --> pdb=" O ALA X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 109 through 111 No H-bonds generated for 'chain 'X' and resid 109 through 111' Processing helix chain 'X' and resid 112 through 122 removed outlier: 3.604A pdb=" N LEU X 116 " --> pdb=" O ALA X 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 20 removed outlier: 3.633A pdb=" N ASP Y 9 " --> pdb=" O ASN Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 44 removed outlier: 3.574A pdb=" N VAL Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 94 removed outlier: 3.645A pdb=" N ASN Y 92 " --> pdb=" O LYS Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 113 through 119 removed outlier: 3.523A pdb=" N ARG Y 118 " --> pdb=" O GLU Y 114 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 21 Processing helix chain 'c' and resid 24 through 32 removed outlier: 3.508A pdb=" N ALA c 30 " --> pdb=" O GLN c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 38 Processing helix chain 'c' and resid 129 through 135 removed outlier: 3.551A pdb=" N LEU c 133 " --> pdb=" O SER c 129 " (cutoff:3.500A) Processing helix chain 'e' and resid 12 through 17 Processing sheet with id=AA1, first strand: chain 'a' and resid 67 through 68 removed outlier: 6.639A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.642A pdb=" N LYS B 40 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.482A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER B 75 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AA5, first strand: chain 'b' and resid 36 through 43 Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 50 removed outlier: 3.836A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 43 through 50 removed outlier: 3.836A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 13.815A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.103A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N ARG C 213 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N VAL C 212 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C 140 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG C 136 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 103 through 115 removed outlier: 5.609A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 184 through 188 Processing sheet with id=AB1, first strand: chain 'd' and resid 43 through 44 removed outlier: 3.633A pdb=" N ARG d 44 " --> pdb=" O VAL d 30 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL d 30 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS d 27 " --> pdb=" O GLY d 19 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLY d 19 " --> pdb=" O CYS d 27 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'd' and resid 46 through 47 Processing sheet with id=AB3, first strand: chain 'E' and resid 39 through 42 removed outlier: 3.620A pdb=" N GLU E 47 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR E 42 " --> pdb=" O ARG E 45 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N THR E 46 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 50 through 52 removed outlier: 6.129A pdb=" N ILE E 50 " --> pdb=" O GLU E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 147 through 149 Processing sheet with id=AB6, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.734A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N LYS E 141 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 181 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 125 through 126 Processing sheet with id=AB8, first strand: chain 'g' and resid 106 through 107 removed outlier: 4.116A pdb=" N SER g 115 " --> pdb=" O LYS g 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'g' and resid 119 through 120 removed outlier: 4.108A pdb=" N ARG g 119 " --> pdb=" O MET g 132 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR g 140 " --> pdb=" O ALA g 133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 12 through 17 removed outlier: 6.833A pdb=" N LYS H 2 " --> pdb=" O LEU H 109 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU H 111 " --> pdb=" O LYS H 2 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASN H 4 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE H 113 " --> pdb=" O ASN H 4 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER H 6 " --> pdb=" O ILE H 113 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N LYS H 115 " --> pdb=" O SER H 6 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 72 through 77 Processing sheet with id=AC3, first strand: chain 'h' and resid 5 through 6 Processing sheet with id=AC4, first strand: chain 'h' and resid 18 through 22 removed outlier: 3.929A pdb=" N ARG h 57 " --> pdb=" O MET h 42 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'h' and resid 70 through 71 removed outlier: 3.563A pdb=" N ALA h 78 " --> pdb=" O TRP h 90 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER h 80 " --> pdb=" O ARG h 88 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR h 96 " --> pdb=" O ASP h 91 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'h' and resid 110 through 112 removed outlier: 3.527A pdb=" N SER h 110 " --> pdb=" O GLY h 123 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL h 121 " --> pdb=" O ALA h 112 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'h' and resid 130 through 131 removed outlier: 4.014A pdb=" N TYR h 140 " --> pdb=" O LEU h 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 154 through 155 removed outlier: 3.504A pdb=" N VAL h 166 " --> pdb=" O ARG h 155 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL h 176 " --> pdb=" O THR h 186 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR h 186 " --> pdb=" O VAL h 176 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 195 through 200 Processing sheet with id=AD1, first strand: chain 'h' and resid 236 through 241 removed outlier: 4.966A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 47 through 53 removed outlier: 4.115A pdb=" N ARG I 57 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 185 through 188 removed outlier: 8.445A pdb=" N ASN I 186 " --> pdb=" O ARG I 152 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE I 154 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N GLU I 188 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL I 156 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE Y 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 3 through 4 removed outlier: 4.166A pdb=" N ILE J 3 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 37 through 38 removed outlier: 6.387A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 62 through 67 removed outlier: 5.577A pdb=" N ARG J 77 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU J 103 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL J 81 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE J 101 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N GLY J 187 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN J 64 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL J 189 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER J 66 " --> pdb=" O VAL J 189 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 135 through 137 Processing sheet with id=AD8, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AD9, first strand: chain 'N' and resid 32 through 33 removed outlier: 3.750A pdb=" N VAL N 109 " --> pdb=" O VAL N 51 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N CYS N 50 " --> pdb=" O ILE N 77 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 76 through 78 removed outlier: 3.896A pdb=" N VAL Q 76 " --> pdb=" O MET Q 93 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL Q 94 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL Q 105 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 20 through 27 removed outlier: 3.594A pdb=" N LYS R 33 " --> pdb=" O ILE R 68 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL R 70 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 96 through 98 removed outlier: 5.983A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'T' and resid 12 through 15 Processing sheet with id=AE5, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE6, first strand: chain 'V' and resid 54 through 55 Processing sheet with id=AE7, first strand: chain 'V' and resid 54 through 55 Processing sheet with id=AE8, first strand: chain 'V' and resid 63 through 66 Processing sheet with id=AE9, first strand: chain 'W' and resid 32 through 39 removed outlier: 5.494A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 6 through 15 removed outlier: 5.989A pdb=" N ILE Z 7 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU Z 28 " --> pdb=" O ILE Z 7 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N THR Z 9 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASP Z 26 " --> pdb=" O THR Z 9 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LYS Z 11 " --> pdb=" O VAL Z 24 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL Z 24 " --> pdb=" O LYS Z 11 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LYS Z 68 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N THR Z 62 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 75 through 76 Processing sheet with id=AF3, first strand: chain 'M' and resid 98 through 99 removed outlier: 4.143A pdb=" N ASN M 98 " --> pdb=" O ILE M 114 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 102 through 103 removed outlier: 4.482A pdb=" N ILE M 102 " --> pdb=" O ALA M 110 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 146 through 148 removed outlier: 3.544A pdb=" N ILE M 147 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N HIS M 138 " --> pdb=" O ILE M 129 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE M 129 " --> pdb=" O HIS M 138 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL M 140 " --> pdb=" O ARG M 127 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR M 159 " --> pdb=" O PHE M 172 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE M 172 " --> pdb=" O THR M 159 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN M 161 " --> pdb=" O THR M 170 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 192 through 194 removed outlier: 5.702A pdb=" N LYS M 230 " --> pdb=" O LEU M 180 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N MET M 182 " --> pdb=" O ILE M 228 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE M 228 " --> pdb=" O MET M 182 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS M 233 " --> pdb=" O LYS M 230 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 207 through 211 Processing sheet with id=AF8, first strand: chain 'O' and resid 72 through 82 removed outlier: 17.783A pdb=" N ILE O 72 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 14.998A pdb=" N LEU O 93 " --> pdb=" O ILE O 72 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N SER O 74 " --> pdb=" O ASP O 91 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASP O 91 " --> pdb=" O SER O 74 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL O 87 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N MET O 80 " --> pdb=" O THR O 85 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THR O 85 " --> pdb=" O MET O 80 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N PHE O 140 " --> pdb=" O ASN O 108 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER O 110 " --> pdb=" O PHE O 140 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N VAL O 142 " --> pdb=" O SER O 110 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N HIS O 112 " --> pdb=" O VAL O 142 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N LYS O 144 " --> pdb=" O HIS O 112 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR O 127 " --> pdb=" O LEU O 143 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL O 145 " --> pdb=" O ILE O 125 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE O 125 " --> pdb=" O VAL O 145 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.072A pdb=" N GLY X 29 " --> pdb=" O HIS X 94 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LYS X 96 " --> pdb=" O GLY X 29 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE X 33 " --> pdb=" O ARG X 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'X' and resid 28 through 30 removed outlier: 6.072A pdb=" N GLY X 29 " --> pdb=" O HIS X 94 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LYS X 96 " --> pdb=" O GLY X 29 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU X 93 " --> pdb=" O ILE X 126 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG X 128 " --> pdb=" O LEU X 93 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'X' and resid 44 through 45 removed outlier: 3.754A pdb=" N VAL X 44 " --> pdb=" O ILE X 53 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y' and resid 71 through 74 Processing sheet with id=AG4, first strand: chain 'Y' and resid 71 through 74 removed outlier: 6.871A pdb=" N VAL Y 103 " --> pdb=" O LEU Y 126 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE Y 128 " --> pdb=" O PHE Y 101 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE Y 101 " --> pdb=" O PHE Y 128 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'c' and resid 46 through 55 removed outlier: 6.983A pdb=" N ARG c 71 " --> pdb=" O LEU c 52 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS c 54 " --> pdb=" O CYS c 69 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N CYS c 69 " --> pdb=" O LYS c 54 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE c 120 " --> pdb=" O THR c 82 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU c 101 " --> pdb=" O VAL c 123 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'e' and resid 45 through 47 1195 hydrogen bonds defined for protein. 3354 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1181 hydrogen bonds 1828 hydrogen bond angles 0 basepair planarities 481 basepair parallelities 980 stacking parallelities Total time for adding SS restraints: 65.44 Time building geometry restraints manager: 32.