Starting phenix.real_space_refine on Mon Dec 11 08:12:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j79_2660/12_2023/3j79_2660.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j79_2660/12_2023/3j79_2660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j79_2660/12_2023/3j79_2660.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j79_2660/12_2023/3j79_2660.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j79_2660/12_2023/3j79_2660.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j79_2660/12_2023/3j79_2660.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 3460 5.49 5 Mg 163 5.21 5 S 223 5.16 5 C 65240 2.51 5 N 22831 2.21 5 O 32592 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 36": "OE1" <-> "OE2" Residue "D GLU 117": "OE1" <-> "OE2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D ARG 242": "NH1" <-> "NH2" Residue "E GLU 38": "OE1" <-> "OE2" Residue "E ARG 58": "NH1" <-> "NH2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E GLU 187": "OE1" <-> "OE2" Residue "E ARG 234": "NH1" <-> "NH2" Residue "E ARG 241": "NH1" <-> "NH2" Residue "E ARG 256": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E ARG 281": "NH1" <-> "NH2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "F ARG 33": "NH1" <-> "NH2" Residue "F ARG 48": "NH1" <-> "NH2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 113": "NH1" <-> "NH2" Residue "F GLU 179": "OE1" <-> "OE2" Residue "F ARG 190": "NH1" <-> "NH2" Residue "F GLU 349": "OE1" <-> "OE2" Residue "G GLU 25": "OE1" <-> "OE2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 92": "NH1" <-> "NH2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G ARG 137": "NH1" <-> "NH2" Residue "G ARG 141": "NH1" <-> "NH2" Residue "G ARG 145": "NH1" <-> "NH2" Residue "H ARG 39": "NH1" <-> "NH2" Residue "H ARG 70": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H GLU 112": "OE1" <-> "OE2" Residue "H ARG 114": "NH1" <-> "NH2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H ARG 167": "NH1" <-> "NH2" Residue "I ARG 36": "NH1" <-> "NH2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I GLU 55": "OE1" <-> "OE2" Residue "I ARG 102": "NH1" <-> "NH2" Residue "I ARG 170": "NH1" <-> "NH2" Residue "I ARG 211": "NH1" <-> "NH2" Residue "J ARG 76": "NH1" <-> "NH2" Residue "J GLU 119": "OE1" <-> "OE2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J GLU 223": "OE1" <-> "OE2" Residue "J ARG 269": "NH1" <-> "NH2" Residue "K GLU 5": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "K ARG 81": "NH1" <-> "NH2" Residue "K ARG 84": "NH1" <-> "NH2" Residue "K ARG 124": "NH1" <-> "NH2" Residue "K GLU 156": "OE1" <-> "OE2" Residue "K ARG 193": "NH1" <-> "NH2" Residue "L ARG 19": "NH1" <-> "NH2" Residue "L ARG 22": "NH1" <-> "NH2" Residue "L ARG 34": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L GLU 78": "OE1" <-> "OE2" Residue "L ARG 100": "NH1" <-> "NH2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L GLU 113": "OE1" <-> "OE2" Residue "L GLU 164": "OE1" <-> "OE2" Residue "L GLU 172": "OE1" <-> "OE2" Residue "L ARG 191": "NH1" <-> "NH2" Residue "L ARG 197": "NH1" <-> "NH2" Residue "L ARG 198": "NH1" <-> "NH2" Residue "L ARG 201": "NH1" <-> "NH2" Residue "M GLU 91": "OE1" <-> "OE2" Residue "M GLU 98": "OE1" <-> "OE2" Residue "M GLU 123": "OE1" <-> "OE2" Residue "N GLU 9": "OE1" <-> "OE2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N GLU 79": "OE1" <-> "OE2" Residue "N GLU 137": "OE1" <-> "OE2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 42": "NH1" <-> "NH2" Residue "O ARG 59": "NH1" <-> "NH2" Residue "O GLU 89": "OE1" <-> "OE2" Residue "P ARG 24": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 44": "NH1" <-> "NH2" Residue "P ARG 67": "NH1" <-> "NH2" Residue "P GLU 103": "OE1" <-> "OE2" Residue "P ARG 186": "NH1" <-> "NH2" Residue "P ARG 195": "NH1" <-> "NH2" Residue "P ARG 196": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 24": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q GLU 56": "OE1" <-> "OE2" Residue "Q GLU 58": "OE1" <-> "OE2" Residue "Q ARG 98": "NH1" <-> "NH2" Residue "Q ARG 153": "NH1" <-> "NH2" Residue "Q GLU 202": "OE1" <-> "OE2" Residue "R GLU 25": "OE1" <-> "OE2" Residue "R ARG 85": "NH1" <-> "NH2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "R ARG 160": "NH1" <-> "NH2" Residue "R ARG 195": "NH1" <-> "NH2" Residue "R ARG 281": "NH1" <-> "NH2" Residue "S ARG 57": "NH1" <-> "NH2" Residue "S GLU 113": "OE1" <-> "OE2" Residue "S ARG 145": "NH1" <-> "NH2" Residue "S ARG 177": "NH1" <-> "NH2" Residue "T ARG 37": "NH1" <-> "NH2" Residue "T ARG 109": "NH1" <-> "NH2" Residue "U ARG 21": "NH1" <-> "NH2" Residue "U ARG 35": "NH1" <-> "NH2" Residue "U GLU 66": "OE1" <-> "OE2" Residue "U ARG 76": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U GLU 102": "OE1" <-> "OE2" Residue "U ARG 104": "NH1" <-> "NH2" Residue "U GLU 109": "OE1" <-> "OE2" Residue "U ARG 122": "NH1" <-> "NH2" Residue "U ARG 124": "NH1" <-> "NH2" Residue "U ARG 126": "NH1" <-> "NH2" Residue "U ARG 134": "NH1" <-> "NH2" Residue "U ARG 144": "NH1" <-> "NH2" Residue "U ARG 178": "NH1" <-> "NH2" Residue "V ARG 13": "NH1" <-> "NH2" Residue "V ARG 80": "NH1" <-> "NH2" Residue "V ARG 84": "NH1" <-> "NH2" Residue "V GLU 86": "OE1" <-> "OE2" Residue "V ARG 98": "NH1" <-> "NH2" Residue "V ARG 109": "NH1" <-> "NH2" Residue "V GLU 153": "OE1" <-> "OE2" Residue "W GLU 53": "OE1" <-> "OE2" Residue "W ARG 113": "NH1" <-> "NH2" Residue "W ARG 127": "NH1" <-> "NH2" Residue "W ARG 128": "NH1" <-> "NH2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X ARG 121": "NH1" <-> "NH2" Residue "Y GLU 125": "OE1" <-> "OE2" Residue "Y GLU 182": "OE1" <-> "OE2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 59": "NH1" <-> "NH2" Residue "0 ARG 19": "NH1" <-> "NH2" Residue "1 ARG 17": "NH1" <-> "NH2" Residue "1 ARG 18": "NH1" <-> "NH2" Residue "1 GLU 47": "OE1" <-> "OE2" Residue "1 GLU 110": "OE1" <-> "OE2" Residue "1 GLU 132": "OE1" <-> "OE2" Residue "2 GLU 106": "OE1" <-> "OE2" Residue "3 GLU 27": "OE1" <-> "OE2" Residue "3 ARG 105": "NH1" <-> "NH2" Residue "4 ARG 32": "NH1" <-> "NH2" Residue "4 ARG 41": "NH1" <-> "NH2" Residue "5 GLU 62": "OE1" <-> "OE2" Residue "5 GLU 73": "OE1" <-> "OE2" Residue "5 GLU 89": "OE1" <-> "OE2" Residue "5 ARG 109": "NH1" <-> "NH2" Residue "5 ARG 113": "NH1" <-> "NH2" Residue "5 ARG 116": "NH1" <-> "NH2" Residue "5 GLU 140": "OE1" <-> "OE2" Residue "5 ARG 160": "NH1" <-> "NH2" Residue "5 ARG 170": "NH1" <-> "NH2" Residue "5 ARG 173": "NH1" <-> "NH2" Residue "5 ARG 231": "NH1" <-> "NH2" Residue "5 ARG 245": "NH1" <-> "NH2" Residue "5 GLU 246": "OE1" <-> "OE2" Residue "6 ARG 30": "NH1" <-> "NH2" Residue "6 ARG 38": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 43": "OE1" <-> "OE2" Residue "7 ARG 58": "NH1" <-> "NH2" Residue "7 GLU 84": "OE1" <-> "OE2" Residue "8 ARG 19": "NH1" <-> "NH2" Residue "8 ARG 41": "NH1" <-> "NH2" Residue "8 ARG 45": "NH1" <-> "NH2" Residue "8 ARG 111": "NH1" <-> "NH2" Residue "9 GLU 42": "OE1" <-> "OE2" Residue "9 ARG 132": "NH1" <-> "NH2" Residue "a ARG 58": "NH1" <-> "NH2" Residue "a ARG 66": "NH1" <-> "NH2" Residue "b ARG 3": "NH1" <-> "NH2" Residue "b ARG 26": "NH1" <-> "NH2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b ARG 94": "NH1" <-> "NH2" Residue "c ARG 14": "NH1" <-> "NH2" Residue "c ARG 24": "NH1" <-> "NH2" Residue "c ARG 74": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 57": "NH1" <-> "NH2" Residue "e ARG 17": "NH1" <-> "NH2" Residue "e ARG 18": "NH1" <-> "NH2" Residue "e ARG 46": "NH1" <-> "NH2" Residue "f GLU 3": "OE1" <-> "OE2" Residue "f ARG 30": "NH1" <-> "NH2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "g ARG 12": "NH1" <-> "NH2" Residue "g ARG 39": "NH1" <-> "NH2" Residue "h ARG 3": "NH1" <-> "NH2" Residue "h ARG 49": "NH1" <-> "NH2" Residue "i GLU 32": "OE1" <-> "OE2" Residue "i GLU 91": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 124514 Number of models: 1 Model: "" Number of chains: 55 Chain: "A" Number of atoms: 67935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3191, 67935 Classifications: {'RNA': 3191} Modifications used: {'rna2p_pur': 313, 'rna2p_pyr': 214, 'rna3p_pur': 1394, 'rna3p_pyr': 1270} Link IDs: {'rna2p': 527, 'rna3p': 2663} Chain breaks: 32 Chain: "B" Number of atoms: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2525 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 58, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3224 Classifications: {'RNA': 151} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 7, 'rna3p_pur': 69, 'rna3p_pyr': 59} Link IDs: {'rna2p': 23, 'rna3p': 127} Chain breaks: 2 Chain: "D" Number of atoms: 1866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1866 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "E" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3061 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 21, 'TRANS': 358} Chain: "F" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3094 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain: "G" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1010 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 3 Chain: "H" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1460 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 178} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1684 