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 12716 1.33 - 1.45: 28341 1.45 - 1.57: 35202 1.57 - 1.70: 3381 1.70 - 1.82: 274 Bond restraints: 79914 Sorted by residual: bond pdb=" C ASP E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.337 1.387 -0.050 9.80e-03 1.04e+04 2.63e+01 bond pdb=" C VAL B 197 " pdb=" N MET B 198 " ideal model delta sigma weight residual 1.331 1.263 0.068 2.83e-02 1.25e+03 5.69e+00 bond pdb=" C LYS S 129 " pdb=" N THR S 130 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.83e-02 1.25e+03 5.37e+00 bond pdb=" C ILE c 115 " pdb=" N PRO c 116 " ideal model delta sigma weight residual 1.335 1.315 0.020 8.70e-03 1.32e+04 5.30e+00 bond pdb=" CA ARG J 5 " pdb=" CB ARG J 5 " ideal model delta sigma weight residual 1.536 1.444 0.092 4.10e-02 5.95e+02 5.06e+00 ... (remaining 79909 not shown) Histogram of bond angle deviations from ideal: 98.27 - 106.48: 10572 106.48 - 114.68: 50829 114.68 - 122.88: 43008 122.88 - 131.09: 11009 131.09 - 139.29: 588 Bond angle restraints: 116006 Sorted by residual: angle pdb=" C VAL P 22 " pdb=" N PRO P 23 " pdb=" CD PRO P 23 " ideal model delta sigma weight residual 120.60 108.48 12.12 2.20e+00 2.07e-01 3.03e+01 angle pdb=" C GLY O 26 " pdb=" N GLU O 27 " pdb=" CA GLU O 27 " ideal model delta sigma weight residual 121.70 131.30 -9.60 1.80e+00 3.09e-01 2.84e+01 angle pdb=" C3' U A 688 " pdb=" O3' U A 688 " pdb=" P U A 689 " ideal model delta sigma weight residual 120.20 128.11 -7.91 1.50e+00 4.44e-01 2.78e+01 angle pdb=" O3' U A 688 " pdb=" C3' U A 688 " pdb=" C2' U A 688 " ideal model delta sigma weight residual 109.50 117.24 -7.74 1.50e+00 4.44e-01 2.66e+01 angle pdb=" N ASP X 138 " pdb=" CA ASP X 138 " pdb=" C ASP X 138 " ideal model delta sigma weight residual 110.35 117.53 -7.18 1.40e+00 5.10e-01 2.63e+01 ... (remaining 116001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 45984 35.99 - 71.98: 4336 71.98 - 107.96: 527 107.96 - 143.95: 14 143.95 - 179.94: 39 Dihedral angle restraints: 50900 sinusoidal: 36940 harmonic: 13960 Sorted by residual: dihedral pdb=" C5' C A1395 " pdb=" C4' C A1395 " pdb=" C3' C A1395 " pdb=" O3' C A1395 " ideal model delta sinusoidal sigma weight residual 147.00 74.03 72.97 1 8.00e+00 1.56e-02 1.06e+02 dihedral pdb=" C4' C A1395 " pdb=" C3' C A1395 " pdb=" C2' C A1395 " pdb=" C1' C A1395 " ideal model delta sinusoidal sigma weight residual -35.00 35.15 -70.15 1 8.00e+00 1.56e-02 9.91e+01 dihedral pdb=" CA GLY X 127 " pdb=" C GLY X 127 " pdb=" N ARG X 128 " pdb=" CA ARG X 128 " ideal model delta harmonic sigma weight residual 180.00 130.55 49.45 0 5.00e+00 4.00e-02 9.78e+01 ... (remaining 50897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 13309 0.083 - 0.167: 962 0.167 - 0.250: 58 0.250 - 0.334: 8 0.334 - 0.417: 10 Chirality restraints: 14347 Sorted by residual: chirality pdb=" C3' U A 110 " pdb=" C4' U A 110 " pdb=" O3' U A 110 " pdb=" C2' U A 110 " both_signs ideal model delta sigma weight residual False -2.48 -2.06 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CB VAL c 128 " pdb=" CA VAL c 128 " pdb=" CG1 VAL c 128 " pdb=" CG2 VAL c 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.39 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CB VAL e 62 " pdb=" CA VAL e 62 " pdb=" CG1 VAL e 62 " pdb=" CG2 VAL e 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 14344 not shown) Planarity restraints: 8425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA M 28 " 0.066 5.00e-02 4.00e+02 9.99e-02 1.60e+01 pdb=" N PRO M 29 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO M 29 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO M 29 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL M 89 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C VAL M 89 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL M 89 " -0.024 2.00e-02 2.50e+03 pdb=" N ILE M 90 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS O 147 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C LYS O 147 " 0.063 2.00e-02 2.50e+03 pdb=" O LYS O 147 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA O 148 " -0.022 2.00e-02 2.50e+03 ... (remaining 8422 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 12403 2.75 - 3.29: 64838 3.29 - 3.83: 153970 3.83 - 4.36: 186199 4.36 - 4.90: 259543 Nonbonded interactions: 676953 Sorted by model distance: nonbonded pdb=" O2' G A1324 " pdb=" O2' G A1510 " model vdw 2.217 2.440 nonbonded pdb=" OG SER h 201 " pdb=" OD1 ASP h 203 " model vdw 2.217 2.440 nonbonded pdb=" O2' G A1236 " pdb=" O PRO Q 131 " model vdw 2.228 2.440 nonbonded pdb=" O2 C A1568 " pdb=" O2' C A1627 " model vdw 2.229 2.440 nonbonded pdb=" O ILE E 66 " pdb=" OG1 THR E 70 " model vdw 2.246 2.440 ... (remaining 676948 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.380 Construct map_model_manager: 0.080 Extract box with map and model: 9.680 Check model and map are aligned: 0.850 Set scattering table: 0.510 Process input model: 209.630 Find NCS groups from input model: 1.750 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:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 237.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 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 : 0.007 0.092 79914 Z= 0.442 Angle : 0.828 16.229 116006 Z= 0.429 Chirality : 0.047 0.417 14347 Planarity : 0.006 0.100 8425 Dihedral : 22.437 179.940 41896 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.91 % Favored : 93.03 % Rotamer: Outliers : 0.36 % Allowed : 8.51 % Favored : 91.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.02 % Twisted Proline : 0.51 % Twisted General : 0.26 % 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: -4.40 (0.10), residues: 4789 helix: -4.23 (0.06), residues: 1334 sheet: -2.28 (0.16), residues: 836 loop : -2.39 (0.10), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 82 HIS 0.008 0.001 HIS P 5 PHE 0.051 0.002 PHE D 236 TYR 0.018 0.002 TYR a 109 ARG 0.009 0.001 ARG S 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 897 time to evaluate : 4.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 68 ILE cc_start: 0.6800 (mm) cc_final: 0.6503 (mm) REVERT: B 31 ASP cc_start: 0.8010 (t0) cc_final: 0.7521 (t0) REVERT: B 35 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7511 (tm-30) REVERT: B 36 GLN cc_start: 0.8859 (pt0) cc_final: 0.8640 (pt0) REVERT: B 40 LYS cc_start: 0.8500 (tttm) cc_final: 0.7940 (ttmt) REVERT: B 70 ASN cc_start: 0.8313 (t0) cc_final: 0.8112 (t0) REVERT: B 75 SER cc_start: 0.8520 (t) cc_final: 0.8278 (t) REVERT: B 206 ASP cc_start: 0.7432 (t0) cc_final: 0.7170 (t0) REVERT: C 27 LYS cc_start: 0.8486 (mmpt) cc_final: 0.8259 (tptp) REVERT: C 89 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8479 (mt-10) REVERT: C 95 ASN cc_start: 0.8661 (m-40) cc_final: 0.8237 (m-40) REVERT: D 63 VAL cc_start: 0.9207 (m) cc_final: 0.8984 (p) REVERT: D 103 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7627 (mttm) REVERT: D 117 ARG cc_start: 0.8035 (ttp-110) cc_final: 0.7080 (ttm-80) REVERT: d 16 LYS cc_start: 0.5817 (tppt) cc_final: 0.5255 (tmtt) REVERT: d 43 ILE cc_start: 0.6834 (mt) cc_final: 0.6596 (tt) REVERT: E 20 GLU cc_start: 0.7277 (tt0) cc_final: 0.7058 (tp30) REVERT: E 81 GLU cc_start: 0.6250 (tp30) cc_final: 0.5996 (mm-30) REVERT: E 143 ARG cc_start: 0.6610 (mpp-170) cc_final: 0.5876 (mtt180) REVERT: E 148 LYS cc_start: 0.8399 (mmpt) cc_final: 0.7808 (mttp) REVERT: E 154 ASP cc_start: 0.7928 (p0) cc_final: 0.7508 (p0) REVERT: E 178 ARG cc_start: 0.7820 (ptm-80) cc_final: 0.7603 (mpp-170) REVERT: E 201 LYS cc_start: 0.8782 (mppt) cc_final: 0.8400 (mppt) REVERT: f 100 LYS cc_start: 0.8521 (mttm) cc_final: 0.8239 (mttm) REVERT: f 109 MET cc_start: 0.8179 (ppp) cc_final: 0.7937 (pp-130) REVERT: G 23 TRP cc_start: 0.5148 (m100) cc_final: 0.4489 (m100) REVERT: G 78 MET cc_start: 0.3969 (mmt) cc_final: 0.3715 (mmp) REVERT: G 137 GLN cc_start: 0.7264 (tt0) cc_final: 0.6733 (tm-30) REVERT: G 148 ASN cc_start: 0.5746 (m-40) cc_final: 0.5308 (m-40) REVERT: H 18 VAL cc_start: 0.8654 (t) cc_final: 0.8346 (p) REVERT: H 120 ASP cc_start: 0.8388 (m-30) cc_final: 0.7851 (t0) REVERT: H 126 ASP cc_start: 0.7475 (m-30) cc_final: 0.6780 (m-30) REVERT: H 225 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7306 (mm-40) REVERT: h 4 GLN cc_start: 0.5270 (mm-40) cc_final: 0.4482 (mm-40) REVERT: h 56 GLN cc_start: 0.7374 (tm-30) cc_final: 0.7014 (tm-30) REVERT: h 63 SER cc_start: 0.3993 (m) cc_final: 0.3740 (p) REVERT: h 116 ASP cc_start: 0.7425 (p0) cc_final: 0.6835 (t70) REVERT: h 285 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6901 (mm-40) REVERT: I 28 LEU cc_start: 0.8423 (pp) cc_final: 0.8095 (mt) REVERT: J 23 LYS cc_start: 0.8191 (ptpt) cc_final: 0.7767 (ptmm) REVERT: J 80 ASP cc_start: 0.7841 (t70) cc_final: 0.7498 (t0) REVERT: J 146 GLN cc_start: 0.7865 (tp40) cc_final: 0.7654 (tp40) REVERT: J 163 GLU cc_start: 0.7619 (pp20) cc_final: 0.7196 (tm-30) REVERT: K 21 GLU cc_start: 0.7465 (tp30) cc_final: 0.6980 (tm-30) REVERT: K 26 ASP cc_start: 0.7977 (p0) cc_final: 0.7758 (m-30) REVERT: K 55 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7859 (tttm) REVERT: K 93 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7999 (mtmm) REVERT: L 46 MET cc_start: 0.7579 (ptp) cc_final: 0.6759 (pp-130) REVERT: L 65 ARG cc_start: 0.7158 (mtp180) cc_final: 0.6088 (ptp-170) REVERT: Q 62 LYS cc_start: 0.1840 (ttmt) cc_final: 0.1536 (mttt) REVERT: Q 65 LYS cc_start: 0.3849 (mptt) cc_final: 0.3596 (pptt) REVERT: Q 93 MET cc_start: 0.6816 (mtp) cc_final: 0.6341 (mmt) REVERT: Q 118 GLU cc_start: 0.5951 (tt0) cc_final: 0.5603 (tm-30) REVERT: Q 130 ARG cc_start: 0.5502 (mmm160) cc_final: 0.5206 (mmp-170) REVERT: R 22 VAL cc_start: 0.6007 (t) cc_final: 0.5691 (t) REVERT: R 41 MET cc_start: 0.5978 (mmt) cc_final: 0.5769 (tpp) REVERT: R 97 GLN cc_start: 0.6419 (tm-30) cc_final: 0.6165 (tm-30) REVERT: S 11 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7685 (ttmm) REVERT: S 23 ARG cc_start: 0.6554 (mtt-85) cc_final: 0.6267 (mtp180) REVERT: S 60 ARG cc_start: 0.7238 (ttt180) cc_final: 0.6982 (ttt180) REVERT: S 63 ARG cc_start: 0.6707 (mmt90) cc_final: 0.5986 (mtm110) REVERT: S 75 GLU cc_start: 0.6169 (pp20) cc_final: 0.5718 (pm20) REVERT: S 101 ASP cc_start: 0.7925 (p0) cc_final: 0.7652 (p0) REVERT: S 104 GLU cc_start: 0.8202 (mp0) cc_final: 0.7549 (mp0) REVERT: T 116 LYS cc_start: 0.7731 (pptt) cc_final: 0.7319 (mttm) REVERT: U 29 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8280 (tmmt) REVERT: V 34 LYS cc_start: 0.7679 (ptmt) cc_final: 0.7445 (mmpt) REVERT: V 79 ARG cc_start: 0.8165 (mtm-85) cc_final: 0.7707 (mtt90) REVERT: V 82 MET cc_start: 0.7311 (ttt) cc_final: 0.7000 (ttt) REVERT: V 86 LYS cc_start: 0.7190 (ttpt) cc_final: 0.6432 (mtmm) REVERT: W 22 ARG cc_start: 0.8116 (ptp-170) cc_final: 0.7893 (ptp-170) REVERT: W 38 GLU cc_start: 0.7589 (mp0) cc_final: 0.7350 (mp0) REVERT: W 41 LYS cc_start: 0.9012 (tppt) cc_final: 0.8749 (tppp) REVERT: W 49 GLN cc_start: 0.8435 (pt0) cc_final: 0.8055 (pt0) REVERT: W 62 MET cc_start: 0.7825 (ttm) cc_final: 0.7622 (ttm) REVERT: Z 61 ARG cc_start: 0.7762 (mmt180) cc_final: 0.7519 (mpt90) REVERT: Z 68 LYS cc_start: 0.8544 (tttt) cc_final: 0.8289 (ttmt) REVERT: Z 74 MET cc_start: 0.8372 (mtm) cc_final: 0.8131 (mtt) REVERT: Z 109 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7883 (mt-10) REVERT: M 40 GLU cc_start: 0.8200 (pm20) cc_final: 0.7678 (pm20) REVERT: M 62 LYS cc_start: 0.8146 (tptt) cc_final: 0.7694 (ttpp) REVERT: M 66 MET cc_start: 0.8436 (mmt) cc_final: 0.8149 (mmm) REVERT: M 127 ARG cc_start: 0.7649 (mtp180) cc_final: 0.7080 (mmm-85) REVERT: M 199 GLU cc_start: 0.7124 (mp0) cc_final: 0.6818 (mp0) REVERT: M 211 LYS cc_start: 0.8260 (tttm) cc_final: 0.7968 (ttmm) REVERT: M 214 ASN cc_start: 0.8710 (m-40) cc_final: 0.8227 (m-40) REVERT: M 237 SER cc_start: 0.8201 (t) cc_final: 0.7921 (t) REVERT: M 242 LYS cc_start: 0.8247 (mptt) cc_final: 0.8002 (mmtp) REVERT: M 251 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7590 (mt-10) REVERT: O 1 MET cc_start: 0.4031 (ttp) cc_final: 0.3452 (ttp) REVERT: O 8 ARG cc_start: 0.8282 (mtp180) cc_final: 0.7725 (mtm110) REVERT: O 57 ASP cc_start: 0.8305 (t0) cc_final: 0.7819 (t0) REVERT: O 79 LYS cc_start: 0.7736 (mttm) cc_final: 0.7339 (mtpt) REVERT: O 97 ARG cc_start: 0.6988 (ptm160) cc_final: 0.6370 (ttm110) REVERT: O 104 LYS cc_start: 0.7995 (tttm) cc_final: 0.7613 (tptm) REVERT: O 121 GLN cc_start: 0.8053 (pt0) cc_final: 0.6970 (pm20) REVERT: O 124 ASP cc_start: 0.6873 (m-30) cc_final: 0.6296 (m-30) REVERT: P 30 SER cc_start: 0.8709 (p) cc_final: 0.8373 (t) REVERT: P 57 SER cc_start: 0.8348 (t) cc_final: 0.8139 (p) REVERT: P 69 ASN cc_start: 0.8193 (m-40) cc_final: 0.7838 (m-40) REVERT: P 103 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7288 (mm-30) REVERT: X 63 LYS cc_start: 0.5892 (mmtt) cc_final: 0.5600 (mptp) REVERT: Y 90 GLN cc_start: 0.8287 (pt0) cc_final: 0.8061 (pt0) REVERT: c 53 GLU cc_start: 0.7417 (pt0) cc_final: 0.6926 (pm20) REVERT: e 14 GLU cc_start: 0.8227 (pt0) cc_final: 0.7889 (pt0) REVERT: e 15 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7609 (mm-30) REVERT: e 16 LYS cc_start: 0.8449 (tptp) cc_final: 0.8115 (tttp) REVERT: e 79 PHE cc_start: 0.9095 (p90) cc_final: 0.8892 (p90) REVERT: e 81 ARG cc_start: 0.7899 (ttt180) cc_final: 0.7626 (ttt-90) outliers start: 15 outliers final: 9 residues processed: 910 average time/residue: 1.7697 time to fit residues: 2068.6022 Evaluate side-chains 626 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 617 time to evaluate : 4.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain c residue 125 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 3.9990 chunk 485 optimal weight: 20.0000 chunk 269 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 327 optimal weight: 4.9990 chunk 259 optimal weight: 0.9980 chunk 501 optimal weight: 30.0000 chunk 194 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 373 optimal weight: 0.4980 chunk 581 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 64 ASN a 112 ASN B 84 GLN B 141 ASN b 17 HIS C 149 GLN C 158 HIS C 186 ASN D 267 GLN D 272 HIS d 24 GLN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 ASN E 57 ASN f 88 GLN f 117 ASN ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 177 GLN H 225 GLN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 187 ASN h 215 GLN h 296 GLN h 305 ASN I 25 GLN I 44 ASN I 97 GLN I 162 GLN J 64 ASN K 125 HIS L 39 ASN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 GLN R 11 GLN R 77 HIS R 80 GLN ** R 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 HIS T 17 ASN T 19 ASN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN F 178 ASN M 17 HIS M 50 ASN M 67 GLN M 98 ASN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 112 HIS O 154 GLN P 5 HIS X 32 HIS e 26 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 79914 Z= 0.187 Angle : 0.621 12.944 116006 Z= 0.315 Chirality : 0.039 0.243 14347 Planarity : 0.005 0.073 8425 Dihedral : 23.487 179.994 31900 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.20 % Favored : 94.78 % Rotamer: Outliers : 3.01 % Allowed : 16.67 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.94 (0.11), residues: 4789 helix: -2.14 (0.11), residues: 1390 sheet: -1.68 (0.17), residues: 808 loop : -1.90 (0.11), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 7 HIS 0.005 0.001 HIS J 22 PHE 0.020 0.001 PHE D 236 TYR 0.014 0.001 TYR K 35 ARG 0.009 0.000 ARG D 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 652 time to evaluate : 4.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 68 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.5718 (tp) REVERT: a 69 THR cc_start: 0.7230 (OUTLIER) cc_final: 0.6796 (t) REVERT: a 106 GLN cc_start: 0.6812 (tp40) cc_final: 0.6609 (tp40) REVERT: B 35 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7306 (tm-30) REVERT: B 36 GLN cc_start: 0.8825 (pt0) cc_final: 0.8586 (pt0) REVERT: B 40 LYS cc_start: 0.8548 (tttm) cc_final: 0.8150 (ttmt) REVERT: b 19 GLN cc_start: 0.8298 (pm20) cc_final: 0.7921 (pm20) REVERT: b 62 TYR cc_start: 0.8411 (t80) cc_final: 0.8118 (t80) REVERT: C 89 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8328 (mt-10) REVERT: C 95 ASN cc_start: 0.8687 (m-40) cc_final: 0.8163 (m-40) REVERT: C 103 MET cc_start: 0.8388 (ptm) cc_final: 0.8158 (ttp) REVERT: C 120 MET cc_start: 0.8869 (ttp) cc_final: 0.8647 (ttp) REVERT: D 92 GLU cc_start: 0.8527 (mp0) cc_final: 0.7801 (mp0) REVERT: D 103 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7662 (mttm) REVERT: D 104 ASP cc_start: 0.7957 (p0) cc_final: 0.7739 (p0) REVERT: D 187 ARG cc_start: 0.8813 (mtp-110) cc_final: 0.8474 (mtp180) REVERT: d 16 LYS cc_start: 0.5806 (tppt) cc_final: 0.5076 (tmtt) REVERT: d 24 GLN cc_start: 0.5179 (mp10) cc_final: 0.4945 (mp10) REVERT: d 45 ASN cc_start: 0.5620 (OUTLIER) cc_final: 0.5228 (p0) REVERT: E 81 GLU cc_start: 0.6513 (tp30) cc_final: 0.6248 (mm-30) REVERT: E 143 ARG cc_start: 0.6714 (mpp-170) cc_final: 0.5794 (mtt180) REVERT: E 148 LYS cc_start: 0.8505 (mmpt) cc_final: 0.7983 (mttp) REVERT: E 150 MET cc_start: 0.7501 (mmm) cc_final: 0.7026 (mtt) REVERT: E 178 ARG cc_start: 0.7762 (ptm-80) cc_final: 0.7546 (mpp-170) REVERT: E 193 ASP cc_start: 0.5609 (p0) cc_final: 0.5280 (p0) REVERT: E 201 LYS cc_start: 0.8800 (mppt) cc_final: 0.8516 (mppt) REVERT: f 100 LYS cc_start: 0.8528 (mttm) cc_final: 0.8273 (mttm) REVERT: f 113 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7353 (mtm-85) REVERT: G 78 MET cc_start: 0.3739 (mmt) cc_final: 0.3472 (mmp) REVERT: G 137 GLN cc_start: 0.7115 (tt0) cc_final: 0.6597 (tm-30) REVERT: G 191 LYS cc_start: 0.6132 (tptp) cc_final: 0.5839 (mtpp) REVERT: H 120 ASP cc_start: 0.8350 (m-30) cc_final: 0.7940 (t0) REVERT: H 133 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6736 (pp) REVERT: H 155 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7894 (mm-40) REVERT: H 225 GLN cc_start: 0.7604 (mm110) cc_final: 0.7291 (mm-40) REVERT: h 116 ASP cc_start: 0.7392 (p0) cc_final: 0.6912 (t70) REVERT: h 118 ARG cc_start: 0.7209 (tpt170) cc_final: 0.6879 (ttp80) REVERT: h 196 ASN cc_start: 0.8048 (t0) cc_final: 0.7639 (t0) REVERT: I 28 LEU cc_start: 0.8208 (pp) cc_final: 0.7634 (mt) REVERT: I 32 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8565 (mpp) REVERT: I 37 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7795 (mmtp) REVERT: I 184 ASP cc_start: 0.8566 (p0) cc_final: 0.8261 (p0) REVERT: J 23 LYS cc_start: 0.8179 (ptpt) cc_final: 0.7788 (ptmm) REVERT: J 71 CYS cc_start: 0.8437 (t) cc_final: 0.7612 (m) REVERT: J 80 ASP cc_start: 0.7865 (t70) cc_final: 0.7607 (t0) REVERT: J 88 ASN cc_start: 0.7707 (m-40) cc_final: 0.7500 (t0) REVERT: J 92 ARG cc_start: 0.7769 (mtm110) cc_final: 0.7515 (ttp-110) REVERT: J 149 TYR cc_start: 0.8186 (m-10) cc_final: 0.7935 (m-80) REVERT: K 21 GLU cc_start: 0.7304 (tp30) cc_final: 0.7059 (tt0) REVERT: K 26 ASP cc_start: 0.7758 (p0) cc_final: 0.7484 (m-30) REVERT: K 93 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7876 (mtmm) REVERT: K 122 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.8175 (p) REVERT: L 29 MET cc_start: 0.6050 (ppp) cc_final: 0.5739 (pp-130) REVERT: L 65 ARG cc_start: 0.6905 (mtp180) cc_final: 0.6022 (ptt-90) REVERT: Q 93 MET cc_start: 0.6806 (mtp) cc_final: 0.6231 (mmt) REVERT: Q 111 MET cc_start: 0.1598 (OUTLIER) cc_final: 0.0831 (mtm) REVERT: Q 118 GLU cc_start: 0.5845 (tt0) cc_final: 0.5542 (tm-30) REVERT: Q 124 LYS cc_start: 0.7232 (mptt) cc_final: 0.6918 (mmtm) REVERT: Q 130 ARG cc_start: 0.5389 (mmm160) cc_final: 0.5075 (mmp-170) REVERT: R 27 ARG cc_start: 0.5214 (ptm160) cc_final: 0.4744 (ttm110) REVERT: S 11 LYS cc_start: 0.8002 (ttpt) cc_final: 0.7670 (tptp) REVERT: S 23 ARG cc_start: 0.6554 (mtt-85) cc_final: 0.5776 (mtt90) REVERT: S 66 VAL cc_start: 0.6263 (OUTLIER) cc_final: 0.5971 (m) REVERT: S 84 TYR cc_start: 0.7648 (t80) cc_final: 0.7292 (t80) REVERT: S 94 GLU cc_start: 0.7251 (pm20) cc_final: 0.6865 (mm-30) REVERT: S 120 THR cc_start: 0.8743 (t) cc_final: 0.8378 (p) REVERT: T 116 LYS cc_start: 0.7667 (pptt) cc_final: 0.7294 (mttm) REVERT: U 29 LYS cc_start: 0.8752 (tmtt) cc_final: 0.8295 (tmmt) REVERT: V 75 LYS cc_start: 0.6688 (mptt) cc_final: 0.6218 (mmtm) REVERT: V 77 TRP cc_start: 0.7139 (m100) cc_final: 0.6353 (m-90) REVERT: V 79 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7587 (mtt90) REVERT: V 82 MET cc_start: 0.7197 (ttt) cc_final: 0.6937 (ttt) REVERT: V 86 LYS cc_start: 0.7080 (ttpt) cc_final: 0.6178 (mtmm) REVERT: W 7 GLU cc_start: 0.7391 (mp0) cc_final: 0.7190 (mp0) REVERT: W 41 LYS cc_start: 0.9031 (tppt) cc_final: 0.8738 (tppp) REVERT: Z 68 LYS cc_start: 0.8483 (tttt) cc_final: 0.8268 (ttmm) REVERT: Z 72 PHE cc_start: 0.8016 (m-80) cc_final: 0.7783 (m-80) REVERT: Z 74 MET cc_start: 0.8409 (mtm) cc_final: 0.8186 (mtt) REVERT: Z 109 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7902 (mt-10) REVERT: F 152 ASP cc_start: 0.7999 (t0) cc_final: 0.7623 (t70) REVERT: F 154 TYR cc_start: 0.8222 (m-80) cc_final: 0.7988 (m-80) REVERT: M 40 GLU cc_start: 0.8095 (pm20) cc_final: 0.7476 (pm20) REVERT: M 62 LYS cc_start: 0.7922 (tptt) cc_final: 0.7567 (ttpt) REVERT: M 66 MET cc_start: 0.8160 (mmt) cc_final: 0.7916 (mmm) REVERT: M 211 LYS cc_start: 0.8136 (tttm) cc_final: 0.7828 (ttmm) REVERT: M 242 LYS cc_start: 0.8328 (mptt) cc_final: 0.8090 (mmtp) REVERT: O 1 MET cc_start: 0.3800 (ttp) cc_final: 0.3173 (ttp) REVERT: O 8 ARG cc_start: 0.8212 (mtp180) cc_final: 0.7653 (mtp180) REVERT: O 49 GLU cc_start: 0.8063 (tp30) cc_final: 0.7713 (tp30) REVERT: O 79 LYS cc_start: 0.7664 (mttm) cc_final: 0.7325 (mtpt) REVERT: O 97 ARG cc_start: 0.6992 (ptm160) cc_final: 0.6418 (ttm110) REVERT: O 104 LYS cc_start: 0.8001 (tttm) cc_final: 0.7719 (tptp) REVERT: O 121 GLN cc_start: 0.8053 (pt0) cc_final: 0.7054 (pm20) REVERT: O 124 ASP cc_start: 0.6999 (m-30) cc_final: 0.6332 (m-30) REVERT: O 130 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.6921 (tt0) REVERT: O 144 LYS cc_start: 0.7796 (ttmm) cc_final: 0.7462 (ttpp) REVERT: P 36 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: P 69 ASN cc_start: 0.8074 (m-40) cc_final: 0.7777 (m-40) REVERT: P 103 GLU cc_start: 0.7226 (mm-30) cc_final: 0.7023 (mm-30) REVERT: P 106 ARG cc_start: 0.6754 (tpp80) cc_final: 0.6488 (tpp80) REVERT: X 63 LYS cc_start: 0.5589 (mmtt) cc_final: 0.5309 (mptp) REVERT: X 83 GLN cc_start: 0.8136 (tp-100) cc_final: 0.7777 (tp40) REVERT: X 87 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7552 (mt-10) REVERT: Y 26 LEU cc_start: 0.8841 (tt) cc_final: 0.8595 (tm) REVERT: Y 90 GLN cc_start: 0.7946 (pt0) cc_final: 0.7612 (pt0) REVERT: Y 114 GLU cc_start: 0.8265 (pt0) cc_final: 0.8056 (pt0) REVERT: c 53 GLU cc_start: 0.7304 (pt0) cc_final: 0.6842 (pm20) REVERT: e 1 MET cc_start: 0.5235 (OUTLIER) cc_final: 0.4868 (ppp) REVERT: e 15 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7475 (mm-30) REVERT: e 16 LYS cc_start: 0.8368 (tptp) cc_final: 0.8075 (tttp) REVERT: e 79 PHE cc_start: 0.9142 (p90) cc_final: 0.8899 (p90) REVERT: e 80 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7876 (ttp-110) outliers start: 126 outliers final: 50 residues processed: 724 average time/residue: 1.7213 time to fit residues: 1619.8942 Evaluate side-chains 664 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 600 time to evaluate : 4.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain a residue 69 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 45 ASN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 19 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 32 MET Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 107 LYS Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain U residue 8 ASP Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 75 ILE Chi-restraints excluded: chain Z residue 96 LEU Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 130 GLU Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 58 HIS Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain c residue 15 SER Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 80 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 9.9990 chunk 180 optimal weight: 1.9990 chunk 483 optimal weight: 0.8980 chunk 395 optimal weight: 3.9990 chunk 160 optimal weight: 40.0000 chunk 582 optimal weight: 4.9990 chunk 628 optimal weight: 5.9990 chunk 518 optimal weight: 10.0000 chunk 577 optimal weight: 0.5980 chunk 198 optimal weight: 3.9990 chunk 467 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN D 134 ASN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN G 110 GLN ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 162 GLN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN R 80 GLN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 GLN T 72 GLN Z 106 GLN O 83 GLN O 154 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 79914 Z= 0.212 Angle : 0.581 10.969 116006 Z= 0.298 Chirality : 0.038 0.384 14347 Planarity : 0.005 0.066 8425 Dihedral : 23.278 179.867 31899 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.55 % Favored : 94.42 % Rotamer: Outliers : 4.02 % Allowed : 18.13 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.22 (0.11), residues: 4789 helix: -1.13 (0.13), residues: 1403 sheet: -1.42 (0.18), residues: 816 loop : -1.66 (0.12), residues: 2570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP h 90 HIS 0.006 0.001 HIS J 22 PHE 0.020 0.001 PHE D 236 TYR 0.015 0.001 TYR K 35 ARG 0.010 0.000 ARG d 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 638 time to evaluate : 4.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 68 ILE cc_start: 0.6842 (OUTLIER) cc_final: 0.5879 (tp) REVERT: a 106 GLN cc_start: 0.6810 (tp40) cc_final: 0.6500 (tp40) REVERT: B 31 ASP cc_start: 0.7828 (t0) cc_final: 0.7332 (t0) REVERT: B 35 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7304 (tm-30) REVERT: B 36 GLN cc_start: 0.8804 (pt0) cc_final: 0.8591 (pt0) REVERT: B 40 LYS cc_start: 0.8519 (tttm) cc_final: 0.8189 (ttmm) REVERT: b 55 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: b 62 TYR cc_start: 0.8366 (t80) cc_final: 0.8040 (t80) REVERT: b 82 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8603 (mtmt) REVERT: C 89 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8346 (mt-10) REVERT: C 95 ASN cc_start: 0.8734 (m-40) cc_final: 0.8194 (m-40) REVERT: C 103 MET cc_start: 0.8326 (ptm) cc_final: 0.8123 (ttp) REVERT: C 120 MET cc_start: 0.8873 (ttp) cc_final: 0.8657 (ttp) REVERT: D 72 ASP cc_start: 0.7314 (m-30) cc_final: 0.7099 (m-30) REVERT: D 103 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7682 (mttm) REVERT: D 104 ASP cc_start: 0.8020 (p0) cc_final: 0.7792 (p0) REVERT: D 117 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7184 (ttm-80) REVERT: D 187 ARG cc_start: 0.8837 (mtp-110) cc_final: 0.8420 (mtp180) REVERT: D 227 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.8070 (ttm170) REVERT: d 16 LYS cc_start: 0.5673 (tppt) cc_final: 0.5178 (tmtt) REVERT: d 24 GLN cc_start: 0.5296 (mp10) cc_final: 0.5080 (mp10) REVERT: d 45 ASN cc_start: 0.6008 (OUTLIER) cc_final: 0.5438 (m-40) REVERT: E 1 MET cc_start: 0.5303 (tpt) cc_final: 0.4974 (tpt) REVERT: E 81 GLU cc_start: 0.6572 (tp30) cc_final: 0.6323 (mm-30) REVERT: E 128 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7657 (tp30) REVERT: E 141 LYS cc_start: 0.7411 (ttpt) cc_final: 0.6945 (pttt) REVERT: E 148 LYS cc_start: 0.8464 (mmpt) cc_final: 0.7979 (mttp) REVERT: E 150 MET cc_start: 0.7546 (mmm) cc_final: 0.7044 (mtt) REVERT: E 192 TRP cc_start: 0.7478 (t60) cc_final: 0.7274 (t60) REVERT: E 201 LYS cc_start: 0.8894 (mppt) cc_final: 0.8525 (mppt) REVERT: f 95 GLN cc_start: 0.8524 (pt0) cc_final: 0.8189 (pt0) REVERT: f 100 LYS cc_start: 0.8481 (mttm) cc_final: 0.8227 (mttm) REVERT: f 113 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7206 (mtm-85) REVERT: G 78 MET cc_start: 0.3786 (mmt) cc_final: 0.3469 (mmp) REVERT: G 137 GLN cc_start: 0.7073 (tt0) cc_final: 0.6497 (tm-30) REVERT: G 191 LYS cc_start: 0.6128 (tptp) cc_final: 0.5653 (tttm) REVERT: H 120 ASP cc_start: 0.8440 (m-30) cc_final: 0.7958 (t0) REVERT: H 133 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6850 (pp) REVERT: H 145 PHE cc_start: 0.8597 (m-80) cc_final: 0.8383 (m-10) REVERT: H 155 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7865 (mm-40) REVERT: H 225 GLN cc_start: 0.7561 (mm110) cc_final: 0.7253 (mp10) REVERT: h 116 ASP cc_start: 0.7408 (p0) cc_final: 0.6953 (t70) REVERT: h 118 ARG cc_start: 0.7186 (tpt170) cc_final: 0.6852 (ttp80) REVERT: I 20 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: I 28 LEU cc_start: 0.8317 (pp) cc_final: 0.7669 (mt) REVERT: I 32 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8658 (mpp) REVERT: I 43 LEU cc_start: 0.7854 (mt) cc_final: 0.7271 (mp) REVERT: I 57 ARG cc_start: 0.7207 (tpp-160) cc_final: 0.6936 (mtm110) REVERT: I 127 ASP cc_start: 0.7841 (m-30) cc_final: 0.7604 (m-30) REVERT: I 184 ASP cc_start: 0.8586 (p0) cc_final: 0.8253 (p0) REVERT: J 23 LYS cc_start: 0.8259 (ptpt) cc_final: 0.7900 (ptmm) REVERT: J 71 CYS cc_start: 0.8403 (t) cc_final: 0.7651 (m) REVERT: J 88 ASN cc_start: 0.7672 (m-40) cc_final: 0.7444 (t0) REVERT: J 107 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8103 (p) REVERT: J 205 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.6742 (tmm-80) REVERT: K 21 GLU cc_start: 0.7207 (tp30) cc_final: 0.6979 (tt0) REVERT: K 26 ASP cc_start: 0.7709 (p0) cc_final: 0.7462 (m-30) REVERT: K 93 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7887 (mtmm) REVERT: K 122 SER cc_start: 0.8506 (OUTLIER) cc_final: 0.8251 (p) REVERT: L 29 MET cc_start: 0.5919 (ppp) cc_final: 0.5555 (pp-130) REVERT: L 65 ARG cc_start: 0.6671 (mtp180) cc_final: 0.5695 (mtt90) REVERT: N 42 LEU cc_start: 0.6212 (mp) cc_final: 0.5968 (pt) REVERT: Q 70 MET cc_start: 0.4378 (mmm) cc_final: 0.4154 (mmm) REVERT: Q 93 MET cc_start: 0.6840 (mtp) cc_final: 0.6240 (mmt) REVERT: Q 111 MET cc_start: 0.1631 (OUTLIER) cc_final: 0.0866 (mtm) REVERT: Q 130 ARG cc_start: 0.5449 (mmm160) cc_final: 0.5141 (mmp-170) REVERT: S 11 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7626 (tptp) REVERT: S 18 GLU cc_start: 0.8505 (tt0) cc_final: 0.8234 (tt0) REVERT: S 23 ARG cc_start: 0.6589 (mtt-85) cc_final: 0.6387 (mtp180) REVERT: S 36 GLU cc_start: 0.6911 (tt0) cc_final: 0.6542 (tp30) REVERT: S 45 LYS cc_start: 0.6118 (OUTLIER) cc_final: 0.5311 (tptm) REVERT: S 126 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8653 (ptm) REVERT: U 29 LYS cc_start: 0.8749 (tmtt) cc_final: 0.8222 (tmmt) REVERT: V 34 LYS cc_start: 0.7656 (mmpt) cc_final: 0.7072 (pttt) REVERT: V 75 LYS cc_start: 0.6668 (mptt) cc_final: 0.6297 (mmtm) REVERT: V 77 TRP cc_start: 0.7103 (m100) cc_final: 0.6778 (m-90) REVERT: V 79 ARG cc_start: 0.7887 (mtm-85) cc_final: 0.7575 (mtt90) REVERT: V 82 MET cc_start: 0.7173 (ttt) cc_final: 0.6916 (ttt) REVERT: V 86 LYS cc_start: 0.7265 (ttpt) cc_final: 0.6393 (mtmm) REVERT: W 41 LYS cc_start: 0.9068 (tppt) cc_final: 0.8739 (tppp) REVERT: W 74 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8279 (ttpt) REVERT: Z 39 GLU cc_start: 0.8192 (tp30) cc_final: 0.7644 (tp30) REVERT: Z 46 LYS cc_start: 0.8644 (mptt) cc_final: 0.8392 (tmmt) REVERT: Z 68 LYS cc_start: 0.8571 (tttt) cc_final: 0.8353 (ttmt) REVERT: Z 72 PHE cc_start: 0.8106 (m-80) cc_final: 0.7855 (m-80) REVERT: Z 74 MET cc_start: 0.8430 (mtm) cc_final: 0.8203 (mtt) REVERT: F 152 ASP cc_start: 0.8017 (t0) cc_final: 0.7569 (t70) REVERT: F 154 TYR cc_start: 0.8208 (m-80) cc_final: 0.7943 (m-80) REVERT: M 40 GLU cc_start: 0.8090 (pm20) cc_final: 0.7449 (pm20) REVERT: M 62 LYS cc_start: 0.7841 (tptt) cc_final: 0.7533 (ttpt) REVERT: M 66 MET cc_start: 0.8096 (mmt) cc_final: 0.7816 (mmm) REVERT: M 211 LYS cc_start: 0.8094 (tttm) cc_final: 0.7815 (ttmm) REVERT: M 246 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7922 (pp) REVERT: O 1 MET cc_start: 0.3792 (ttp) cc_final: 0.3235 (ttp) REVERT: O 8 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7797 (mtm110) REVERT: O 49 GLU cc_start: 0.8083 (tp30) cc_final: 0.7759 (tp30) REVERT: O 57 ASP cc_start: 0.7704 (t0) cc_final: 0.6728 (t70) REVERT: O 79 LYS cc_start: 0.7677 (mttm) cc_final: 0.7345 (mtpt) REVERT: O 97 ARG cc_start: 0.6970 (ptm160) cc_final: 0.6417 (ttm110) REVERT: O 104 LYS cc_start: 0.8034 (tttm) cc_final: 0.7719 (tptp) REVERT: O 121 GLN cc_start: 0.8146 (pt0) cc_final: 0.7222 (pm20) REVERT: O 124 ASP cc_start: 0.7043 (m-30) cc_final: 0.6252 (m-30) REVERT: O 144 LYS cc_start: 0.7839 (ttmm) cc_final: 0.7540 (ttpp) REVERT: P 36 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: P 69 ASN cc_start: 0.8087 (m-40) cc_final: 0.7773 (m-40) REVERT: P 103 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7013 (mm-30) REVERT: X 61 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8555 (mttp) REVERT: X 63 LYS cc_start: 0.5844 (mmtt) cc_final: 0.5522 (mptp) REVERT: X 83 GLN cc_start: 0.8101 (tp-100) cc_final: 0.7734 (tp40) REVERT: X 87 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7556 (mt-10) REVERT: Y 51 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7878 (tt0) REVERT: Y 90 GLN cc_start: 0.7883 (pt0) cc_final: 0.7466 (pt0) REVERT: c 53 GLU cc_start: 0.7325 (pt0) cc_final: 0.6811 (pm20) REVERT: c 96 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7381 (mm-30) REVERT: e 15 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7495 (mm-30) outliers start: 168 outliers final: 79 residues processed: 737 average time/residue: 1.6160 time to fit residues: 1561.4362 Evaluate side-chains 693 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 595 time to evaluate : 4.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 90 GLU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain d residue 45 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 32 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 205 ARG Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 75 ILE Chi-restraints excluded: chain Z residue 84 LYS Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 58 HIS Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 61 LYS Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 105 PHE Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain e residue 80 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 3.9990 chunk 437 optimal weight: 40.0000 chunk 302 optimal weight: 3.9990 chunk 64 optimal weight: 50.0000 chunk 277 optimal weight: 40.0000 chunk 390 optimal weight: 0.0050 chunk 584 optimal weight: 0.2980 chunk 618 optimal weight: 5.9990 chunk 305 optimal weight: 6.9990 chunk 553 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 overall best weight: 2.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 ASN G 110 GLN ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN I 97 GLN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 11 GLN R 80 GLN Z 106 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 79914 Z= 0.219 Angle : 0.575 12.616 116006 Z= 0.294 Chirality : 0.038 0.246 14347 Planarity : 0.004 0.063 8425 Dihedral : 23.193 179.809 31899 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.26 % Favored : 94.72 % Rotamer: Outliers : 3.97 % Allowed : 20.04 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.85 (0.12), residues: 4789 helix: -0.68 (0.14), residues: 1403 sheet: -1.25 (0.18), residues: 832 loop : -1.51 (0.12), residues: 2554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 23 HIS 0.006 0.001 HIS J 22 PHE 0.023 0.001 PHE E 125 TYR 0.019 0.001 TYR M 121 ARG 0.010 0.000 ARG H 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 633 time to evaluate : 4.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 58 LEU cc_start: 0.4783 (tp) cc_final: 0.4360 (mp) REVERT: a 106 GLN cc_start: 0.6688 (tp40) cc_final: 0.6464 (tp40) REVERT: B 31 ASP cc_start: 0.7754 (t0) cc_final: 0.7398 (t0) REVERT: B 35 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7292 (tm-30) REVERT: B 40 LYS cc_start: 0.8540 (tttm) cc_final: 0.8211 (ttmt) REVERT: b 62 TYR cc_start: 0.8382 (t80) cc_final: 0.8110 (t80) REVERT: b 82 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8596 (mtmt) REVERT: C 89 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8354 (mt-10) REVERT: C 95 ASN cc_start: 0.8745 (m-40) cc_final: 0.8230 (m-40) REVERT: C 103 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8055 (ttp) REVERT: C 120 MET cc_start: 0.8925 (ttp) cc_final: 0.8718 (ttp) REVERT: D 72 ASP cc_start: 0.7287 (m-30) cc_final: 0.7057 (m-30) REVERT: D 103 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7680 (mttm) REVERT: D 117 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7082 (ttm-80) REVERT: D 145 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8155 (mtmt) REVERT: D 152 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7795 (ttp80) REVERT: D 187 ARG cc_start: 0.8802 (mtp-110) cc_final: 0.8544 (mtp180) REVERT: D 227 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.8043 (ttm170) REVERT: d 16 LYS cc_start: 0.5803 (tppt) cc_final: 0.5096 (tmtt) REVERT: E 1 MET cc_start: 0.5507 (tpt) cc_final: 0.5207 (tpt) REVERT: E 81 GLU cc_start: 0.6398 (tp30) cc_final: 0.6152 (mm-30) REVERT: E 141 LYS cc_start: 0.7362 (ttpt) cc_final: 0.6971 (pttp) REVERT: E 148 LYS cc_start: 0.8457 (mmpt) cc_final: 0.7960 (mttt) REVERT: E 150 MET cc_start: 0.7590 (mmm) cc_final: 0.7125 (mtt) REVERT: E 176 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8584 (mm) REVERT: E 192 TRP cc_start: 0.7495 (t60) cc_final: 0.7224 (t60) REVERT: E 201 LYS cc_start: 0.8924 (mppt) cc_final: 0.8515 (mppt) REVERT: f 95 GLN cc_start: 0.8537 (pt0) cc_final: 0.8217 (pt0) REVERT: f 100 LYS cc_start: 0.8476 (mttm) cc_final: 0.8220 (mttm) REVERT: f 113 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7319 (mtm-85) REVERT: G 78 MET cc_start: 0.3726 (mmt) cc_final: 0.3486 (mmp) REVERT: G 137 GLN cc_start: 0.7111 (tt0) cc_final: 0.6564 (tm-30) REVERT: G 191 LYS cc_start: 0.6119 (tptp) cc_final: 0.5800 (mtpp) REVERT: H 22 ARG cc_start: 0.8626 (mtm110) cc_final: 0.8412 (ttp-110) REVERT: H 120 ASP cc_start: 0.8433 (m-30) cc_final: 0.7972 (t0) REVERT: H 133 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6808 (pp) REVERT: H 225 GLN cc_start: 0.7612 (mm110) cc_final: 0.7300 (mp10) REVERT: h 116 ASP cc_start: 0.7404 (p0) cc_final: 0.6953 (t70) REVERT: h 118 ARG cc_start: 0.7117 (tpt170) cc_final: 0.6783 (ttp80) REVERT: I 20 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: I 28 LEU cc_start: 0.8375 (pp) cc_final: 0.7606 (mt) REVERT: I 32 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8702 (mpp) REVERT: I 43 LEU cc_start: 0.7854 (mt) cc_final: 0.7290 (mp) REVERT: I 57 ARG cc_start: 0.7285 (tpp-160) cc_final: 0.6999 (mtm110) REVERT: I 127 ASP cc_start: 0.7762 (m-30) cc_final: 0.7549 (m-30) REVERT: I 131 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: I 184 ASP cc_start: 0.8574 (p0) cc_final: 0.8222 (p0) REVERT: J 23 LYS cc_start: 0.8278 (ptpt) cc_final: 0.7953 (ptmm) REVERT: J 88 ASN cc_start: 0.7722 (m-40) cc_final: 0.7478 (t0) REVERT: J 107 THR cc_start: 0.8420 (m) cc_final: 0.8178 (p) REVERT: J 205 ARG cc_start: 0.7105 (OUTLIER) cc_final: 0.6836 (tmm-80) REVERT: K 21 GLU cc_start: 0.7128 (tp30) cc_final: 0.6925 (tt0) REVERT: K 26 ASP cc_start: 0.7696 (p0) cc_final: 0.7453 (m-30) REVERT: K 79 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.6876 (ttp-170) REVERT: K 93 LYS cc_start: 0.8113 (mtpt) cc_final: 0.7883 (mtmm) REVERT: K 122 SER cc_start: 0.8482 (OUTLIER) cc_final: 0.8232 (p) REVERT: L 29 MET cc_start: 0.5908 (ppp) cc_final: 0.5424 (pp-130) REVERT: L 65 ARG cc_start: 0.6583 (mtp180) cc_final: 0.5805 (mtt90) REVERT: N 42 LEU cc_start: 0.6083 (mp) cc_final: 0.5746 (pt) REVERT: Q 93 MET cc_start: 0.6794 (mtp) cc_final: 0.6199 (mmt) REVERT: Q 130 ARG cc_start: 0.5543 (mmm160) cc_final: 0.5243 (mmp-170) REVERT: R 24 HIS cc_start: 0.6027 (t70) cc_final: 0.5724 (t70) REVERT: R 27 ARG cc_start: 0.5242 (ptm160) cc_final: 0.4821 (ttm110) REVERT: S 11 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7634 (tptp) REVERT: S 18 GLU cc_start: 0.8493 (tt0) cc_final: 0.8205 (tt0) REVERT: S 45 LYS cc_start: 0.6232 (OUTLIER) cc_final: 0.5434 (tptm) REVERT: U 74 SER cc_start: 0.4773 (t) cc_final: 0.4476 (m) REVERT: V 56 MET cc_start: 0.8184 (mmp) cc_final: 0.7660 (mmm) REVERT: V 79 ARG cc_start: 0.7845 (mtm-85) cc_final: 0.7540 (mtt90) REVERT: V 86 LYS cc_start: 0.7283 (ttpt) cc_final: 0.6540 (mtmm) REVERT: W 41 LYS cc_start: 0.9063 (tppt) cc_final: 0.8713 (tppp) REVERT: Z 39 GLU cc_start: 0.8210 (tp30) cc_final: 0.7710 (tp30) REVERT: Z 46 LYS cc_start: 0.8596 (mptt) cc_final: 0.8372 (tmmt) REVERT: Z 68 LYS cc_start: 0.8541 (tttt) cc_final: 0.8182 (ttmm) REVERT: Z 72 PHE cc_start: 0.8134 (m-80) cc_final: 0.7905 (m-80) REVERT: Z 74 MET cc_start: 0.8415 (mtm) cc_final: 0.8183 (mtt) REVERT: F 152 ASP cc_start: 0.8040 (t0) cc_final: 0.7833 (t70) REVERT: F 154 TYR cc_start: 0.8176 (m-80) cc_final: 0.7919 (m-80) REVERT: M 40 GLU cc_start: 0.8076 (pm20) cc_final: 0.7417 (pm20) REVERT: M 62 LYS cc_start: 0.7838 (tptt) cc_final: 0.7514 (ttpt) REVERT: M 66 MET cc_start: 0.8088 (mmt) cc_final: 0.7815 (mmm) REVERT: M 211 LYS cc_start: 0.8126 (tttm) cc_final: 0.7828 (ttmm) REVERT: M 246 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7789 (pp) REVERT: M 251 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7413 (mt-10) REVERT: O 1 MET cc_start: 0.3727 (ttp) cc_final: 0.3215 (ttp) REVERT: O 8 ARG cc_start: 0.8127 (mtp180) cc_final: 0.7804 (mtm110) REVERT: O 49 GLU cc_start: 0.8143 (tp30) cc_final: 0.7807 (tp30) REVERT: O 57 ASP cc_start: 0.7661 (t0) cc_final: 0.6708 (t70) REVERT: O 79 LYS cc_start: 0.7672 (mttm) cc_final: 0.7379 (mtpt) REVERT: O 97 ARG cc_start: 0.7052 (ptm160) cc_final: 0.6474 (ttm110) REVERT: O 104 LYS cc_start: 0.8030 (tttm) cc_final: 0.7801 (tptp) REVERT: O 121 GLN cc_start: 0.8147 (pt0) cc_final: 0.7146 (pm20) REVERT: O 124 ASP cc_start: 0.7052 (m-30) cc_final: 0.6228 (m-30) REVERT: O 144 LYS cc_start: 0.7866 (ttmm) cc_final: 0.7568 (ttpp) REVERT: P 36 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: P 69 ASN cc_start: 0.8187 (m-40) cc_final: 0.7842 (m-40) REVERT: P 103 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7130 (mm-30) REVERT: X 63 LYS cc_start: 0.5867 (mmtt) cc_final: 0.5529 (mptp) REVERT: X 70 SER cc_start: 0.8474 (t) cc_final: 0.8108 (p) REVERT: X 83 GLN cc_start: 0.8065 (tp-100) cc_final: 0.7785 (tp40) REVERT: X 87 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7592 (mt-10) REVERT: Y 23 ARG cc_start: 0.7687 (mmm160) cc_final: 0.7403 (mtp180) REVERT: Y 26 LEU cc_start: 0.8787 (tt) cc_final: 0.8515 (tm) REVERT: Y 90 GLN cc_start: 0.7910 (pt0) cc_final: 0.7517 (pt0) REVERT: c 53 GLU cc_start: 0.7268 (pt0) cc_final: 0.6714 (pm20) REVERT: e 15 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7574 (mm-30) outliers start: 166 outliers final: 93 residues processed: 727 average time/residue: 1.6313 time to fit residues: 1557.7875 Evaluate side-chains 725 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 617 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 90 GLU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 227 ARG Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 45 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 176 VAL Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 32 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 205 ARG Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 122 SER Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 75 ILE Chi-restraints excluded: chain Z residue 84 LYS Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 58 HIS Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 105 PHE Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 127 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 2.9990 chunk 351 optimal weight: 30.0000 chunk 8 optimal weight: 8.9990 chunk 460 optimal weight: 0.9990 chunk 255 optimal weight: 30.0000 chunk 527 optimal weight: 4.9990 chunk 427 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 315 optimal weight: 6.9990 chunk 555 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 ASN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 ASN ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 ASN I 97 GLN J 146 GLN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN S 118 GLN Z 106 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 79914 Z= 0.213 Angle : 0.565 12.267 116006 Z= 0.288 Chirality : 0.038 0.242 14347 Planarity : 0.004 0.062 8425 Dihedral : 23.126 179.867 31899 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.39 % Favored : 94.59 % Rotamer: Outliers : 4.38 % Allowed : 20.95 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.57 (0.12), residues: 4789 helix: -0.34 (0.14), residues: 1400 sheet: -1.14 (0.18), residues: 839 loop : -1.38 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 23 HIS 0.006 0.001 HIS J 22 PHE 0.017 0.001 PHE K 147 TYR 0.021 0.001 TYR T 77 ARG 0.012 0.000 ARG d 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 631 time to evaluate : 4.