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1873 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "K" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1659 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 192} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1761 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 9, 'TRANS': 201} Chain: "M" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 996 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "N" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1197 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1172 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "P" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1697 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 195} Chain: "Q" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1544 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 10, 'TRANS': 178} Chain breaks: 1 Chain: "R" Number of atoms: 2045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2045 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 245} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1502 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 10, 'TRANS': 175} Chain: "T" Number of atoms: 1505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1505 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 178} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "U" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1496 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain: "V" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1275 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "W" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1318 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "X" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 824 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "Y" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 796 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "Z" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1000 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "0" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 521 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "1" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1134 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain breaks: 1 Chain: "2" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 830 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain breaks: 3 Chain: "3" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 994 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "4" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 555 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "5" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1879 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "6" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 740 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 1, 'TRANS': 96} Chain: "7" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 793 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain breaks: 1 Chain: "8" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1036 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "9" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 844 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "a" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 858 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "b" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 756 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain breaks: 1 Chain: "c" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 705 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "d" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 603 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain breaks: 1 Chain: "e" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 388 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain breaks: 1 Chain: "f" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 413 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "g" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 342 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "h" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "i" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 153 Unusual residues: {' MG': 153} Classifications: {'undetermined': 153} Link IDs: {None: 152} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0ET8 SG CYS a 44 122.067 155.220 194.614 1.00117.20 S ATOM A0F1O SG CYS a 84 119.011 156.949 196.168 1.00126.62 S ATOM A0FWH SG CYS c 22 141.316 112.603 161.075 1.00 80.77 S ATOM A0G00 SG CYS c 37 138.465 111.727 159.206 1.00 78.43 S ATOM A0G0H SG CYS c 40 140.553 108.483 160.792 1.00 85.94 S ATOM A0H7P SG CYS f 20 80.869 128.507 66.301 1.00 96.22 S ATOM A0H8F SG CYS f 23 84.565 130.749 66.859 1.00104.00 S ATOM A0HAX SG CYS f 34 83.442 128.631 64.224 1.00102.33 S ATOM A0HC4 SG CYS f 39 84.166 127.565 67.399 1.00118.41 S ATOM A0HWZ SG CYS h 39 104.011 159.354 189.465 1.00 87.90 S ATOM A0HXN SG CYS h 42 105.422 162.468 189.973 1.00107.61 S ATOM A0I0S SG CYS h 57 106.430 160.661 187.415 1.00105.99 S ATOM A0I1G SG CYS h 60 107.494 159.643 190.689 1.00117.58 S ATOM A0I96 SG CYS i 12 69.768 53.121 145.217 1.00120.19 S ATOM A0I9Z SG CYS i 16 68.323 49.730 146.981 1.00165.24 S ATOM A0IMZ SG CYS i 73 67.054 53.412 147.392 1.00127.64 S ATOM A0INL SG CYS i 76 70.340 51.604 149.624 1.00176.39 S Time building chain proxies: 46.53, per 1000 atoms: 0.37 Number of scatterers: 124514 At special positions: 0 Unit cell: (210.38, 227.8, 247.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 223 16.00 P 3460 15.00 Mg 163 11.99 O 32592 8.00 N 22831 7.00 C 65240 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: 45.27 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 200 " pdb="ZN ZN a 200 " - pdb=" SG CYS a 44 " pdb="ZN ZN a 200 " - pdb=" SG CYS a 84 " pdb=" ZN c 100 " pdb="ZN ZN c 100 " - pdb=" SG CYS c 22 " pdb="ZN ZN c 100 " - pdb=" SG CYS c 37 " pdb="ZN ZN c 100 " - pdb=" SG CYS c 40 " pdb=" ZN f 100 " pdb="ZN ZN f 100 " - pdb=" SG CYS f 39 " pdb="ZN ZN f 100 " - pdb=" SG CYS f 34 " pdb="ZN ZN f 100 " - pdb=" SG CYS f 23 " pdb="ZN ZN f 100 " - pdb=" SG CYS f 20 " pdb=" ZN h 100 " pdb="ZN ZN h 100 " - pdb=" SG CYS h 60 " pdb="ZN ZN h 100 " - pdb=" SG CYS h 42 " pdb="ZN ZN h 100 " - pdb=" SG CYS h 57 " pdb="ZN ZN h 100 " - pdb=" SG CYS h 39 " pdb=" ZN i 201 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 73 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 76 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 12 " pdb="ZN ZN i 201 " - pdb=" SG CYS i 16 " Number of angles added : 18 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11712 Finding SS restraints... Secondary structure from input PDB file: 226 helices and 67 sheets defined 40.7% alpha, 13.8% beta 1044 base pairs and 1897 stacking pairs defined. Time for finding SS restraints: 40.59 Creating SS restraints... Processing helix chain 'D' and resid 5 through 12 removed outlier: 3.972A pdb=" N GLY D 11 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG D 12 " --> pdb=" O GLN D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 39 Processing helix chain 'D' and resid 105 through 107 No H-bonds generated for 'chain 'D' and resid 105 through 107' Processing helix chain 'D' and resid 173 through 177 removed outlier: 3.745A pdb=" N LYS D 177 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 190 removed outlier: 3.545A pdb=" N ALA D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'E' and resid 13 through 17 removed outlier: 3.692A pdb=" N LEU E 17 " --> pdb=" O LEU E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 117 removed outlier: 3.613A pdb=" N ARG E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 152 removed outlier: 3.811A pdb=" N LYS E 141 " --> pdb=" O PRO E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'E' and resid 184 through 196 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'E' and resid 344 through 349 Processing helix chain 'E' and resid 369 through 378 Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 33 through 47 removed outlier: 3.538A pdb=" N ASN F 47 " --> pdb=" O ASN F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 133 Processing helix chain 'F' and resid 133 through 141 Processing helix chain 'F' and resid 156 through 161 Processing helix chain 'F' and resid 163 through 175 Processing helix chain 'F' and resid 176 through 186 Processing helix chain 'F' and resid 191 through 197 removed outlier: 4.424A pdb=" N GLY F 194 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS F 195 " --> pdb=" O GLY F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 222 Processing helix chain 'F' and resid 236 through 241 Processing helix chain 'F' and resid 242 through 245 Processing helix chain 'F' and resid 254 through 264 Processing helix chain 'F' and resid 288 through 295 Processing helix chain 'F' and resid 295 through 302 Processing helix chain 'F' and resid 321 through 329 Processing helix chain 'F' and resid 331 through 345 removed outlier: 3.601A pdb=" N LYS F 345 " --> pdb=" O LEU F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 395 removed outlier: 