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 58 LEU cc_start: 0.4910 (tp) cc_final: 0.4572 (mp) REVERT: a 106 GLN cc_start: 0.6774 (tp40) cc_final: 0.6373 (tp40) REVERT: B 31 ASP cc_start: 0.7686 (t0) cc_final: 0.7370 (t0) REVERT: B 35 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7300 (tm-30) REVERT: B 40 LYS cc_start: 0.8548 (tttm) cc_final: 0.8265 (ttmt) REVERT: b 55 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: b 62 TYR cc_start: 0.8363 (t80) cc_final: 0.8043 (t80) REVERT: b 82 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8581 (mtmt) REVERT: C 89 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8373 (mt-10) REVERT: C 95 ASN cc_start: 0.8756 (m-40) cc_final: 0.8210 (m-40) REVERT: D 72 ASP cc_start: 0.7229 (m-30) cc_final: 0.7023 (m-30) REVERT: D 103 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7806 (mttm) REVERT: D 117 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7118 (ttm-80) REVERT: D 145 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8128 (mtmt) REVERT: D 152 ARG cc_start: 0.8105 (ttp-110) cc_final: 0.7841 (ttp80) REVERT: D 187 ARG cc_start: 0.8822 (mtp-110) cc_final: 0.8568 (mtp180) REVERT: D 215 MET cc_start: 0.7996 (mtm) cc_final: 0.7759 (mtt) REVERT: d 16 LYS cc_start: 0.5601 (tppt) cc_final: 0.5127 (tmtt) REVERT: d 31 ARG cc_start: 0.6625 (ttp80) cc_final: 0.6393 (ttm-80) REVERT: d 43 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6628 (tt) REVERT: d 45 ASN cc_start: 0.5048 (p0) cc_final: 0.4711 (p0) REVERT: E 1 MET cc_start: 0.5556 (tpt) cc_final: 0.5006 (mmm) REVERT: E 141 LYS cc_start: 0.7295 (ttpt) cc_final: 0.6931 (pttp) REVERT: E 148 LYS cc_start: 0.8498 (mmpt) cc_final: 0.7989 (mttt) REVERT: E 150 MET cc_start: 0.7446 (mmm) cc_final: 0.7046 (mtt) REVERT: E 176 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8491 (mm) REVERT: E 178 ARG cc_start: 0.7534 (mmp80) cc_final: 0.7137 (mmp80) REVERT: E 192 TRP cc_start: 0.7540 (t60) cc_final: 0.7229 (t60) REVERT: E 201 LYS cc_start: 0.8918 (mppt) cc_final: 0.8510 (mppt) REVERT: f 95 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: f 100 LYS cc_start: 0.8474 (mttm) cc_final: 0.8218 (mttm) REVERT: f 113 ARG cc_start: 0.7587 (mtm110) cc_final: 0.7299 (mtm-85) REVERT: G 78 MET cc_start: 0.3680 (mmt) cc_final: 0.3379 (mmp) REVERT: G 137 GLN cc_start: 0.7090 (tt0) cc_final: 0.6627 (tm-30) REVERT: G 140 ASP cc_start: 0.7070 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: G 191 LYS cc_start: 0.6153 (tptp) cc_final: 0.5659 (ttpp) REVERT: H 18 VAL cc_start: 0.8539 (t) cc_final: 0.8253 (p) REVERT: H 22 ARG cc_start: 0.8587 (mtm110) cc_final: 0.8329 (ttp-110) REVERT: H 25 ARG cc_start: 0.8053 (ttp-110) cc_final: 0.7825 (mtp85) REVERT: H 48 TYR cc_start: 0.8263 (m-80) cc_final: 0.8038 (m-10) REVERT: H 120 ASP cc_start: 0.8423 (m-30) cc_final: 0.7943 (t0) REVERT: H 133 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6768 (pp) REVERT: H 145 PHE cc_start: 0.8399 (m-10) cc_final: 0.8152 (m-10) REVERT: H 146 ASN cc_start: 0.8601 (m110) cc_final: 0.8136 (p0) REVERT: H 155 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8016 (mm110) REVERT: H 225 GLN cc_start: 0.7627 (mm110) cc_final: 0.7389 (mp10) REVERT: h 116 ASP cc_start: 0.7376 (p0) cc_final: 0.6935 (t70) REVERT: h 118 ARG cc_start: 0.7126 (tpt170) cc_final: 0.6740 (ttp80) REVERT: I 28 LEU cc_start: 0.8449 (pp) cc_final: 0.7553 (tp) REVERT: I 43 LEU cc_start: 0.7825 (mt) cc_final: 0.7261 (mp) REVERT: I 57 ARG cc_start: 0.7337 (tpp-160) cc_final: 0.7024 (mtm110) REVERT: I 127 ASP cc_start: 0.7689 (m-30) cc_final: 0.7479 (m-30) REVERT: I 131 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7351 (mm-30) REVERT: I 184 ASP cc_start: 0.8568 (p0) cc_final: 0.8208 (p0) REVERT: J 23 LYS cc_start: 0.8370 (ptpt) cc_final: 0.8066 (ptmm) REVERT: J 71 CYS cc_start: 0.8352 (t) cc_final: 0.8023 (t) REVERT: J 107 THR cc_start: 0.8339 (m) cc_final: 0.8087 (p) REVERT: J 206 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7461 (ptpp) REVERT: K 26 ASP cc_start: 0.7671 (p0) cc_final: 0.7445 (m-30) REVERT: K 79 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.6831 (ttp-170) REVERT: L 29 MET cc_start: 0.5897 (ppp) cc_final: 0.5447 (pp-130) REVERT: L 43 LEU cc_start: 0.6954 (mp) cc_final: 0.6061 (tp) REVERT: L 65 ARG cc_start: 0.6504 (mtp180) cc_final: 0.5713 (mtt180) REVERT: L 85 LEU cc_start: 0.7677 (mt) cc_final: 0.6665 (tt) REVERT: N 42 LEU cc_start: 0.6067 (mp) cc_final: 0.5735 (tp) REVERT: Q 93 MET cc_start: 0.6848 (mtp) cc_final: 0.6269 (mmt) REVERT: Q 130 ARG cc_start: 0.5580 (mmm160) cc_final: 0.5236 (mmp-170) REVERT: R 24 HIS cc_start: 0.6097 (t70) cc_final: 0.5766 (t70) REVERT: R 143 LYS cc_start: 0.5597 (tptt) cc_final: 0.5321 (tptt) REVERT: S 11 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7619 (tptp) REVERT: S 45 LYS cc_start: 0.6235 (OUTLIER) cc_final: 0.5503 (tptm) REVERT: S 126 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.8633 (ptm) REVERT: T 70 ILE cc_start: 0.4464 (mm) cc_final: 0.4000 (tp) REVERT: U 74 SER cc_start: 0.4811 (t) cc_final: 0.4561 (m) REVERT: V 34 LYS cc_start: 0.7683 (mmpt) cc_final: 0.7068 (ptmm) REVERT: V 56 MET cc_start: 0.8238 (mmp) cc_final: 0.7658 (mmm) REVERT: V 79 ARG cc_start: 0.7841 (mtm-85) cc_final: 0.7542 (mtt90) REVERT: V 86 LYS cc_start: 0.7292 (ttpt) cc_final: 0.6547 (mtmm) REVERT: V 91 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.5107 (tt) REVERT: W 21 ASN cc_start: 0.8712 (t0) cc_final: 0.7993 (t0) REVERT: W 41 LYS cc_start: 0.9069 (tppt) cc_final: 0.8704 (tppp) REVERT: W 74 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8212 (ttpt) REVERT: W 81 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8484 (tppt) REVERT: Z 39 GLU cc_start: 0.8211 (tp30) cc_final: 0.7727 (tp30) REVERT: Z 68 LYS cc_start: 0.8452 (tttt) cc_final: 0.8103 (ttmm) REVERT: Z 72 PHE cc_start: 0.8148 (m-80) cc_final: 0.7899 (m-80) REVERT: Z 74 MET cc_start: 0.8410 (mtm) cc_final: 0.8174 (mtt) REVERT: F 152 ASP cc_start: 0.8046 (t0) cc_final: 0.7671 (t70) REVERT: M 40 GLU cc_start: 0.8073 (pm20) cc_final: 0.7411 (pm20) REVERT: M 62 LYS cc_start: 0.7876 (tptt) cc_final: 0.7523 (ttpt) REVERT: M 66 MET cc_start: 0.8117 (mmt) cc_final: 0.7844 (mmm) REVERT: M 200 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7929 (mtm180) REVERT: M 211 LYS cc_start: 0.8113 (tttm) cc_final: 0.7797 (ttmm) REVERT: M 246 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7896 (pp) REVERT: M 251 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7290 (mt-10) REVERT: O 49 GLU cc_start: 0.8104 (tp30) cc_final: 0.7664 (tp30) REVERT: O 57 ASP cc_start: 0.7660 (t0) cc_final: 0.6691 (t70) REVERT: O 79 LYS cc_start: 0.7671 (mttm) cc_final: 0.7373 (mtpt) REVERT: O 97 ARG cc_start: 0.7033 (ptm160) cc_final: 0.6492 (ttm110) REVERT: O 104 LYS cc_start: 0.8017 (tttm) cc_final: 0.7773 (tptp) REVERT: O 121 GLN cc_start: 0.8214 (pt0) cc_final: 0.7181 (pm20) REVERT: O 124 ASP cc_start: 0.7077 (m-30) cc_final: 0.6310 (m-30) REVERT: O 144 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7575 (ttpp) REVERT: P 36 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: P 69 ASN cc_start: 0.8184 (m-40) cc_final: 0.7866 (m-40) REVERT: P 103 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7110 (mm-30) REVERT: X 63 LYS cc_start: 0.5788 (mmtt) cc_final: 0.5428 (mptp) REVERT: X 70 SER cc_start: 0.8514 (t) cc_final: 0.8132 (p) REVERT: X 83 GLN cc_start: 0.8041 (tp-100) cc_final: 0.7826 (tp40) REVERT: X 87 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7618 (mt-10) REVERT: Y 12 LYS cc_start: 0.7316 (OUTLIER) cc_final: 0.7082 (tppp) REVERT: Y 23 ARG cc_start: 0.7631 (mmm160) cc_final: 0.7421 (mtp180) REVERT: Y 26 LEU cc_start: 0.8786 (tt) cc_final: 0.8492 (tm) REVERT: Y 90 GLN cc_start: 0.7865 (pt0) cc_final: 0.7469 (pt0) REVERT: c 53 GLU cc_start: 0.7301 (pt0) cc_final: 0.6729 (pm20) REVERT: e 15 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7606 (mm-30) outliers start: 183 outliers final: 98 residues processed: 737 average time/residue: 1.6428 time to fit residues: 1595.9699 Evaluate side-chains 722 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 604 time to evaluate : 4.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 90 GLU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain d residue 43 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain f residue 95 GLN Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 155 GLN Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 176 VAL Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 38 GLU Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 75 ILE Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 84 LYS Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 250 GLU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 99 TYR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 58 HIS Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 107 SER Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 105 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 5.9990 chunk 557 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 363 optimal weight: 5.9990 chunk 152 optimal weight: 8.9990 chunk 619 optimal weight: 2.9990 chunk 514 optimal weight: 6.9990 chunk 286 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 325 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN I 97 GLN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 GLN ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 49 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 79914 Z= 0.364 Angle : 0.645 14.178 116006 Z= 0.327 Chirality : 0.042 0.268 14347 Planarity : 0.005 0.066 8425 Dihedral : 23.165 179.867 31898 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.12 % Favored : 93.86 % Rotamer: Outliers : 4.50 % Allowed : 21.90 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.54 (0.12), residues: 4789 helix: -0.30 (0.14), residues: 1395 sheet: -1.12 (0.18), residues: 847 loop : -1.37 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP T 82 HIS 0.009 0.001 HIS J 22 PHE 0.025 0.002 PHE K 147 TYR 0.025 0.002 TYR M 121 ARG 0.010 0.001 ARG J 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 603 time to evaluate : 4.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 58 LEU cc_start: 0.5253 (tp) cc_final: 0.4780 (mp) REVERT: B 35 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7342 (tm-30) REVERT: B 40 LYS cc_start: 0.8487 (tttm) cc_final: 0.8140 (ttmt) REVERT: b 38 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8403 (ttmm) REVERT: b 62 TYR cc_start: 0.8312 (t80) cc_final: 0.8048 (t80) REVERT: b 82 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8580 (mtmt) REVERT: C 89 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8484 (mt-10) REVERT: C 95 ASN cc_start: 0.8751 (m-40) cc_final: 0.8195 (m-40) REVERT: D 92 GLU cc_start: 0.8486 (mp0) cc_final: 0.7850 (mp0) REVERT: D 103 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7807 (mttm) REVERT: D 117 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7124 (ttm-80) REVERT: D 145 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8180 (mtmt) REVERT: D 152 ARG cc_start: 0.8126 (ttp-110) cc_final: 0.7890 (ttp-110) REVERT: D 215 MET cc_start: 0.8011 (mtm) cc_final: 0.7774 (mtt) REVERT: d 16 LYS cc_start: 0.5683 (tppt) cc_final: 0.5182 (tmtt) REVERT: d 31 ARG cc_start: 0.6823 (ttp80) cc_final: 0.6617 (ttm-80) REVERT: d 43 ILE cc_start: 0.6720 (mt) cc_final: 0.6479 (tt) REVERT: E 1 MET cc_start: 0.5614 (OUTLIER) cc_final: 0.5125 (tmm) REVERT: E 141 LYS cc_start: 0.7426 (ttpt) cc_final: 0.6943 (pttp) REVERT: E 148 LYS cc_start: 0.8504 (mmpt) cc_final: 0.7991 (mttt) REVERT: E 150 MET cc_start: 0.7492 (mmm) cc_final: 0.7142 (mtt) REVERT: E 178 ARG cc_start: 0.7601 (mmp80) cc_final: 0.7075 (mmp80) REVERT: E 192 TRP cc_start: 0.7545 (t60) cc_final: 0.7222 (t60) REVERT: E 201 LYS cc_start: 0.8873 (mppt) cc_final: 0.8462 (mppt) REVERT: f 95 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8076 (pt0) REVERT: f 100 LYS cc_start: 0.8448 (mttm) cc_final: 0.8210 (mttp) REVERT: G 78 MET cc_start: 0.3774 (mmt) cc_final: 0.3554 (mmp) REVERT: G 137 GLN cc_start: 0.6972 (tt0) cc_final: 0.6480 (tt0) REVERT: G 191 LYS cc_start: 0.6154 (tptp) cc_final: 0.5637 (ttpp) REVERT: H 18 VAL cc_start: 0.8556 (t) cc_final: 0.8269 (p) REVERT: H 25 ARG cc_start: 0.8098 (ttp-110) cc_final: 0.7825 (ttp-110) REVERT: H 120 ASP cc_start: 0.8423 (m-30) cc_final: 0.7942 (t0) REVERT: H 133 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6791 (pp) REVERT: H 145 PHE cc_start: 0.8359 (m-10) cc_final: 0.8027 (m-10) REVERT: H 146 ASN cc_start: 0.8545 (m110) cc_final: 0.8048 (p0) REVERT: H 225 GLN cc_start: 0.7692 (mm110) cc_final: 0.7439 (mp10) REVERT: h 116 ASP cc_start: 0.7460 (p0) cc_final: 0.7048 (t70) REVERT: h 118 ARG cc_start: 0.6966 (tpt170) cc_final: 0.6626 (ttp80) REVERT: h 196 ASN cc_start: 0.8050 (t0) cc_final: 0.7610 (t0) REVERT: I 43 LEU cc_start: 0.7844 (mt) cc_final: 0.7289 (mp) REVERT: I 57 ARG cc_start: 0.7271 (tpp-160) cc_final: 0.6982 (mtm110) REVERT: I 131 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7370 (mm-30) REVERT: I 184 ASP cc_start: 0.8601 (p0) cc_final: 0.8200 (p0) REVERT: J 71 CYS cc_start: 0.8423 (t) cc_final: 0.8106 (t) REVERT: J 107 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8145 (p) REVERT: J 206 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7426 (ptpp) REVERT: K 26 ASP cc_start: 0.7727 (p0) cc_final: 0.7440 (OUTLIER) REVERT: K 79 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6877 (ttp-170) REVERT: K 107 GLU cc_start: 0.7801 (tp30) cc_final: 0.7554 (tp30) REVERT: L 29 MET cc_start: 0.5901 (ppp) cc_final: 0.5408 (pp-130) REVERT: L 43 LEU cc_start: 0.7004 (mp) cc_final: 0.6656 (mp) REVERT: L 65 ARG cc_start: 0.6421 (mtp180) cc_final: 0.5638 (mtt180) REVERT: L 71 LEU cc_start: 0.5469 (OUTLIER) cc_final: 0.4534 (tp) REVERT: L 79 LEU cc_start: 0.5174 (tp) cc_final: 0.4712 (tp) REVERT: L 83 LEU cc_start: 0.8037 (mt) cc_final: 0.7835 (mt) REVERT: L 85 LEU cc_start: 0.7705 (mt) cc_final: 0.6741 (tt) REVERT: N 42 LEU cc_start: 0.6295 (mp) cc_final: 0.5933 (tp) REVERT: Q 93 MET cc_start: 0.6876 (mtp) cc_final: 0.6275 (mmt) REVERT: Q 111 MET cc_start: 0.1507 (OUTLIER) cc_final: 0.0847 (mmm) REVERT: Q 130 ARG cc_start: 0.5579 (mmm160) cc_final: 0.5328 (mmp-170) REVERT: R 24 HIS cc_start: 0.5874 (t70) cc_final: 0.5599 (t70) REVERT: R 42 ILE cc_start: 0.5586 (mm) cc_final: 0.5234 (mm) REVERT: R 143 LYS cc_start: 0.5641 (tptt) cc_final: 0.5351 (tptt) REVERT: S 11 LYS cc_start: 0.7933 (ttpt) cc_final: 0.7656 (ttmm) REVERT: S 23 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6540 (mtp180) REVERT: S 45 LYS cc_start: 0.6453 (OUTLIER) cc_final: 0.5760 (tptm) REVERT: S 126 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8654 (ptm) REVERT: T 71 MET cc_start: 0.5508 (ptm) cc_final: 0.5219 (ptt) REVERT: U 75 MET cc_start: 0.7104 (mmp) cc_final: 0.6752 (mmm) REVERT: V 34 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7088 (ptmm) REVERT: V 86 LYS cc_start: 0.7286 (ttpt) cc_final: 0.6618 (mtmm) REVERT: V 91 LEU cc_start: 0.5552 (OUTLIER) cc_final: 0.5132 (tt) REVERT: W 21 ASN cc_start: 0.8678 (t0) cc_final: 0.7973 (t0) REVERT: W 41 LYS cc_start: 0.9084 (tppt) cc_final: 0.8701 (tppp) REVERT: W 74 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8261 (ttpt) REVERT: Z 39 GLU cc_start: 0.8242 (tp30) cc_final: 0.7773 (tp30) REVERT: Z 68 LYS cc_start: 0.8547 (tttt) cc_final: 0.8276 (ttmt) REVERT: Z 72 PHE cc_start: 0.8225 (m-80) cc_final: 0.7994 (m-80) REVERT: Z 74 MET cc_start: 0.8393 (mtm) cc_final: 0.8165 (mtt) REVERT: Z 101 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7529 (mppt) REVERT: F 154 TYR cc_start: 0.8272 (m-80) cc_final: 0.8016 (m-80) REVERT: M 40 GLU cc_start: 0.8082 (pm20) cc_final: 0.7413 (pm20) REVERT: M 62 LYS cc_start: 0.7908 (tptt) cc_final: 0.7577 (ttpp) REVERT: M 66 MET cc_start: 0.8162 (mmt) cc_final: 0.7875 (mmm) REVERT: M 127 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7240 (mtt180) REVERT: M 200 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7924 (mtm180) REVERT: M 211 LYS cc_start: 0.8127 (tttm) cc_final: 0.7823 (ttmm) REVERT: M 246 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8010 (pp) REVERT: M 251 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7425 (mt-10) REVERT: O 49 GLU cc_start: 0.8111 (tp30) cc_final: 0.7679 (tp30) REVERT: O 57 ASP cc_start: 0.7748 (t0) cc_final: 0.6736 (t70) REVERT: O 79 LYS cc_start: 0.7727 (mttm) cc_final: 0.7388 (mttt) REVERT: O 97 ARG cc_start: 0.7084 (ptm160) cc_final: 0.6529 (ttm110) REVERT: O 121 GLN cc_start: 0.8240 (pt0) cc_final: 0.7131 (pm20) REVERT: O 124 ASP cc_start: 0.7424 (m-30) cc_final: 0.6587 (m-30) REVERT: P 36 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7960 (mp10) REVERT: P 69 ASN cc_start: 0.8326 (m-40) cc_final: 0.7915 (m-40) REVERT: P 103 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7116 (mm-30) REVERT: X 63 LYS cc_start: 0.5896 (mmtt) cc_final: 0.5377 (mptp) REVERT: X 70 SER cc_start: 0.8619 (t) cc_final: 0.8228 (p) REVERT: X 83 GLN cc_start: 0.8059 (tp-100) cc_final: 0.7834 (tp40) REVERT: Y 87 GLU cc_start: 0.7602 (tp30) cc_final: 0.7368 (tp30) REVERT: e 1 MET cc_start: 0.5105 (OUTLIER) cc_final: 0.4261 (ppp) REVERT: e 15 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7693 (mm-30) REVERT: e 18 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8090 (mtpt) outliers start: 188 outliers final: 120 residues processed: 710 average time/residue: 1.6316 time to fit residues: 1519.3967 Evaluate side-chains 727 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 585 time to evaluate : 4.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 90 GLU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain f residue 95 GLN Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain H residue 163 ASN Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 159 ASN Chi-restraints excluded: chain h residue 176 VAL Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 56 ARG Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 142 SER Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 23 ARG Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 78 ARG Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 38 GLU Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 75 ILE Chi-restraints excluded: chain Z residue 84 LYS Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 250 GLU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 99 TYR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain P residue 133 ARG Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 90 CYS Chi-restraints excluded: chain c residue 105 PHE Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 18 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 352 optimal weight: 30.0000 chunk 452 optimal weight: 7.9990 chunk 350 optimal weight: 50.0000 chunk 521 optimal weight: 1.9990 chunk 345 optimal weight: 30.0000 chunk 616 optimal weight: 0.8980 chunk 386 optimal weight: 0.9980 chunk 376 optimal weight: 8.9990 chunk 284 optimal weight: 20.0000 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 ASN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 163 ASN I 97 GLN I 162 GLN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 79914 Z= 0.332 Angle : 0.627 12.989 116006 Z= 0.318 Chirality : 0.041 0.267 14347 Planarity : 0.005 0.073 8425 Dihedral : 23.162 179.627 31898 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.95 % Favored : 94.03 % Rotamer: Outliers : 4.52 % Allowed : 22.50 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.46 (0.12), residues: 4789 helix: -0.24 (0.14), residues: 1393 sheet: -1.08 (0.18), residues: 858 loop : -1.31 (0.12), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 82 HIS 0.008 0.001 HIS J 22 PHE 0.023 0.002 PHE K 147 TYR 0.027 0.002 TYR M 121 ARG 0.013 0.001 ARG J 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 790 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 601 time to evaluate : 4.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 58 LEU cc_start: 0.5310 (tp) cc_final: 0.4897 (mp) REVERT: B 35 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7340 (tm-30) REVERT: B 40 LYS cc_start: 0.8501 (tttm) cc_final: 0.8138 (ttmt) REVERT: B 198 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7803 (ptp) REVERT: b 38 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8390 (ttmm) REVERT: b 55 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7608 (mp0) REVERT: b 62 TYR cc_start: 0.8310 (t80) cc_final: 0.7993 (t80) REVERT: b 82 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8588 (mtmt) REVERT: C 89 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8474 (mt-10) REVERT: C 95 ASN cc_start: 0.8754 (m-40) cc_final: 0.8191 (m-40) REVERT: D 92 GLU cc_start: 0.8445 (mp0) cc_final: 0.7786 (mp0) REVERT: D 103 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7809 (mttm) REVERT: D 117 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7136 (ttm-80) REVERT: D 145 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8157 (mtmt) REVERT: D 152 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7907 (ttp-110) REVERT: D 215 MET cc_start: 0.7995 (mtm) cc_final: 0.7760 (mtt) REVERT: d 16 LYS cc_start: 0.5615 (tppt) cc_final: 0.5064 (tmtt) REVERT: d 31 ARG cc_start: 0.6758 (ttp80) cc_final: 0.6557 (ttm-80) REVERT: E 1 MET cc_start: 0.5712 (OUTLIER) cc_final: 0.5037 (mmm) REVERT: E 141 LYS cc_start: 0.7482 (ttpt) cc_final: 0.6940 (pttp) REVERT: E 148 LYS cc_start: 0.8500 (mmpt) cc_final: 0.8022 (mttt) REVERT: E 150 MET cc_start: 0.7503 (mmm) cc_final: 0.7191 (mtt) REVERT: E 178 ARG cc_start: 0.7680 (mmp80) cc_final: 0.7124 (mmp80) REVERT: E 192 TRP cc_start: 0.7585 (t60) cc_final: 0.7244 (t60) REVERT: E 201 LYS cc_start: 0.8880 (mppt) cc_final: 0.8455 (mppt) REVERT: f 100 LYS cc_start: 0.8538 (mttm) cc_final: 0.8289 (mttm) REVERT: G 137 GLN cc_start: 0.6849 (tt0) cc_final: 0.6392 (tt0) REVERT: G 191 LYS cc_start: 0.6167 (tptp) cc_final: 0.5664 (ttpp) REVERT: H 18 VAL cc_start: 0.8524 (t) cc_final: 0.8229 (p) REVERT: H 25 ARG cc_start: 0.8045 (ttp-110) cc_final: 0.7832 (ttp-110) REVERT: H 120 ASP cc_start: 0.8427 (m-30) cc_final: 0.7924 (t0) REVERT: H 133 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6937 (pp) REVERT: H 145 PHE cc_start: 0.8382 (m-10) cc_final: 0.7999 (m-10) REVERT: H 146 ASN cc_start: 0.8537 (m110) cc_final: 0.8027 (p0) REVERT: H 225 GLN cc_start: 0.7695 (mm110) cc_final: 0.7431 (mp10) REVERT: h 12 LYS cc_start: 0.4219 (pptt) cc_final: 0.3977 (mmmm) REVERT: h 116 ASP cc_start: 0.7531 (p0) cc_final: 0.7156 (t70) REVERT: h 118 ARG cc_start: 0.6971 (tpt170) cc_final: 0.6625 (ttp80) REVERT: h 196 ASN cc_start: 0.8065 (t0) cc_final: 0.7614 (t0) REVERT: I 43 LEU cc_start: 0.7846 (mt) cc_final: 0.7277 (mp) REVERT: I 57 ARG cc_start: 0.7260 (tpp-160) cc_final: 0.6945 (mtm110) REVERT: I 131 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7271 (mm-30) REVERT: I 184 ASP cc_start: 0.8609 (p0) cc_final: 0.8216 (p0) REVERT: J 71 CYS cc_start: 0.8358 (t) cc_final: 0.8052 (t) REVERT: J 107 THR cc_start: 0.8406 (m) cc_final: 0.8144 (p) REVERT: J 206 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7415 (ptpp) REVERT: K 26 ASP cc_start: 0.7713 (p0) cc_final: 0.7454 (p0) REVERT: K 79 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6867 (ttp-170) REVERT: K 107 GLU cc_start: 0.7824 (tp30) cc_final: 0.7550 (tp30) REVERT: L 29 MET cc_start: 0.5822 (ppp) cc_final: 0.5478 (pp-130) REVERT: L 53 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7426 (ttpt) REVERT: L 65 ARG cc_start: 0.6472 (mtp180) cc_final: 0.5679 (mtt180) REVERT: L 71 LEU cc_start: 0.5246 (OUTLIER) cc_final: 0.4409 (tp) REVERT: L 79 LEU cc_start: 0.5176 (tp) cc_final: 0.4776 (tp) REVERT: L 83 LEU cc_start: 0.8051 (mt) cc_final: 0.7800 (mt) REVERT: L 85 LEU cc_start: 0.7678 (mt) cc_final: 0.6778 (tt) REVERT: Q 93 MET cc_start: 0.7061 (mtp) cc_final: 0.6410 (mmt) REVERT: Q 111 MET cc_start: 0.1495 (OUTLIER) cc_final: 0.0840 (mmm) REVERT: Q 130 ARG cc_start: 0.5689 (mmm160) cc_final: 0.5454 (mmp-170) REVERT: R 24 HIS cc_start: 0.5731 (t70) cc_final: 0.5477 (t70) REVERT: R 42 ILE cc_start: 0.5988 (mm) cc_final: 0.5620 (mm) REVERT: S 11 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7741 (ttmm) REVERT: S 45 LYS cc_start: 0.6488 (OUTLIER) cc_final: 0.5838 (tptm) REVERT: S 126 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8641 (ptm) REVERT: T 116 LYS cc_start: 0.6434 (pptt) cc_final: 0.5862 (mmmt) REVERT: U 75 MET cc_start: 0.7114 (mmp) cc_final: 0.6907 (mmt) REVERT: V 34 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7193 (ptmm) REVERT: V 56 MET cc_start: 0.8080 (mmp) cc_final: 0.7567 (mmm) REVERT: V 86 LYS cc_start: 0.7323 (ttpt) cc_final: 0.6709 (mtmm) REVERT: V 91 LEU cc_start: 0.5562 (OUTLIER) cc_final: 0.5176 (tt) REVERT: W 21 ASN cc_start: 0.8679 (t0) cc_final: 0.7979 (t0) REVERT: W 41 LYS cc_start: 0.9037 (tppt) cc_final: 0.8721 (tppp) REVERT: Z 39 GLU cc_start: 0.8252 (tp30) cc_final: 0.7774 (tp30) REVERT: Z 68 LYS cc_start: 0.8534 (tttt) cc_final: 0.8270 (ttmt) REVERT: Z 72 PHE cc_start: 0.8268 (m-80) cc_final: 0.8037 (m-80) REVERT: Z 74 MET cc_start: 0.8380 (mtm) cc_final: 0.8149 (mtt) REVERT: Z 101 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7528 (mppt) REVERT: F 154 TYR cc_start: 0.8260 (m-80) cc_final: 0.7990 (m-80) REVERT: M 40 GLU cc_start: 0.8077 (pm20) cc_final: 0.7389 (pm20) REVERT: M 62 LYS cc_start: 0.7896 (tptt) cc_final: 0.7528 (ttpt) REVERT: M 66 MET cc_start: 0.8157 (mmt) cc_final: 0.7868 (mmm) REVERT: M 127 ARG cc_start: 0.7729 (mtp180) cc_final: 0.7231 (mtt180) REVERT: M 200 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7945 (mtm180) REVERT: M 211 LYS cc_start: 0.8112 (tttm) cc_final: 0.7797 (ttmm) REVERT: M 246 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8028 (pp) REVERT: M 251 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7301 (mt-10) REVERT: O 49 GLU cc_start: 0.8095 (tp30) cc_final: 0.7681 (tp30) REVERT: O 57 ASP cc_start: 0.7687 (t0) cc_final: 0.6695 (t70) REVERT: O 79 LYS cc_start: 0.7715 (mttm) cc_final: 0.7383 (mttt) REVERT: O 97 ARG cc_start: 0.7102 (ptm160) cc_final: 0.6515 (ttm110) REVERT: O 121 GLN cc_start: 0.8287 (pt0) cc_final: 0.7160 (pm20) REVERT: O 124 ASP cc_start: 0.7498 (m-30) cc_final: 0.6621 (m-30) REVERT: P 36 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: P 69 ASN cc_start: 0.8327 (m-40) cc_final: 0.7904 (m-40) REVERT: P 103 GLU cc_start: 0.7312 (mm-30) cc_final: 0.7085 (mm-30) REVERT: X 63 LYS cc_start: 0.5793 (mmtt) cc_final: 0.5331 (mptp) REVERT: X 70 SER cc_start: 0.8602 (t) cc_final: 0.8236 (p) REVERT: X 87 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7551 (mt-10) REVERT: e 15 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7576 (mm-30) outliers start: 189 outliers final: 123 residues processed: 714 average time/residue: 1.6787 time to fit residues: 1579.5917 Evaluate side-chains 726 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 583 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain b residue 90 GLU Chi-restraints excluded: chain b residue 96 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain d residue 45 ASN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 140 ASP Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 159 ASN Chi-restraints excluded: chain h residue 176 VAL Chi-restraints excluded: chain h residue 189 ILE Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain h residue 241 PHE Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 56 ARG Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 93 THR Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 186 ASP Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 126 MET Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 59 LYS Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 38 GLU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 75 ILE Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 84 LYS Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 250 GLU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 85 THR Chi-restraints excluded: chain O residue 99 TYR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain P residue 4 MET Chi-restraints excluded: chain P residue 11 LEU Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 133 ARG Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 105 PHE Chi-restraints excluded: chain c residue 127 ASN Chi-restraints excluded: chain e residue 53 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 0.6980 chunk 246 optimal weight: 0.8980 chunk 368 optimal weight: 8.9990 chunk 185 optimal weight: 0.2980 chunk 121 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 392 optimal weight: 8.9990 chunk 420 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 484 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 ASN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN M 98 ASN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.165 79914 Z= 0.161 Angle : 0.561 12.479 116006 Z= 0.284 Chirality : 0.036 0.236 14347 Planarity : 0.004 0.061 8425 Dihedral : 23.095 179.841 31896 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.30 % Favored : 94.68 % Rotamer: Outliers : 3.73 % Allowed : 23.51 % Favored : 72.76 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.24 (0.12), residues: 4789 helix: -0.01 (0.14), residues: 1392 sheet: -0.95 (0.18), residues: 852 loop : -1.21 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP h 259 HIS 0.007 0.001 HIS Q 79 PHE 0.019 0.001 PHE E 125 TYR 0.025 0.001 TYR M 121 ARG 0.009 0.000 ARG O 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 614 time to evaluate : 4.