3.939A pdb=" N LYS F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS F 355 " --> pdb=" O SER F 351 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU F 356 " --> pdb=" O LYS F 352 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE F 363 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLN F 364 " --> pdb=" O GLN F 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 41 Processing helix chain 'G' and resid 72 through 85 removed outlier: 3.998A pdb=" N LYS G 85 " --> pdb=" O GLU G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 141 removed outlier: 3.893A pdb=" N ARG G 140 " --> pdb=" O TYR G 136 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 155 through 166 Processing helix chain 'H' and resid 62 through 85 removed outlier: 3.537A pdb=" N LEU H 66 " --> pdb=" O VAL H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 165 Processing helix chain 'I' and resid 112 through 114 No H-bonds generated for 'chain 'I' and resid 112 through 114' Processing helix chain 'I' and resid 116 through 119 removed outlier: 4.082A pdb=" N LYS I 119 " --> pdb=" O ASN I 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 116 through 119' Processing helix chain 'I' and resid 120 through 131 removed outlier: 3.553A pdb=" N PHE I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 149 removed outlier: 3.664A pdb=" N LEU I 149 " --> pdb=" O LYS I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 173 Processing helix chain 'I' and resid 173 through 197 Proline residue: I 192 - end of helix Processing helix chain 'I' and resid 197 through 206 Processing helix chain 'J' and resid 72 through 88 removed outlier: 6.320A pdb=" N GLN J 78 " --> pdb=" O TYR J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 97 Processing helix chain 'J' and resid 102 through 116 removed outlier: 3.955A pdb=" N ALA J 115 " --> pdb=" O ASN J 111 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR J 116 " --> pdb=" O PHE J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 120 through 131 Processing helix chain 'J' and resid 152 through 162 Processing helix chain 'J' and resid 177 through 191 removed outlier: 4.547A pdb=" N PHE J 182 " --> pdb=" O GLU J 178 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU J 183 " --> pdb=" O LEU J 179 " (cutoff:3.500A) Proline residue: J 184 - end of helix Processing helix chain 'J' and resid 199 through 206 Processing helix chain 'J' and resid 224 through 239 Processing helix chain 'J' and resid 242 through 248 removed outlier: 3.999A pdb=" N ARG J 246 " --> pdb=" O ASN J 242 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 268 Processing helix chain 'J' and resid 268 through 283 Processing helix chain 'K' and resid 14 through 30 removed outlier: 3.946A pdb=" N GLN K 30 " --> pdb=" O LEU K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 39 Processing helix chain 'K' and resid 45 through 59 Processing helix chain 'K' and resid 74 through 86 Processing helix chain 'K' and resid 92 through 100 Processing helix chain 'K' and resid 119 through 122 Processing helix chain 'K' and resid 123 through 128 Processing helix chain 'K' and resid 137 through 144 Processing helix chain 'K' and resid 149 through 186 removed outlier: 4.141A pdb=" N ASN K 186 " --> pdb=" O THR K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 199 Processing helix chain 'L' and resid 16 through 19 Processing helix chain 'L' and resid 26 through 45 Processing helix chain 'L' and resid 60 through 65 removed outlier: 4.055A pdb=" N TYR L 64 " --> pdb=" O PRO L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 83 Processing helix chain 'L' and resid 85 through 92 Processing helix chain 'L' and resid 104 through 122 Processing helix chain 'L' and resid 144 through 154 Processing helix chain 'L' and resid 177 through 179 No H-bonds generated for 'chain 'L' and resid 177 through 179' Processing helix chain 'L' and resid 184 through 195 Processing helix chain 'L' and resid 195 through 211 Processing helix chain 'M' and resid 121 through 126 Processing helix chain 'M' and resid 128 through 134 removed outlier: 3.789A pdb=" N ALA M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 16 removed outlier: 3.763A pdb=" N TYR N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 74 No H-bonds generated for 'chain 'N' and resid 72 through 74' Processing helix chain 'N' and resid 88 through 100 Processing helix chain 'N' and resid 100 through 108 Processing helix chain 'N' and resid 108 through 123 Processing helix chain 'N' and resid 124 through 150 Processing helix chain 'O' and resid 2 through 5 Processing helix chain 'O' and resid 6 through 11 removed outlier: 3.659A pdb=" N LYS O 10 " --> pdb=" O LYS O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 41 through 49 Processing helix chain 'O' and resid 76 through 82 removed outlier: 4.299A pdb=" N TRP O 79 " --> pdb=" O ASP O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 93 Processing helix chain 'O' and resid 130 through 140 Processing helix chain 'P' and resid 3 through 14 removed outlier: 3.534A pdb=" N LYS P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS P 14 " --> pdb=" O ILE P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 33 removed outlier: 3.519A pdb=" N GLN P 32 " --> pdb=" O TRP P 28 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 51 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 97 through 109 removed outlier: 4.287A pdb=" N SER P 109 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 removed outlier: 3.816A pdb=" N ASN P 146 " --> pdb=" O ALA P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 158 Proline residue: P 155 - end of helix Processing helix chain 'P' and resid 159 through 164 removed outlier: 3.639A pdb=" N GLY P 164 " --> pdb=" O GLU P 161 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 173 Processing helix chain 'P' and resid 179 through 183 removed outlier: 3.714A pdb=" N ALA P 183 " --> pdb=" O HIS P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 198 Processing helix chain 'Q' and resid 61 through 80 Processing helix chain 'Q' and resid 144 through 157 Processing helix chain 'Q' and resid 177 through 187 Processing helix chain 'R' and resid 9 through 16 Processing helix chain 'R' and resid 20 through 26 Processing helix chain 'R' and resid 30 through 38 removed outlier: 3.538A pdb=" N ALA R 35 " --> pdb=" O ARG R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 87 removed outlier: 4.043A pdb=" N ILE R 84 " --> pdb=" O LYS R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 114 Processing helix chain 'R' and resid 159 through 171 removed outlier: 3.708A pdb=" N ALA R 163 " --> pdb=" O ASN R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 182 removed outlier: 4.460A pdb=" N ARG R 181 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE R 182 " --> pdb=" O ASN R 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 178 through 182' Processing helix chain 'R' and resid 190 through 200 removed outlier: 3.634A pdb=" N LEU R 194 " --> pdb=" O ASN R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 213 Processing helix chain 'R' and resid 214 through 222 Processing helix chain 'R' and resid 222 through 229 Processing helix chain 'R' and resid 233 through 249 removed outlier: 4.518A pdb=" N GLN R 237 " --> pdb=" O ASP R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 293 Processing helix chain 'S' and resid 23 through 40 Processing helix chain 'S' and resid 43 through 54 Processing helix chain 'S' and resid 55 through 59 Processing helix chain 'S' and resid 64 through 72 Processing helix chain 'S' and resid 105 through 115 Processing helix chain 'S' and resid 121 through 129 Processing helix chain 'S' and resid 147 through 151 Processing helix chain 'T' and resid 3 through 15 Processing helix chain 'T' and resid 17 through 19 No H-bonds generated for 'chain 'T' and resid 17 through 19' Processing helix chain 'T' and resid 27 through 33 Processing helix chain 'T' and resid 36 through 47 Processing helix chain 'T' and resid 59 through 71 Processing helix chain 'T' and resid 76 through 80 removed outlier: 3.723A pdb=" N ARG T 80 " --> pdb=" O ILE T 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 88 Processing helix chain 'T' and resid 89 through 111 Processing helix chain 'T' and resid 115 through 129 Processing helix chain 'T' and resid 133 through 182 Processing helix chain 'U' and resid 42 through 58 Processing helix chain 'U' and resid 61 through 63 No H-bonds generated for 'chain 'U' and resid 61 through 63' Processing helix chain 'U' and resid 107 through 124 Processing helix chain 'U' and resid 126 through 128 No H-bonds generated for 'chain 'U' and resid 126 through 128' Processing helix chain 'U' and resid 145 through 150 Processing helix chain 'V' and resid 29 through 33 removed outlier: 3.595A pdb=" N GLU V 33 " --> pdb=" O LYS V 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 59 Processing helix chain 'V' and resid 101 through 124 Processing helix chain 'V' and resid 145 through 149 removed outlier: 3.983A pdb=" N ILE V 149 " --> pdb=" O PRO V 146 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 12 No H-bonds generated for 'chain 'W' and resid 10 through 12' Processing helix chain 'W' and resid 25 