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 58 LEU cc_start: 0.5330 (tp) cc_final: 0.4916 (mp) REVERT: a 68 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.5397 (tp) REVERT: B 35 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7328 (tm-30) REVERT: B 40 LYS cc_start: 0.8552 (tttm) cc_final: 0.8238 (ttmt) REVERT: B 155 ARG cc_start: 0.8451 (ttm-80) cc_final: 0.8204 (ttm170) REVERT: b 38 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8409 (ttmm) REVERT: b 55 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: b 62 TYR cc_start: 0.8258 (t80) cc_final: 0.7967 (t80) REVERT: b 82 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8562 (mtmt) REVERT: C 89 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8477 (mt-10) REVERT: C 95 ASN cc_start: 0.8710 (m-40) cc_final: 0.8194 (m-40) REVERT: D 103 LYS cc_start: 0.8437 (mtpt) cc_final: 0.7866 (mttm) REVERT: D 117 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7153 (ttm-80) REVERT: D 145 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8055 (mtmt) REVERT: D 152 ARG cc_start: 0.8119 (ttp-110) cc_final: 0.7699 (ttp80) REVERT: D 215 MET cc_start: 0.7984 (mtm) cc_final: 0.7744 (mtt) REVERT: d 16 LYS cc_start: 0.5603 (tppt) cc_final: 0.5057 (tmtt) REVERT: d 45 ASN cc_start: 0.6130 (OUTLIER) cc_final: 0.5467 (m110) REVERT: E 1 MET cc_start: 0.5433 (OUTLIER) cc_final: 0.4748 (mmm) REVERT: E 141 LYS cc_start: 0.7300 (ttpt) cc_final: 0.6877 (pttp) REVERT: E 148 LYS cc_start: 0.8451 (mmpt) cc_final: 0.7978 (mttt) REVERT: E 150 MET cc_start: 0.7446 (mmm) cc_final: 0.7102 (mtt) REVERT: E 178 ARG cc_start: 0.7664 (mmp80) cc_final: 0.7120 (mmp80) REVERT: E 192 TRP cc_start: 0.7591 (t60) cc_final: 0.7175 (t60) REVERT: E 201 LYS cc_start: 0.8874 (mppt) cc_final: 0.8436 (mppt) REVERT: f 91 LYS cc_start: 0.9148 (tppt) cc_final: 0.8615 (tppt) REVERT: f 100 LYS cc_start: 0.8465 (mttm) cc_final: 0.8229 (mttm) REVERT: G 137 GLN cc_start: 0.6917 (tt0) cc_final: 0.6511 (tt0) REVERT: G 191 LYS cc_start: 0.6174 (tptp) cc_final: 0.5826 (mtpp) REVERT: H 18 VAL cc_start: 0.8508 (t) cc_final: 0.8215 (p) REVERT: H 22 ARG cc_start: 0.8546 (ttp-110) cc_final: 0.8323 (mtm110) REVERT: H 48 TYR cc_start: 0.8283 (m-80) cc_final: 0.8046 (m-10) REVERT: H 105 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8325 (p0) REVERT: H 120 ASP cc_start: 0.8394 (m-30) cc_final: 0.7895 (t0) REVERT: H 133 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6758 (pp) REVERT: H 145 PHE cc_start: 0.8385 (m-10) cc_final: 0.8054 (m-10) REVERT: H 146 ASN cc_start: 0.8551 (m110) cc_final: 0.8075 (p0) REVERT: H 225 GLN cc_start: 0.7664 (mm110) cc_final: 0.7414 (mp10) REVERT: h 60 ARG cc_start: 0.6404 (mtt-85) cc_final: 0.6052 (mmm-85) REVERT: h 118 ARG cc_start: 0.7002 (tpt170) cc_final: 0.6705 (ttp80) REVERT: h 196 ASN cc_start: 0.8086 (t0) cc_final: 0.7646 (t0) REVERT: I 18 GLU cc_start: 0.7546 (pm20) cc_final: 0.7214 (pm20) REVERT: I 37 LYS cc_start: 0.8209 (mttt) cc_final: 0.7936 (mmtp) REVERT: I 57 ARG cc_start: 0.7291 (tpp-160) cc_final: 0.7002 (mtm110) REVERT: I 131 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7301 (mm-30) REVERT: I 184 ASP cc_start: 0.8609 (p0) cc_final: 0.8233 (p0) REVERT: J 71 CYS cc_start: 0.8309 (t) cc_final: 0.8013 (t) REVERT: J 107 THR cc_start: 0.8341 (m) cc_final: 0.8113 (p) REVERT: J 206 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7388 (ptpp) REVERT: K 26 ASP cc_start: 0.7649 (p0) cc_final: 0.7436 (m-30) REVERT: K 79 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6935 (ttp-170) REVERT: K 107 GLU cc_start: 0.7834 (tp30) cc_final: 0.7575 (tp30) REVERT: L 29 MET cc_start: 0.5798 (ppp) cc_final: 0.5475 (pp-130) REVERT: L 53 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7410 (ttpt) REVERT: L 65 ARG cc_start: 0.6489 (mtp180) cc_final: 0.5723 (mtt180) REVERT: L 71 LEU cc_start: 0.5030 (OUTLIER) cc_final: 0.4172 (tp) REVERT: Q 41 GLN cc_start: 0.4442 (mp10) cc_final: 0.4227 (mp10) REVERT: Q 111 MET cc_start: 0.1517 (OUTLIER) cc_final: 0.0825 (mmm) REVERT: Q 130 ARG cc_start: 0.5705 (mmm160) cc_final: 0.5476 (mmp-170) REVERT: R 24 HIS cc_start: 0.5705 (t70) cc_final: 0.5421 (t70) REVERT: R 41 MET cc_start: 0.6121 (mtt) cc_final: 0.5547 (ttt) REVERT: S 11 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7687 (ttmm) REVERT: T 116 LYS cc_start: 0.6461 (pptt) cc_final: 0.5884 (mmmt) REVERT: V 34 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7267 (ptmm) REVERT: V 56 MET cc_start: 0.8085 (mmp) cc_final: 0.7665 (mmm) REVERT: V 83 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7854 (ttm-80) REVERT: V 86 LYS cc_start: 0.7324 (ttpt) cc_final: 0.6680 (mtmm) REVERT: V 91 LEU cc_start: 0.5283 (OUTLIER) cc_final: 0.5064 (tt) REVERT: W 21 ASN cc_start: 0.8635 (t0) cc_final: 0.7905 (t0) REVERT: W 41 LYS cc_start: 0.9033 (tppt) cc_final: 0.8709 (tppp) REVERT: Z 39 GLU cc_start: 0.8240 (tp30) cc_final: 0.7770 (tp30) REVERT: Z 74 MET cc_start: 0.8371 (mtm) cc_final: 0.8131 (mtt) REVERT: Z 101 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7530 (mppt) REVERT: F 154 TYR cc_start: 0.8144 (m-80) cc_final: 0.7868 (m-80) REVERT: F 176 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7393 (mp0) REVERT: M 40 GLU cc_start: 0.8070 (pm20) cc_final: 0.7388 (pm20) REVERT: M 62 LYS cc_start: 0.7863 (tptt) cc_final: 0.7525 (ttpt) REVERT: M 66 MET cc_start: 0.8128 (mmt) cc_final: 0.7848 (mmm) REVERT: M 211 LYS cc_start: 0.8037 (tttm) cc_final: 0.7739 (ttmm) REVERT: M 246 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.7990 (pp) REVERT: M 251 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7299 (mt-10) REVERT: M 253 ASP cc_start: 0.8439 (m-30) cc_final: 0.8164 (m-30) REVERT: O 1 MET cc_start: 0.4965 (ttp) cc_final: 0.3402 (ptm) REVERT: O 49 GLU cc_start: 0.8092 (tp30) cc_final: 0.7692 (tp30) REVERT: O 57 ASP cc_start: 0.7633 (t0) cc_final: 0.6696 (t70) REVERT: O 79 LYS cc_start: 0.7654 (mttm) cc_final: 0.7355 (mtpt) REVERT: O 97 ARG cc_start: 0.7013 (ptm160) cc_final: 0.6476 (ttm110) REVERT: O 121 GLN cc_start: 0.8213 (pt0) cc_final: 0.7187 (pm20) REVERT: O 124 ASP cc_start: 0.7404 (m-30) cc_final: 0.6597 (m-30) REVERT: P 36 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: P 69 ASN cc_start: 0.8237 (m-40) cc_final: 0.7887 (m-40) REVERT: P 103 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7190 (mm-30) REVERT: P 119 GLU cc_start: 0.7080 (mt-10) cc_final: 0.6855 (mm-30) REVERT: X 63 LYS cc_start: 0.5681 (mmtt) cc_final: 0.5233 (mptp) REVERT: X 70 SER cc_start: 0.8608 (t) cc_final: 0.8241 (p) REVERT: Y 12 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7175 (tppp) REVERT: Y 26 LEU cc_start: 0.8796 (tt) cc_final: 0.8507 (tm) REVERT: Y 90 GLN cc_start: 0.7782 (pt0) cc_final: 0.7422 (pt0) REVERT: c 1 MET cc_start: 0.2593 (mtp) cc_final: 0.1272 (mtp) REVERT: c 15 SER cc_start: 0.7261 (t) cc_final: 0.7003 (m) REVERT: e 15 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7506 (mm-30) outliers start: 156 outliers final: 97 residues processed: 717 average time/residue: 1.6154 time to fit residues: 1530.7864 Evaluate side-chains 708 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 591 time to evaluate : 4.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 68 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 192 SER Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain d residue 45 ASN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 176 VAL Chi-restraints excluded: chain h residue 217 MET Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain J residue 56 ARG Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 123 VAL Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 101 ASP Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 34 LYS Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 59 LYS Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 38 GLU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 75 ILE Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 250 GLU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 58 HIS Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 133 ARG Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain c residue 77 ASN Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 90 CYS Chi-restraints excluded: chain c residue 105 PHE Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain e residue 53 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 3.9990 chunk 590 optimal weight: 0.9980 chunk 539 optimal weight: 0.9980 chunk 574 optimal weight: 1.9990 chunk 345 optimal weight: 40.0000 chunk 250 optimal weight: 10.0000 chunk 451 optimal weight: 30.0000 chunk 176 optimal weight: 0.6980 chunk 519 optimal weight: 9.9990 chunk 543 optimal weight: 6.9990 chunk 572 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 112 ASN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 ASN f 110 GLN ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 85 HIS Z 106 GLN M 98 ASN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 GLN ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.168 79914 Z= 0.143 Angle : 0.546 14.722 116006 Z= 0.275 Chirality : 0.036 0.294 14347 Planarity : 0.004 0.060 8425 Dihedral : 22.978 179.830 31896 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.11 % Allowed : 24.39 % Favored : 72.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.02 (0.12), residues: 4789 helix: 0.19 (0.14), residues: 1395 sheet: -0.75 (0.18), residues: 825 loop : -1.11 (0.12), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP h 259 HIS 0.007 0.001 HIS Q 79 PHE 0.014 0.001 PHE K 147 TYR 0.024 0.001 TYR M 121 ARG 0.015 0.000 ARG J 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 626 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 58 LEU cc_start: 0.5418 (tp) cc_final: 0.5022 (mp) REVERT: B 35 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7340 (tm-30) REVERT: B 40 LYS cc_start: 0.8489 (tttm) cc_final: 0.8222 (ttmt) REVERT: b 38 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8408 (ttmm) REVERT: b 51 ARG cc_start: 0.7608 (mtp85) cc_final: 0.7336 (mtp85) REVERT: b 55 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: b 62 TYR cc_start: 0.8209 (t80) cc_final: 0.7925 (t80) REVERT: b 82 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8508 (mtmt) REVERT: C 89 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8376 (mt-10) REVERT: C 94 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8163 (mmtm) REVERT: C 95 ASN cc_start: 0.8680 (m-40) cc_final: 0.8202 (m-40) REVERT: D 103 LYS cc_start: 0.8424 (mtpt) cc_final: 0.7865 (mttm) REVERT: D 117 ARG cc_start: 0.8231 (ttp80) cc_final: 0.7158 (ttm-80) REVERT: D 145 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7989 (mtmt) REVERT: D 152 ARG cc_start: 0.8052 (ttp-110) cc_final: 0.7748 (ttp80) REVERT: D 215 MET cc_start: 0.7987 (mtm) cc_final: 0.7753 (mtt) REVERT: d 16 LYS cc_start: 0.5697 (tppt) cc_final: 0.5010 (tmtt) REVERT: E 1 MET cc_start: 0.5606 (OUTLIER) cc_final: 0.4924 (mmm) REVERT: E 141 LYS cc_start: 0.7232 (ttpt) cc_final: 0.6922 (pttp) REVERT: E 143 ARG cc_start: 0.6653 (mpp-170) cc_final: 0.5873 (mtt180) REVERT: E 148 LYS cc_start: 0.8439 (mmpt) cc_final: 0.7962 (mttt) REVERT: E 150 MET cc_start: 0.7389 (mmm) cc_final: 0.7054 (mtt) REVERT: E 178 ARG cc_start: 0.7695 (mmp80) cc_final: 0.7154 (mmp80) REVERT: E 192 TRP cc_start: 0.7581 (t60) cc_final: 0.7141 (t60) REVERT: E 201 LYS cc_start: 0.8886 (mppt) cc_final: 0.8436 (mppt) REVERT: f 91 LYS cc_start: 0.9150 (tppt) cc_final: 0.8620 (tppt) REVERT: f 100 LYS cc_start: 0.8468 (mttm) cc_final: 0.8230 (mttm) REVERT: G 137 GLN cc_start: 0.6846 (tt0) cc_final: 0.6384 (tt0) REVERT: G 191 LYS cc_start: 0.6232 (tptp) cc_final: 0.5872 (mtpp) REVERT: H 12 CYS cc_start: 0.7694 (m) cc_final: 0.6615 (m) REVERT: H 22 ARG cc_start: 0.8567 (ttp-110) cc_final: 0.8325 (mtm110) REVERT: H 48 TYR cc_start: 0.8310 (m-80) cc_final: 0.8071 (m-10) REVERT: H 120 ASP cc_start: 0.8350 (m-30) cc_final: 0.7862 (t0) REVERT: H 133 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6732 (pp) REVERT: H 145 PHE cc_start: 0.8375 (m-10) cc_final: 0.8050 (m-10) REVERT: H 146 ASN cc_start: 0.8537 (m110) cc_final: 0.8099 (p0) REVERT: H 225 GLN cc_start: 0.7672 (mm110) cc_final: 0.7309 (mp10) REVERT: h 60 ARG cc_start: 0.6671 (mtt-85) cc_final: 0.6318 (mmm-85) REVERT: h 118 ARG cc_start: 0.7132 (tpt170) cc_final: 0.6656 (ttp80) REVERT: h 196 ASN cc_start: 0.8111 (t0) cc_final: 0.7658 (t0) REVERT: I 37 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.8003 (mmtp) REVERT: I 43 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7258 (mp) REVERT: I 57 ARG cc_start: 0.7306 (tpp-160) cc_final: 0.7048 (mtm110) REVERT: I 131 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: I 184 ASP cc_start: 0.8563 (p0) cc_final: 0.8184 (p0) REVERT: J 71 CYS cc_start: 0.8114 (t) cc_final: 0.7878 (t) REVERT: J 107 THR cc_start: 0.8274 (m) cc_final: 0.8047 (p) REVERT: J 110 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7769 (tpp80) REVERT: J 151 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7959 (mm-30) REVERT: J 206 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7378 (ptpp) REVERT: K 79 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.6866 (ttp-170) REVERT: K 107 GLU cc_start: 0.7833 (tp30) cc_final: 0.7571 (tp30) REVERT: L 29 MET cc_start: 0.5847 (ppp) cc_final: 0.5394 (pp-130) REVERT: L 53 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7449 (ttpt) REVERT: L 65 ARG cc_start: 0.6431 (mtp180) cc_final: 0.5672 (mtt180) REVERT: L 71 LEU cc_start: 0.5018 (OUTLIER) cc_final: 0.4176 (tp) REVERT: Q 41 GLN cc_start: 0.4419 (mp10) cc_final: 0.4165 (mp10) REVERT: Q 89 MET cc_start: 0.6771 (OUTLIER) cc_final: 0.6326 (mpt) REVERT: Q 111 MET cc_start: 0.1533 (OUTLIER) cc_final: 0.0847 (mmm) REVERT: Q 130 ARG cc_start: 0.5736 (mmm160) cc_final: 0.5466 (mmp-170) REVERT: R 24 HIS cc_start: 0.5734 (t70) cc_final: 0.5437 (t70) REVERT: R 41 MET cc_start: 0.6086 (mtt) cc_final: 0.5692 (ttt) REVERT: R 143 LYS cc_start: 0.5476 (tptt) cc_final: 0.5224 (tptt) REVERT: S 11 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7570 (ttmm) REVERT: S 45 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.5724 (tptm) REVERT: T 70 ILE cc_start: 0.4274 (mm) cc_final: 0.4052 (tp) REVERT: T 116 LYS cc_start: 0.6444 (pptt) cc_final: 0.5906 (mmtt) REVERT: V 34 LYS cc_start: 0.7808 (mmpt) cc_final: 0.7180 (ptmm) REVERT: V 56 MET cc_start: 0.8132 (mmp) cc_final: 0.7743 (mmm) REVERT: V 79 ARG cc_start: 0.7664 (mtt90) cc_final: 0.7464 (mtt90) REVERT: V 86 LYS cc_start: 0.7300 (ttpt) cc_final: 0.6652 (mtmm) REVERT: V 91 LEU cc_start: 0.5270 (OUTLIER) cc_final: 0.5061 (tt) REVERT: W 21 ASN cc_start: 0.8593 (t0) cc_final: 0.7894 (t0) REVERT: W 41 LYS cc_start: 0.9021 (tppt) cc_final: 0.8694 (tppp) REVERT: Z 39 GLU cc_start: 0.8257 (tp30) cc_final: 0.7744 (tp30) REVERT: Z 74 MET cc_start: 0.8388 (mtm) cc_final: 0.8144 (mtt) REVERT: F 154 TYR cc_start: 0.7983 (m-80) cc_final: 0.7759 (m-80) REVERT: M 40 GLU cc_start: 0.8021 (pm20) cc_final: 0.7363 (pm20) REVERT: M 54 TYR cc_start: 0.8683 (m-80) cc_final: 0.8367 (m-80) REVERT: M 62 LYS cc_start: 0.7829 (tptt) cc_final: 0.7528 (ttpt) REVERT: M 66 MET cc_start: 0.8109 (mmt) cc_final: 0.7826 (mmm) REVERT: M 211 LYS cc_start: 0.8070 (tttm) cc_final: 0.7769 (ttmm) REVERT: M 246 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8021 (pp) REVERT: M 251 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7381 (mt-10) REVERT: M 253 ASP cc_start: 0.8452 (m-30) cc_final: 0.8163 (m-30) REVERT: M 255 ARG cc_start: 0.7761 (ttm170) cc_final: 0.7475 (ttp-110) REVERT: O 8 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7005 (mtp85) REVERT: O 49 GLU cc_start: 0.8067 (tp30) cc_final: 0.7672 (tp30) REVERT: O 57 ASP cc_start: 0.7540 (t0) cc_final: 0.6625 (t70) REVERT: O 79 LYS cc_start: 0.7640 (mttm) cc_final: 0.7318 (mtpt) REVERT: O 97 ARG cc_start: 0.6847 (ptm160) cc_final: 0.6348 (ttm110) REVERT: O 121 GLN cc_start: 0.8183 (pt0) cc_final: 0.7199 (pm20) REVERT: O 124 ASP cc_start: 0.7121 (m-30) cc_final: 0.6158 (m-30) REVERT: O 144 LYS cc_start: 0.7898 (ttmm) cc_final: 0.7506 (ttpp) REVERT: P 36 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7853 (mp10) REVERT: P 69 ASN cc_start: 0.8027 (m-40) cc_final: 0.7606 (m-40) REVERT: P 103 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7194 (mm-30) REVERT: X 63 LYS cc_start: 0.5840 (mmtt) cc_final: 0.5261 (mptp) REVERT: X 70 SER cc_start: 0.8583 (t) cc_final: 0.8225 (p) REVERT: X 124 MET cc_start: 0.8070 (mtp) cc_final: 0.7858 (tpt) REVERT: Y 12 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.7112 (tppp) REVERT: Y 22 LYS cc_start: 0.7738 (mmtp) cc_final: 0.7404 (mmtt) REVERT: Y 26 LEU cc_start: 0.8730 (tt) cc_final: 0.8526 (tm) REVERT: Y 90 GLN cc_start: 0.7716 (pt0) cc_final: 0.7371 (pt0) REVERT: Y 107 SER cc_start: 0.8038 (p) cc_final: 0.7642 (m) REVERT: c 1 MET cc_start: 0.2502 (mtp) cc_final: 0.1329 (mtp) REVERT: c 15 SER cc_start: 0.7295 (t) cc_final: 0.7059 (m) REVERT: c 50 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7861 (mm) REVERT: c 95 GLU cc_start: 0.7103 (mp0) cc_final: 0.6831 (mm-30) REVERT: c 96 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7100 (mm-30) REVERT: e 15 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7424 (mm-30) outliers start: 130 outliers final: 81 residues processed: 707 average time/residue: 1.6507 time to fit residues: 1529.6287 Evaluate side-chains 709 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 606 time to evaluate : 4.