through 37 Processing helix chain 'W' and resid 40 through 53 Processing helix chain 'W' and resid 71 through 77 removed outlier: 3.762A pdb=" N LYS W 74 " --> pdb=" O ASN W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 105 Processing helix chain 'W' and resid 108 through 110 No H-bonds generated for 'chain 'W' and resid 108 through 110' Processing helix chain 'W' and resid 188 through 203 Processing helix chain 'X' and resid 46 through 51 Processing helix chain 'X' and resid 56 through 68 Processing helix chain 'X' and resid 99 through 114 removed outlier: 3.700A pdb=" N ILE X 103 " --> pdb=" O SER X 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 106 through 110 Processing helix chain 'Y' and resid 117 through 128 removed outlier: 3.884A pdb=" N ASN Y 128 " --> pdb=" O ILE Y 124 " (cutoff:3.500A) Processing helix chain 'Y' and resid 139 through 151 Processing helix chain 'Y' and resid 179 through 188 Processing helix chain 'Z' and resid 10 through 21 Processing helix chain 'Z' and resid 22 through 29 Processing helix chain 'Z' and resid 35 through 42 Processing helix chain 'Z' and resid 99 through 101 No H-bonds generated for 'chain 'Z' and resid 99 through 101' Processing helix chain 'Z' and resid 111 through 122 Processing helix chain '0' and resid 40 through 49 Processing helix chain '0' and resid 52 through 56 Processing helix chain '0' and resid 59 through 66 Processing helix chain '1' and resid 58 through 66 Processing helix chain '1' and resid 76 through 78 No H-bonds generated for 'chain '1' and resid 76 through 78' Processing helix chain '1' and resid 92 through 97 removed outlier: 3.612A pdb=" N LEU 1 96 " --> pdb=" O ASP 1 92 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA 1 97 " --> pdb=" O ILE 1 93 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 92 through 97' Processing helix chain '1' and resid 98 through 104 removed outlier: 4.159A pdb=" N LYS 1 103 " --> pdb=" O ASP 1 99 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER 1 104 " --> pdb=" O ASP 1 100 " (cutoff:3.500A) Processing helix chain '1' and resid 106 through 124 Processing helix chain '1' and resid 134 through 142 Processing helix chain '2' and resid 5 through 14 Processing helix chain '2' and resid 87 through 96 Processing helix chain '2' and resid 104 through 118 Processing helix chain '3' and resid 5 through 10 removed outlier: 3.937A pdb=" N LEU 3 9 " --> pdb=" O LYS 3 5 " (cutoff:3.500A) Processing helix chain '3' and resid 13 through 37 Processing helix chain '3' and resid 45 through 72 Processing helix chain '3' and resid 87 through 93 Processing helix chain '3' and resid 95 through 101 Processing helix chain '3' and resid 103 through 113 Processing helix chain '4' and resid 11 through 18 Processing helix chain '4' and resid 38 through 67 Processing helix chain '5' and resid 36 through 81 Processing helix chain '5' and resid 105 through 116 Processing helix chain '5' and resid 130 through 139 Processing helix chain '5' and resid 149 through 161 Processing helix chain '5' and resid 179 through 186 removed outlier: 4.389A pdb=" N HIS 5 185 " --> pdb=" O ASP 5 181 " (cutoff:3.500A) Processing helix chain '5' and resid 192 through 203 removed outlier: 4.458A pdb=" N ASP 5 196 " --> pdb=" O HIS 5 192 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET 5 197 " --> pdb=" O GLY 5 193 " (cutoff:3.500A) Processing helix chain '5' and resid 208 through 215 Processing helix chain '5' and resid 248 through 256 Processing helix chain '6' and resid 9 through 23 Processing helix chain '6' and resid 29 through 40 Processing helix chain '6' and resid 52 through 67 Processing helix chain '6' and resid 76 through 84 Processing helix chain '7' and resid 24 through 29 Processing helix chain '7' and resid 35 through 53 Processing helix chain '7' and resid 60 through 69 Processing helix chain '8' and resid 54 through 58 Processing helix chain '8' and resid 78 through 83 removed outlier: 3.649A pdb=" N GLU 8 83 " --> pdb=" O VAL 8 79 " (cutoff:3.500A) Processing helix chain '8' and resid 84 through 86 No H-bonds generated for 'chain '8' and resid 84 through 86' Processing helix chain '8' and resid 101 through 116 Processing helix chain '9' and resid 70 through 77 removed outlier: 3.504A pdb=" N PHE 9 76 " --> pdb=" O LYS 9 72 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR 9 77 " --> pdb=" O HIS 9 73 " (cutoff:3.500A) Processing helix chain '9' and resid 123 through 127 Processing helix chain 'a' and resid 58 through 65 removed outlier: 3.869A pdb=" N TYR a 63 " --> pdb=" O PRO a 59 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG a 64 " --> pdb=" O ALA a 60 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 71 removed outlier: 3.725A pdb=" N ARG a 70 " --> pdb=" O ARG a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 81 through 107 removed outlier: 3.620A pdb=" N GLU a 96 " --> pdb=" O ALA a 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 53 Processing helix chain 'b' and resid 55 through 68 removed outlier: 3.684A pdb=" N GLY b 68 " --> pdb=" O LEU b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 69 through 85 Processing helix chain 'b' and resid 86 through 106 Processing helix chain 'c' and resid 7 through 12 Processing helix chain 'c' and resid 53 through 59 Processing helix chain 'c' and resid 69 through 74 Processing helix chain 'c' and resid 75 through 80 Processing helix chain 'd' and resid 7 through 17 Processing helix chain 'd' and resid 56 through 67 Processing helix chain 'e' and resid 6 through 21 removed outlier: 3.626A pdb=" N ARG e 21 " --> pdb=" O ARG e 17 " (cutoff:3.500A) Processing helix chain 'e' and resid 24 through 30 Processing helix chain 'f' and resid 3 through 15 Processing helix chain 'g' and resid 16 through 39 Processing helix chain 'h' and resid 8 through 14 removed outlier: 3.786A pdb=" N THR h 11 " --> pdb=" O VAL h 8 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS h 13 " --> pdb=" O LEU h 10 " (cutoff:3.500A) Processing helix chain 'h' and resid 19 through 35 Processing helix chain 'h' and resid 73 through 86 Processing helix chain 'i' and resid 36 through 47 Processing sheet with id= A, first strand: chain 'D' and resid 71 through 77 removed outlier: 3.630A pdb=" N ASP D 47 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 62 " --> pdb=" O VAL D 45 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL D 45 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N LYS D 64 " --> pdb=" O GLY D 43 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N GLY D 43 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 101 through 103 removed outlier: 6.124A pdb=" N VAL D 136 " --> pdb=" O ARG D 149 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG D 149 " --> pdb=" O VAL D 136 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 224 through 225 Processing sheet with id= D, first strand: chain 'E' and resid 42 through 43 removed outlier: 4.822A pdb=" N LEU E 155 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL E 154 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY E 91 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG E 156 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE E 89 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE E 158 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL E 87 " --> pdb=" O TRP E 106 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TRP E 106 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE E 89 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N THR E 104 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY E 91 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 42 through 43 removed outlier: 4.822A pdb=" N LEU E 155 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL E 154 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY E 91 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG E 156 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE E 89 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE E 158 " --> pdb=" O VAL E 87 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 353 through 356 removed outlier: 6.424A pdb=" N VAL E 57 " --> pdb=" O LYS E 354 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE E 356 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N HIS E 55 " --> pdb=" O ILE E 356 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL E 217 " --> pdb=" O PRO E 332 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ILE E 212 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS E 278 " --> pdb=" O LYS E 322 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU E 320 " --> pdb=" O TYR E 280 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE E 282 " --> pdb=" O PHE E 318 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N PHE E 318 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE E 72 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N VAL E 57 " --> pdb=" O ILE E 72 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLU E 74 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N HIS E 55 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS E 76 " --> pdb=" O MET E 53 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N MET E 53 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE E 78 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 223 through 224 Processing sheet with id= H, first strand: chain 'F' and resid 7 through 8 Processing sheet with id= I, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.547A pdb=" N LEU F 152 " --> pdb=" O TRP F 252 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 188 through 189 Processing sheet with id= K, first strand: chain 'G' and resid 46 through 48 Processing sheet with id= L, first strand: chain 'H' and resid 5 through 10 Processing sheet with id= M, first strand: chain 'H' and resid 17 through 18 removed outlier: 3.848A pdb=" N VAL H 25 " --> pdb=" O ARG H 36 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 132 through 135 removed outlier: 6.244A pdb=" N ARG H 92 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL H 180 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL H 94 " --> pdb=" O ILE H 178 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE H 178 " --> pdb=" O VAL H 94 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 101 through 105 removed outlier: 4.126A pdb=" N ARG H 110 " --> pdb=" O VAL H 105 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 20 through 22 Processing sheet with id= Q, first strand: chain 'I' and resid 28 through 29 Processing sheet with id= R, first strand: chain 'I' and resid 97 through 99 removed outlier: 6.566A pdb=" N ALA I 84 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS I 58 " --> pdb=" O ILE I 74 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL I 59 " --> pdb=" O THR I 107 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 89 through 90 Processing sheet with id= T, first strand: chain 'J' and resid 150 through 151 removed outlier: 6.688A pdb=" N VAL J 168 " --> pdb=" O CYS J 195 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL J 197 " --> pdb=" O VAL J 168 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE J 170 " --> pdb=" O VAL J 197 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 101 through 103 removed outlier: 6.743A pdb=" N TYR K 6 " --> pdb=" O VAL K 33 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL K 35 " --> pdb=" O TYR K 6 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE K 8 " --> pdb=" O VAL K 35 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 41 through 42 Processing sheet with id= W, first strand: chain 'L' and resid 21 through 22 Processing sheet with id= X, first strand: chain 'L' and resid 56 through 58 Processing sheet with id= Y, first strand: chain 'L' and resid 171 through 175 removed outlier: 8.497A pdb=" N VAL O 123 " --> pdb=" O ILE O 96 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N LYS O 125 " --> pdb=" O PRO O 98 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE O 100 " --> pdb=" O LYS O 125 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 24 through 26 removed outlier: 6.443A pdb=" N LEU M 61 " --> pdb=" O ILE M 39 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL M 41 " --> pdb=" O MET M 59 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N MET M 59 " --> pdb=" O VAL M 41 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN M 77 " --> pdb=" O VAL M 105 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA M 101 " --> pdb=" O CYS M 81 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N GLY M 102 " --> pdb=" O LEU M 24 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN M 26 " --> pdb=" O GLY M 102 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE M 104 " --> pdb=" O ASN M 26 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 87 through 88 removed outlier: 6.241A pdb=" N TYR M 94 " --> pdb=" O LYS 0 27 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE 0 29 " --> pdb=" O TYR M 94 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR M 96 " --> pdb=" O ILE 0 29 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'N' and resid 24 through 25 Processing sheet with id= AC, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.572A pdb=" N ILE N 55 " --> pdb=" O VAL N 46 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE N 48 " --> pdb=" O ARG N 53 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG N 53 " --> pdb=" O ILE N 48 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'O' and resid 72 through 74 removed outlier: 6.019A pdb=" N ILE O 73 " --> pdb=" O LEU O 111 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'P' and resid 36 through 39 removed outlier: 4.329A pdb=" N ILE P 61 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU P 132 " --> pdb=" O TRP P 121 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N TRP P 121 " --> pdb=" O GLU P 132 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE P 134 " --> pdb=" O SER P 119 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N SER P 119 " --> pdb=" O ILE P 134 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N VAL P 136 " --> pdb=" O LEU P 117 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU P 117 " --> pdb=" O VAL P 136 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Q' and resid 35 through 36 removed outlier: 6.599A pdb=" N LEU Q 52 " --> pdb=" O LEU Q 135 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER Q 137 " --> pdb=" O VAL Q 50 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL Q 50 " --> pdb=" O SER Q 137 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG Q 139 " --> pdb=" O GLY Q 48 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLY Q 48 " --> pdb=" O ARG Q 139 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'Q' and resid 98 through 99 Processing sheet with id= AH, first strand: chain 'Q' and resid 190 through 192 Processing sheet with id= AI, first strand: chain 'R' and resid 74 through 79 removed outlier: 3.665A pdb=" N ALA R 76 " --> pdb=" O ILE R 64 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'S' and resid 62 through 63 removed outlier: 6.439A pdb=" N ALA S 79 " --> pdb=" O CYS S 100 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N LEU S 102 " --> pdb=" O ALA S 79 " (cutoff:3.500A) removed outlier: 9.245A pdb=" N VAL S 81 " --> pdb=" O LEU S 102 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N PHE S 104 " --> pdb=" O VAL S 81 " (cutoff:3.500A) removed outlier: 11.097A pdb=" N GLY S 83 " --> pdb=" O PHE S 104 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL S 99 " --> pdb=" O LEU S 120 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'S' and resid 62 through 63 removed outlier: 4.407A pdb=" N VAL S 82 " --> pdb=" O LEU S 138 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'T' and resid 21 through 23 Processing sheet with id= AM, first strand: chain 'U' and resid 33 through 40 removed outlier: 6.456A pdb=" N ARG U 21 " --> pdb=" O LEU U 67 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU U 67 " --> pdb=" O ARG U 21 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'U' and resid 96 through 105 removed outlier: 6.932A pdb=" N ASN U 83 " --> pdb=" O GLU U 137 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU U 137 " --> pdb=" O ASN U 83 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY U 85 " --> pdb=" O ILE U 135 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE U 135 " --> pdb=" O GLY U 85 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU U 87 " --> pdb=" O ILE U 133 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'V' and resid 84 through 93 removed outlier: 6.549A pdb=" N GLY V 72 " --> pdb=" O ILE V 68 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE V 68 " --> pdb=" O GLY V 72 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY V 74 " --> pdb=" O PHE V 66 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASN V 78 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR V 62 " --> pdb=" O ASN V 78 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'V' and resid 140 through 142 Processing sheet with id= AQ, first strand: chain 'W' and resid 14 through 22 removed outlier: 4.194A pdb=" N ASP W 21 " --> pdb=" O CYS W 144 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N CYS W 144 " --> pdb=" O ASP W 21 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS W 145 " --> pdb=" O VAL W 119 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL W 119 " --> pdb=" O HIS W 145 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN W 147 " --> pdb=" O VAL W 117 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL W 117 " --> pdb=" O GLN W 147 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE W 149 " --> pdb=" O ILE W 115 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'W' and resid 58 through 59 Processing sheet with id= AS, first strand: chain 'W' and resid 128 through 131 Processing sheet with id= AT, first strand: chain 'X' and resid 81 through 85 removed outlier: 7.927A pdb=" N TYR X 130 " --> pdb=" O LYS X 41 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL X 43 " --> pdb=" O TYR X 130 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE X 132 " --> pdb=" O VAL X 43 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASP X 45 " --> pdb=" O PHE X 132 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ALA X 129 " --> pdb=" O LYS X 125 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Y' and resid 111 through 114 Processing sheet with id= AV, first strand: chain 