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain D residue 145 LYS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain d residue 45 ASN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 176 VAL Chi-restraints excluded: chain h residue 217 MET Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain I residue 37 LYS Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain J residue 56 ARG Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 59 LYS Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 38 GLU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 75 ILE Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 250 GLU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 58 HIS Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain P residue 133 ARG Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain c residue 50 ILE Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain c residue 105 PHE Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain e residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 3.9990 chunk 607 optimal weight: 5.9990 chunk 371 optimal weight: 9.9990 chunk 288 optimal weight: 7.9990 chunk 422 optimal weight: 30.0000 chunk 637 optimal weight: 9.9990 chunk 586 optimal weight: 10.0000 chunk 507 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 392 optimal weight: 7.9990 chunk 311 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 112 ASN B 84 GLN B 141 ASN D 134 ASN ** d 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 ASN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 197 GLN ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 143 GLN I 97 GLN I 162 GLN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 GLN M 98 ASN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 GLN ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.154 79914 Z= 0.491 Angle : 0.726 16.873 116006 Z= 0.364 Chirality : 0.047 0.308 14347 Planarity : 0.006 0.077 8425 Dihedral : 23.115 179.146 31895 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.43 % Favored : 93.55 % Rotamer: Outliers : 3.42 % Allowed : 24.37 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.12), residues: 4789 helix: -0.14 (0.14), residues: 1404 sheet: -0.93 (0.18), residues: 859 loop : -1.25 (0.12), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP T 82 HIS 0.012 0.001 HIS J 22 PHE 0.029 0.002 PHE K 147 TYR 0.030 0.002 TYR M 121 ARG 0.015 0.001 ARG J 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9578 Ramachandran restraints generated. 4789 Oldfield, 0 Emsley, 4789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 578 time to evaluate : 4.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 58 LEU cc_start: 0.5339 (tp) cc_final: 0.4995 (mp) REVERT: B 35 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7378 (tm-30) REVERT: B 40 LYS cc_start: 0.8398 (tttm) cc_final: 0.8052 (ttmt) REVERT: b 38 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8389 (ttmm) REVERT: b 55 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: b 62 TYR cc_start: 0.8299 (t80) cc_final: 0.7990 (t80) REVERT: b 82 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8570 (mtmt) REVERT: C 89 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8484 (mt-10) REVERT: C 95 ASN cc_start: 0.8728 (m-40) cc_final: 0.8201 (m-40) REVERT: D 103 LYS cc_start: 0.8397 (mtpt) cc_final: 0.7793 (mttm) REVERT: D 215 MET cc_start: 0.8010 (mtm) cc_final: 0.7766 (mtt) REVERT: d 11 LEU cc_start: 0.8004 (mt) cc_final: 0.7564 (pp) REVERT: d 16 LYS cc_start: 0.5603 (tppt) cc_final: 0.5013 (tmtt) REVERT: d 45 ASN cc_start: 0.5680 (OUTLIER) cc_final: 0.4989 (m-40) REVERT: E 1 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5423 (tmm) REVERT: E 141 LYS cc_start: 0.7392 (ttpt) cc_final: 0.6831 (pttp) REVERT: E 143 ARG cc_start: 0.6626 (mpp-170) cc_final: 0.6079 (mpt-90) REVERT: E 148 LYS cc_start: 0.8425 (mmpt) cc_final: 0.7926 (mttt) REVERT: E 150 MET cc_start: 0.7458 (mmm) cc_final: 0.7093 (mtt) REVERT: E 178 ARG cc_start: 0.7773 (mmp80) cc_final: 0.7189 (mmp80) REVERT: E 192 TRP cc_start: 0.7509 (t60) cc_final: 0.7149 (t60) REVERT: E 201 LYS cc_start: 0.8876 (mppt) cc_final: 0.8443 (mppt) REVERT: f 94 LYS cc_start: 0.8433 (tppt) cc_final: 0.8165 (mttm) REVERT: f 100 LYS cc_start: 0.8499 (mttm) cc_final: 0.8236 (mttp) REVERT: G 137 GLN cc_start: 0.6984 (tt0) cc_final: 0.6576 (tt0) REVERT: G 191 LYS cc_start: 0.6445 (tptp) cc_final: 0.6086 (mtpp) REVERT: H 25 ARG cc_start: 0.8053 (ttp-110) cc_final: 0.7839 (ttp-110) REVERT: H 120 ASP cc_start: 0.8380 (m-30) cc_final: 0.7863 (t0) REVERT: H 133 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6920 (pp) REVERT: H 145 PHE cc_start: 0.8438 (m-10) cc_final: 0.8112 (m-10) REVERT: H 146 ASN cc_start: 0.8478 (m110) cc_final: 0.8047 (p0) REVERT: H 225 GLN cc_start: 0.7748 (mm110) cc_final: 0.7485 (mp10) REVERT: h 118 ARG cc_start: 0.7054 (tpt170) cc_final: 0.6606 (ttp80) REVERT: h 196 ASN cc_start: 0.8093 (t0) cc_final: 0.7623 (t0) REVERT: I 37 LYS cc_start: 0.8161 (mttt) cc_final: 0.7915 (mmtp) REVERT: I 43 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7384 (mp) REVERT: I 57 ARG cc_start: 0.7315 (tpp-160) cc_final: 0.6941 (mtm110) REVERT: I 131 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: I 184 ASP cc_start: 0.8608 (p0) cc_final: 0.8226 (p0) REVERT: J 71 CYS cc_start: 0.8374 (t) cc_final: 0.8069 (t) REVERT: J 107 THR cc_start: 0.8390 (m) cc_final: 0.8104 (p) REVERT: J 110 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7873 (ttm-80) REVERT: K 66 LYS cc_start: 0.8500 (mmpt) cc_final: 0.8170 (mmpt) REVERT: K 79 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.6834 (ttp-170) REVERT: L 53 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7432 (ttpt) REVERT: L 65 ARG cc_start: 0.6464 (mtp180) cc_final: 0.5703 (mtt180) REVERT: L 71 LEU cc_start: 0.5121 (OUTLIER) cc_final: 0.4281 (tp) REVERT: L 85 LEU cc_start: 0.7632 (mp) cc_final: 0.6981 (tt) REVERT: Q 41 GLN cc_start: 0.4430 (mp10) cc_final: 0.4181 (mp10) REVERT: Q 89 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6289 (mpt) REVERT: Q 111 MET cc_start: 0.1831 (OUTLIER) cc_final: 0.1143 (mmm) REVERT: Q 130 ARG cc_start: 0.5822 (mmm160) cc_final: 0.5589 (mmp-170) REVERT: S 11 LYS cc_start: 0.8013 (ttpt) cc_final: 0.7751 (ttmm) REVERT: S 45 LYS cc_start: 0.6500 (OUTLIER) cc_final: 0.5903 (tptm) REVERT: S 63 ARG cc_start: 0.6612 (mmt90) cc_final: 0.5870 (ttm110) REVERT: T 115 LYS cc_start: 0.7340 (OUTLIER) cc_final: 0.7113 (tptt) REVERT: T 116 LYS cc_start: 0.6538 (pptt) cc_final: 0.6053 (mmtp) REVERT: T 144 ARG cc_start: 0.4031 (mmt-90) cc_final: 0.3668 (mpp-170) REVERT: V 34 LYS cc_start: 0.7755 (mmpt) cc_final: 0.7154 (ptmm) REVERT: V 56 MET cc_start: 0.8103 (mmp) cc_final: 0.7541 (mmm) REVERT: V 86 LYS cc_start: 0.7322 (ttpt) cc_final: 0.6701 (mtmm) REVERT: V 91 LEU cc_start: 0.5326 (OUTLIER) cc_final: 0.5052 (tt) REVERT: W 21 ASN cc_start: 0.8616 (t0) cc_final: 0.7955 (t0) REVERT: W 41 LYS cc_start: 0.9047 (tppt) cc_final: 0.8726 (tppp) REVERT: W 74 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8234 (ttpt) REVERT: Z 39 GLU cc_start: 0.8310 (tp30) cc_final: 0.7838 (tp30) REVERT: Z 74 MET cc_start: 0.8392 (mtm) cc_final: 0.8169 (mtt) REVERT: Z 101 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7508 (mppt) REVERT: F 154 TYR cc_start: 0.8293 (m-80) cc_final: 0.8040 (m-80) REVERT: M 40 GLU cc_start: 0.8060 (pm20) cc_final: 0.7375 (pm20) REVERT: M 62 LYS cc_start: 0.7918 (tptt) cc_final: 0.7565 (ttpp) REVERT: M 66 MET cc_start: 0.8146 (mmt) cc_final: 0.7861 (mmm) REVERT: M 127 ARG cc_start: 0.7742 (mtp180) cc_final: 0.7135 (mmm-85) REVERT: M 200 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7952 (mtm180) REVERT: M 211 LYS cc_start: 0.8187 (tttm) cc_final: 0.7884 (ttmm) REVERT: M 237 SER cc_start: 0.8313 (t) cc_final: 0.8046 (t) REVERT: M 246 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8208 (pp) REVERT: M 251 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7264 (mt-10) REVERT: O 4 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7952 (mp) REVERT: O 49 GLU cc_start: 0.8106 (tp30) cc_final: 0.7696 (tp30) REVERT: O 57 ASP cc_start: 0.7743 (t0) cc_final: 0.6707 (t70) REVERT: O 79 LYS cc_start: 0.7819 (mttm) cc_final: 0.7449 (mttt) REVERT: O 97 ARG cc_start: 0.7342 (ptm160) cc_final: 0.6737 (ttm110) REVERT: O 121 GLN cc_start: 0.8307 (pt0) cc_final: 0.7076 (pm20) REVERT: O 124 ASP cc_start: 0.7464 (m-30) cc_final: 0.6421 (m-30) REVERT: P 36 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: P 69 ASN cc_start: 0.8298 (m-40) cc_final: 0.7921 (m-40) REVERT: P 105 ASN cc_start: 0.7844 (m110) cc_final: 0.7489 (m-40) REVERT: X 63 LYS cc_start: 0.5979 (mmtt) cc_final: 0.5289 (mptp) REVERT: X 67 ASP cc_start: 0.7648 (m-30) cc_final: 0.7447 (OUTLIER) REVERT: X 70 SER cc_start: 0.8618 (t) cc_final: 0.8318 (p) REVERT: X 113 GLN cc_start: 0.7418 (mm110) cc_final: 0.7120 (mm-40) REVERT: e 15 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7581 (mm-30) outliers start: 143 outliers final: 92 residues processed: 666 average time/residue: 1.6838 time to fit residues: 1463.5141 Evaluate side-chains 681 residues out of total 4185 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 568 time to evaluate : 4.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain b residue 38 LYS Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 82 LYS Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 45 ASN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 167 TYR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain f residue 102 THR Chi-restraints excluded: chain f residue 109 MET Chi-restraints excluded: chain f residue 118 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain h residue 107 ASP Chi-restraints excluded: chain h residue 137 VAL Chi-restraints excluded: chain h residue 176 VAL Chi-restraints excluded: chain h residue 235 ILE Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 131 GLU Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 4 SER Chi-restraints excluded: chain J residue 56 ARG Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 110 ARG Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 79 ARG Chi-restraints excluded: chain K residue 102 ILE Chi-restraints excluded: chain K residue 152 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 53 LYS Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 89 MET Chi-restraints excluded: chain Q residue 111 MET Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain S residue 8 THR Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 45 LYS Chi-restraints excluded: chain S residue 75 GLU Chi-restraints excluded: chain S residue 130 THR Chi-restraints excluded: chain T residue 12 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 115 LYS Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 87 VAL Chi-restraints excluded: chain V residue 30 LYS Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 59 LYS Chi-restraints excluded: chain V residue 91 LEU Chi-restraints excluded: chain V residue 114 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 75 ILE Chi-restraints excluded: chain Z residue 80 ASP Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 200 ARG Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 254 LYS Chi-restraints excluded: chain O residue 4 ILE Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 99 TYR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 36 GLN Chi-restraints excluded: chain P residue 76 LYS Chi-restraints excluded: chain P residue 133 ARG Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 91 THR Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain Y residue 12 LYS Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 76 SER Chi-restraints excluded: chain Y residue 104 LEU Chi-restraints excluded: chain Y residue 111 MET Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain c residue 82 THR Chi-restraints excluded: chain e residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 0.9990 chunk 540 optimal weight: 0.9990 chunk 155 optimal weight: 30.0000 chunk 468 optimal weight: 10.0000 chunk 74 optimal weight: 50.0000 chunk 141 optimal weight: 30.0000 chunk 508 optimal weight: 8.9990 chunk 212 optimal weight: 7.9990 chunk 522 optimal weight: 0.0570 chunk 64 optimal weight: 50.0000 chunk 93 optimal weight: 0.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 112 ASN B 141 ASN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 45 ASN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 110 GLN ** g 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 GLN H 197 GLN ** h 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN I 162 GLN ** Q 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 HIS Z 106 GLN M 98 ASN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 103 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.176929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.135940 restraints weight = 100133.894| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.84 r_work: 0.3331 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 79914 Z= 0.205 Angle : 0.587 15.755 116006 Z= 0.297 Chirality : 0.038 0.243 14347 Planarity : 0.004 0.063 8425 Dihedral : 23.066 179.195 31895 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.43 % Favored : 94.55 % Rotamer: Outliers : 2.89 % Allowed : 25.11 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.11 (0.12), residues: 4789 helix: 0.11 (0.14), residues: 1396 sheet: -0.84 (0.18), residues: 851 loop : -1.14 (0.12), residues: 2542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 77 HIS 0.008 0.001 HIS D 136 PHE 0.018 0.001 PHE K 147 TYR 0.029 0.001 TYR M 121 ARG 0.015 0.000 ARG d 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24671.60 seconds wall clock time: 434 minutes 58.27 seconds (26098.27 seconds total)