'Z' and resid 46 through 48 removed outlier: 8.546A pdb=" N SER Z 31 " --> pdb=" O VAL Z 103 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LEU Z 105 " --> pdb=" O SER Z 31 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS Z 33 " --> pdb=" O LEU Z 105 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N LYS Z 107 " --> pdb=" O LYS Z 33 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LEU Z 105 " --> pdb=" O LEU Z 56 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU Z 56 " --> pdb=" O LEU Z 105 " (cutoff:3.500A) removed outlier: 11.115A pdb=" N GLU Z 66 " --> pdb=" O VAL Z 84 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL Z 84 " --> pdb=" O GLU Z 66 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS Z 68 " --> pdb=" O GLU Z 82 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR Z 80 " --> pdb=" O VAL Z 70 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE Z 72 " --> pdb=" O LYS Z 78 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS Z 78 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL Z 81 " --> pdb=" O ILE Z 96 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE Z 96 " --> pdb=" O VAL Z 81 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N ARG Z 83 " --> pdb=" O THR Z 94 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N THR Z 94 " --> pdb=" O ARG Z 83 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain '0' and resid 11 through 12 Processing sheet with id= AX, first strand: chain '1' and resid 69 through 73 removed outlier: 6.775A pdb=" N LYS 1 69 " --> pdb=" O GLU 1 47 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS 1 22 " --> pdb=" O ILE 1 46 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS 1 9 " --> pdb=" O ILE 1 25 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL 1 10 " --> pdb=" O THR 1 83 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '2' and resid 20 through 22 Processing sheet with id= AZ, first strand: chain '2' and resid 57 through 58 Processing sheet with id= BA, first strand: chain '5' and resid 143 through 146 removed outlier: 5.150A pdb=" N ASN 5 122 " --> pdb=" O ARG 5 97 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain '5' and resid 162 through 164 Processing sheet with id= BC, first strand: chain '6' and resid 24 through 28 removed outlier: 6.212A pdb=" N LYS 6 25 " --> pdb=" O THR 6 96 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain '7' and resid 17 through 23 removed outlier: 3.526A pdb=" N TYR 7 98 " --> pdb=" O LYS 7 86 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain '8' and resid 4 through 5 removed outlier: 3.613A pdb=" N LYS 8 11 " --> pdb=" O LYS 8 4 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain '8' and resid 72 through 76 Processing sheet with id= BG, first strand: chain '9' and resid 97 through 102 removed outlier: 4.998A pdb=" N VAL 9 85 " --> pdb=" O ARG 9 130 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARG 9 130 " --> pdb=" O VAL 9 85 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU 9 62 " --> pdb=" O LEU 9 47 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG 9 106 " --> pdb=" O ARG 9 115 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'a' and resid 19 through 24 removed outlier: 4.716A pdb=" N LYS a 19 " --> pdb=" O VAL a 35 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'c' and resid 19 through 20 Processing sheet with id= BJ, first strand: chain 'd' and resid 3 through 4 removed outlier: 6.712A pdb=" N LYS d 3 " --> pdb=" O THR d 51 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL d 53 " --> pdb=" O LYS d 3 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA d 22 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL d 23 " --> pdb=" O ILE d 74 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'f' and resid 26 through 27 Processing sheet with id= BL, first strand: chain 'h' and resid 48 through 49 Processing sheet with id= BM, first strand: chain 'i' and resid 3 through 4 Processing sheet with id= BN, first strand: chain 'i' and resid 7 through 11 Processing sheet with id= BO, first strand: chain 'i' and resid 65 through 66 removed outlier: 4.630A pdb=" N LYS i 65 " --> pdb=" O CYS i 87 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N CYS i 87 " --> pdb=" O LYS i 65 " (cutoff:3.500A) No H-bonds generated for sheet with id= BO 2080 hydrogen bonds defined for protein. 5862 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2500 hydrogen bonds 4186 hydrogen bond angles 0 basepair planarities 1044 basepair parallelities 1897 stacking parallelities Total time for adding SS restraints: 209.59 Time building geometry restraints manager: 49.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 13024 1.32 - 1.44: 55472 1.44 - 1.57: 58224 1.57 - 1.70: 6896 1.70 - 1.82: 319 Bond restraints: 133935 Sorted by residual: bond pdb=" CA GLN F 38 " pdb=" C GLN F 38 " ideal model delta sigma weight residual 1.524 1.468 0.057 1.24e-02 6.50e+03 2.09e+01 bond pdb=" O3' U A2463 " pdb=" P G A2464 " ideal model delta sigma weight residual 1.607 1.541 0.066 1.50e-02 4.44e+03 1.91e+01 bond pdb=" CA ILE Y 187 " pdb=" CB ILE Y 187 " ideal model delta sigma weight residual 1.540 1.594 -0.055 1.29e-02 6.01e+03 1.81e+01 bond pdb=" CA TYR K 167 " pdb=" C TYR K 167 " ideal model delta sigma weight residual 1.523 1.471 0.052 1.30e-02 5.92e+03 1.61e+01 bond pdb=" C VAL 3 59 " pdb=" O VAL 3 59 " ideal model delta sigma weight residual 1.237 1.281 -0.044 1.13e-02 7.83e+03 1.50e+01 ... (remaining 133930 not shown) Histogram of bond angle deviations from ideal: 97.26 - 104.72: 15285 104.72 - 112.19: 69867 112.19 - 119.65: 52751 119.65 - 127.12: 50375 127.12 - 134.58: 8744 Bond angle restraints: 197022 Sorted by residual: angle pdb=" C4' A A 683 " pdb=" C3' A A 683 " pdb=" O3' A A 683 " ideal model delta sigma weight residual 109.40 125.61 -16.21 1.50e+00 4.44e-01 1.17e+02 angle pdb=" O3' U A1805 " pdb=" C3' U A1805 " pdb=" C2' U A1805 " ideal model delta sigma weight residual 113.70 128.62 -14.92 1.50e+00 4.44e-01 9.90e+01 angle pdb=" O3' A A 289 " pdb=" C3' A A 289 " pdb=" C2' A A 289 " ideal model delta sigma weight residual 113.70 127.98 -14.28 1.50e+00 4.44e-01 9.07e+01 angle pdb=" C4' C A1574 " pdb=" C3' C A1574 " pdb=" O3' C A1574 " ideal model delta sigma weight residual 109.40 123.52 -14.12 1.50e+00 4.44e-01 8.86e+01 angle pdb=" C4' A A 773 " pdb=" C3' A A 773 " pdb=" O3' A A 773 " ideal model delta sigma weight residual 109.40 123.49 -14.09 1.50e+00 4.44e-01 8.83e+01 ... (remaining 197017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 72311 35.99 - 71.98: 7367 71.98 - 107.97: 880 107.97 - 143.96: 51 143.96 - 179.95: 110 Dihedral angle restraints: 80719 sinusoidal: 62589 harmonic: 18130 Sorted by residual: dihedral pdb=" CA TRP D 196 " pdb=" C TRP D 196 " pdb=" N PRO D 197 " pdb=" CA PRO D 197 " ideal model delta harmonic sigma weight residual -180.00 -106.57 -73.43 0 5.00e+00 4.00e-02 2.16e+02 dihedral pdb=" CA HIS E 253 " pdb=" C HIS E 253 " pdb=" N PRO E 254 " pdb=" CA PRO E 254 " ideal model delta harmonic sigma weight residual 180.00 112.26 67.74 0 5.00e+00 4.00e-02 1.84e+02 dihedral pdb=" CA TYR 9 136 " pdb=" C TYR 9 136 " pdb=" N PRO 9 137 " pdb=" CA PRO 9 137 " ideal model delta harmonic sigma weight residual -180.00 -120.55 -59.45 0 5.00e+00 4.00e-02 1.41e+02 ... (remaining 80716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 20980 0.154 - 0.308: 3649 0.308 - 0.463: 102 0.463 - 0.617: 35 0.617 - 0.771: 7 Chirality restraints: 24773 Sorted by residual: chirality pdb=" C3' A A3476 " pdb=" C4' A A3476 " pdb=" O3' A A3476 " pdb=" C2' A A3476 " both_signs ideal model delta sigma weight residual False -2.74 -1.97 -0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" C3' U A1750 " pdb=" C4' U A1750 " pdb=" O3' U A1750 " pdb=" C2' U A1750 " both_signs ideal model delta sigma weight residual False -2.74 -2.00 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" C3' U A 889 " pdb=" C4' U A 889 " pdb=" O3' U A 889 " pdb=" C2' U A 889 " both_signs ideal model delta sigma weight residual False -2.74 -2.06 -0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 24770 not shown) Planarity restraints: 12011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP D 196 " -0.100 5.00e-02 4.00e+02 1.53e-01 3.75e+01 pdb=" N PRO D 197 " 0.265 5.00e-02 4.00e+02 pdb=" CA PRO D 197 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO D 197 " -0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR 9 136 " -0.097 5.00e-02 4.00e+02 1.46e-01 3.40e+01 pdb=" N PRO 9 137 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO 9 137 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO 9 137 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 17 " -0.091 5.00e-02 4.00e+02 1.39e-01 3.11e+01 pdb=" N PRO E 18 " 0.241 5.00e-02 4.00e+02 pdb=" CA PRO E 18 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO E 18 " -0.071 5.00e-02 4.00e+02 ... (remaining 12008 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 115 2.18 - 2.86: 38220 2.86 - 3.54: 184669 3.54 - 4.22: 390616 4.22 - 4.90: 534912 Nonbonded interactions: 1148532 Sorted by model distance: nonbonded pdb=" O2' A A3660 " pdb=" O5' A A3661 " model vdw 1.505 2.440 nonbonded pdb=" N7 G A3121 " pdb=" NH2 ARG L 201 " model vdw 1.510 2.600 nonbonded pdb=" OP1 A A3176 " pdb="MG MG A3917 " model vdw 1.748 2.170 nonbonded pdb=" OP2 U C 109 " pdb="MG MG C 202 " model vdw 1.788 2.170 nonbonded pdb=" O2 C A3123 " pdb=" NH2 ARG L 202 " model vdw 1.799 2.520 ... (remaining 1148527 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 14.360 Check model and map are aligned: 1.360 Set scattering table: 0.810 Process input model: 444.140 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 468.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 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 0.066 133935 Z= 0.434 Angle : 1.306 16.210 197022 Z= 0.892 Chirality : 0.102 0.771 24773 Planarity : 0.007 0.153 12011 Dihedral : 23.506 179.949 69007 Min Nonbonded Distance : 1.505 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 2.42 % Allowed : 7.15 % Favored : 90.43 % Rotamer: Outliers : 11.66 % Allowed : 13.68 % Favored : 74.66 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.73 % Twisted General : 0.12 % 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: -1.45 (0.10), residues: 6124 helix: 1.05 (0.09), residues: 2241 sheet: -2.07 (0.15), residues: 863 loop : -2.26 (0.10), residues: 3020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP 5 242 HIS 0.010 0.002 HIS E 253 PHE 0.034 0.003 PHE U 39 TYR 0.046 0.003 TYR 9 136 ARG 0.011 0.001 ARG a 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2765 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 639 poor density : 2126 time to evaluate : 6.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 639 outliers final: 136 residues processed: 2511 average time/residue: 1.3049 time to fit residues: 5336.9894 Evaluate side-chains 1533 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1397 time to evaluate : 6.044 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 136 outliers final: 1 residues processed: 136 average time/residue: 0.9469 time to fit residues: 247.1932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 803 optimal weight: 0.8980 chunk 721 optimal weight: 0.6980 chunk 400 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 486 optimal weight: 9.9990 chunk 385 optimal weight: 6.9990 chunk 746 optimal weight: 0.9990 chunk 288 optimal weight: 9.9990 chunk 453 optimal weight: 5.9990 chunk 555 optimal weight: 0.9990 chunk 864 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 GLN ** E 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 HIS ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 HIS F 276 ASN G 20 ASN G 101 ASN H 21 ASN H 162 GLN I 12 ASN I 47 GLN ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 GLN J 53 ASN J 86 GLN J 96 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 ASN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 ASN K 54 GLN K 64 ASN ** K 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 GLN K 147 ASN K 192 GLN L 24 ASN L 58 HIS L 90 GLN L 153 ASN M 11 ASN M 100 ASN N 86 ASN O 28 HIS O 74 ASN O 118 HIS O 120 GLN P 81 HIS P 141 ASN ** P 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 157 HIS P 159 HIS Q 51 HIS Q 79 ASN Q 84 ASN Q 95 HIS R 59 GLN R 63 GLN R 68 HIS R 180 ASN R 249 ASN S 23 ASN S 45 ASN S 68 GLN S 124 GLN T 57 HIS T 129 ASN T 170 ASN U 58 ASN U 123 HIS ** U 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN W 64 ASN W 80 GLN Y 185 ASN Z 62 ASN Z 73 ASN 1 15 ASN 1 79 HIS 2 95 GLN 3 52 ASN 4 6 ASN 4 17 HIS ** 4 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 63 GLN 5 129 ASN 5 185 HIS 5 244 ASN ** 5 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 254 ASN 6 12 ASN ** 6 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 23 ASN 7 29 HIS 7 64 ASN ** 8 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 60 ASN 8 116 ASN 9 53 GLN 9 108 HIS 9 110 ASN ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN a 52 GLN b 87 HIS ** c 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 79 ASN f 14 ASN ** f 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 33 GLN i 19 HIS i 22 HIS i 26 GLN Total number of N/Q/H flips: 90 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 133935 Z= 0.194 Angle : 0.737 15.152 197022 Z= 0.380 Chirality : 0.041 0.393 24773 Planarity : 0.006 0.151 12011 Dihedral : 22.987 179.875 55388 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.75 % Allowed : 5.13 % Favored : 94.12 % Rotamer: Outliers : 5.22 % Allowed : 21.11 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.11), residues: 6124 helix: 2.56 (0.11), residues: 2228 sheet: -1.42 (0.17), residues: 859 loop : -1.55 (0.10), residues: 3037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 5 242 HIS 0.007 0.001 HIS a 12 PHE 0.044 0.002 PHE c 81 TYR 0.024 0.002 TYR P 172 ARG 0.011 0.001 ARG E 366 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1868 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1582 time to evaluate : 6.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 286 outliers final: 125 residues processed: 1733 average time/residue: 1.1365 time to fit residues: 3338.1559 Evaluate side-chains 1434 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1309 time to evaluate : 7.196 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 125 outliers final: 1 residues processed: 125 average time/residue: 0.8179 time to fit residues: 198.5300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 480 optimal weight: 0.1980 chunk 268 optimal weight: 9.9990 chunk 719 optimal weight: 9.9990 chunk 588 optimal weight: 0.7980 chunk 238 optimal weight: 10.0000 chunk 866 optimal weight: 3.9990 chunk 935 optimal weight: 5.9990 chunk 771 optimal weight: 6.9990 chunk 858 optimal weight: 5.9990 chunk 295 optimal weight: 10.0000 chunk 694 optimal weight: 7.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 HIS D 86 GLN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS E 55 HIS E 174 HIS ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS E 260 GLN F 285 HIS F 314 GLN G 152 HIS H 75 HIS H 97 HIS H 103 ASN H 152 ASN H 162 GLN ** I 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN J 98 ASN J 154 ASN J 225 GLN J 240 ASN ** J 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 HIS O 14 HIS ** O 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 HIS O 120 GLN P 145 ASN P 154 ASN P 159 HIS ** Q 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 GLN S 73 ASN T 130 GLN U 7 ASN ** U 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 97 HIS ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 133 HIS Y 165 ASN ** 4 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 63 GLN ** 5 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 21 GLN 8 89 HIS a 6 HIS ** a 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 ASN a 69 ASN ** c 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 8 GLN f 33 ASN i 19 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 133935 Z= 0.311 Angle : 0.746 12.263 197022 Z= 0.385 Chirality : 0.042 0.330 24773 Planarity : 0.007 0.136 12011 Dihedral : 22.581 179.786 55388 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.29 % Favored : 93.06 % Rotamer: Outliers : 5.51 % Allowed : 23.24 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.11), residues: 6124 helix: 1.74 (0.11), residues: 2218 sheet: -1.34 (0.17), residues: 852 loop : -1.36 (0.11), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 5 242 HIS 0.035 0.002 HIS U 17 PHE 0.041 0.003 PHE F 257 TYR 0.099 0.003 TYR F 375 ARG 0.026 0.001 ARG L 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1960 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1658 time to evaluate : 6.108 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 outliers start: 302 outliers final: 133 residues processed: 1833 average time/residue: 1.1964 time to fit residues: 3712.1340 Evaluate side-chains 1500 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1367 time to evaluate : 6.068 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 133 outliers final: 1 residues processed: 133 average time/residue: 0.8866 time to fit residues: 234.9769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 855 optimal weight: 2.9990 chunk 651 optimal weight: 0.8980 chunk 449 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 413 optimal weight: 10.0000 chunk 581 optimal weight: 7.9990 chunk 869 optimal weight: 7.9990 chunk 920 optimal weight: 5.9990 chunk 454 optimal weight: 4.9990 chunk 823 optimal weight: 0.9990 chunk 247 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 100 ASN ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 HIS ** I 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN ** I 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN J 225 GLN J 240 ASN J 252 GLN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN L 24 ASN N 84 ASN ** O 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 120 GLN P 86 HIS P 139 ASN P 154 ASN ** P 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN ** Q 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 HIS S 34 ASN S 73 ASN T 74 HIS T 90 GLN U 7 ASN U 12 ASN U 15 GLN U 17 HIS ** U 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 77 ASN 1 54 ASN 2 37 ASN 3 3 ASN 3 47 HIS ** 3 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 63 GLN 5 129 ASN ** 5 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 23 ASN 8 60 ASN ** 8 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 12 HIS a 52 GLN a 69 ASN e 43 HIS i 46 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.6257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 133935 Z= 0.235 Angle : 0.652 12.668 197022 Z= 0.334 Chirality : 0.038 0.310 24773 Planarity : 0.006 0.131 12011 Dihedral : 22.414 179.885 55388 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.96 % Favored : 94.46 % Rotamer: Outliers : 3.99 % Allowed : 24.72 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 6124 helix: 1.82 (0.11), residues: 2217 sheet: -1.03 (0.17), residues: 810 loop : -1.20 (0.11), residues: 3097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 5 242 HIS 0.008 0.001 HIS U 162 PHE 0.030 0.002 PHE J 231 TYR 0.027 0.002 TYR F 332 ARG 0.010 0.001 ARG F 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1714 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1495 time to evaluate : 6.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 219 outliers final: 115 residues processed: 1617 average time/residue: 1.1700 time to fit residues: 3206.2601 Evaluate side-chains 1478 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1363 time to evaluate : 6.029 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 115 outliers final: 1 residues processed: 115 average time/residue: 0.9281 time to fit residues: 206.7361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 766 optimal weight: 3.9990 chunk 522 optimal weight: 4.9990 chunk 13 optimal weight: 30.0000 chunk 685 optimal weight: 7.9990 chunk 379 optimal weight: 0.6980 chunk 785 optimal weight: 0.9980 chunk 636 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 469 optimal weight: 8.9990 chunk 825 optimal weight: 10.0000 chunk 232 optimal weight: 40.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 HIS ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 HIS F 94 ASN F 268 HIS F 285 HIS ** I 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN J 252 GLN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 ASN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 106 ASN ** O 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 HIS P 154 ASN ** P 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 GLN R 68 HIS R 202 HIS T 74 HIS T 130 GLN U 7 ASN 2 79 GLN 3 43 ASN 3 52 ASN ** 3 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 6 ASN 4 51 GLN 4 63 GLN ** 5 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 36 GLN 9 59 ASN a 10 HIS a 33 HIS a 69 ASN e 20 ASN f 36 ASN ** f 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 19 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 133935 Z= 0.292 Angle : 0.675 12.372 197022 Z= 0.346 Chirality : 0.039 0.304 24773 Planarity : 0.006 0.134 12011 Dihedral : 22.301 179.923 55388 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.78 % Favored : 93.62 % Rotamer: Outliers : 3.74 % Allowed : 25.99 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.11), residues: 6124 helix: 1.53 (0.11), residues: 2227 sheet: -1.15 (0.17), residues: 858 loop : -1.23 (0.11), residues: 3039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 5 242 HIS 0.011 0.002 HIS T 74 PHE 0.027 0.002 PHE Y 151 TYR 0.026 0.002 TYR 9 136 ARG 0.010 0.001 ARG V 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1697 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1492 time to evaluate : 6.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 205 outliers final: 116 residues processed: 1596 average time/residue: 1.1914 time to fit residues: 3243.4502 Evaluate side-chains 1467 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1351 time to evaluate : 6.083 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 116 outliers final: 1 residues processed: 116 average time/residue: 0.9222 time to fit residues: 210.4001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 309 optimal weight: 20.0000 chunk 828 optimal weight: 20.0000 chunk 181 optimal weight: 30.0000 chunk 540 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 921 optimal weight: 4.9990 chunk 764 optimal weight: 0.0170 chunk 426 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 304 optimal weight: 20.0000 chunk 483 optimal weight: 1.9990 overall best weight: 3.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS E 258 GLN F 285 HIS ** I 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 225 GLN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 204 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN P 154 ASN ** P 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 HIS R 94 ASN T 130 GLN U 7 ASN V 56 ASN Y 162 ASN Y 165 ASN 1 78 ASN ** 3 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 52 ASN ** 3 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 106 GLN ** 4 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 114 ASN 8 70 ASN 9 36 GLN 9 59 ASN a 69 ASN e 19 GLN e 20 ASN f 8 GLN ** f 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.7427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 133935 Z= 0.281 Angle : 0.658 11.412 197022 Z= 0.336 Chirality : 0.039 0.296 24773 Planarity : 0.006 0.136 12011 Dihedral : 22.258 179.949 55388 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.19 % Favored : 94.25 % Rotamer: Outliers : 3.25 % Allowed : 27.16 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.11), residues: 6124 helix: 1.49 (0.11), residues: 2216 sheet: -1.09 (0.17), residues: 876 loop : -1.25 (0.11), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 5 242 HIS 0.008 0.001 HIS U 162 PHE 0.028 0.002 PHE J 231 TYR 0.032 0.002 TYR P 172 ARG 0.012 0.001 ARG 5 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1415 time to evaluate : 6.122 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 outliers start: 178 outliers final: 104 residues processed: 1499 average time/residue: 1.2113 time to fit residues: 3080.1207 Evaluate side-chains 1438 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1334 time to evaluate : 6.074 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 104 outliers final: 1 residues processed: 104 average time/residue: 0.9985 time to fit residues: 197.9795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 888 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 524 optimal weight: 5.9990 chunk 672 optimal weight: 1.9990 chunk 521 optimal weight: 0.9980 chunk 775 optimal weight: 7.9990 chunk 514 optimal weight: 6.9990 chunk 917 optimal weight: 8.9990 chunk 574 optimal weight: 8.9990 chunk 559 optimal weight: 9.9990 chunk 423 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS E 364 HIS F 285 HIS F 362 GLN G 95 ASN J 225 GLN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 ASN K 49 ASN K 71 HIS N 84 ASN ** O 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN P 154 ASN P 159 HIS Q 73 ASN Q 84 ASN ** Q 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 HIS U 7 ASN Y 165 ASN 1 78 ASN 4 63 GLN ** 5 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 27 GLN 7 114 ASN 8 60 ASN 8 70 ASN 9 59 ASN a 69 ASN e 19 GLN e 20 ASN f 16 GLN f 44 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.7708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 133935 Z= 0.261 Angle : 0.646 13.017 197022 Z= 0.330 Chirality : 0.038 0.291 24773 Planarity : 0.005 0.136 12011 Dihedral : 22.201 179.945 55388 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.99 % Favored : 93.44 % Rotamer: Outliers : 2.46 % Allowed : 28.40 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.11), residues: 6124 helix: 1.48 (0.11), residues: 2214 sheet: -1.13 (0.17), residues: 872 loop : -1.22 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 196 HIS 0.008 0.001 HIS U 162 PHE 0.025 0.002 PHE J 231 TYR 0.026 0.002 TYR X 102 ARG 0.013 0.001 ARG 5 231 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1537 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1402 time to evaluate : 6.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 78 residues processed: 1466 average time/residue: 1.1967 time to fit residues: 2979.7180 Evaluate side-chains 1404 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1326 time to evaluate : 6.120 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 78 outliers final: 1 residues processed: 78 average time/residue: 0.9425 time to fit residues: 146.4085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 567 optimal weight: 0.0770 chunk 366 optimal weight: 9.9990 chunk 548 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 180 optimal weight: 30.0000 chunk 177 optimal weight: 10.0000 chunk 583 optimal weight: 5.9990 chunk 625 optimal weight: 10.0000 chunk 453 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 721 optimal weight: 5.9990 overall best weight: 6.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 ASN ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 HIS E 162 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS F 268 HIS F 285 HIS F 362 GLN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 ASN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 HIS P 154 ASN P 159 HIS Q 73 ASN ** Q 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN R 59 GLN R 68 HIS U 7 ASN Y 165 ASN 1 78 ASN 3 43 ASN 3 115 GLN 4 11 ASN ** 4 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 27 GLN 7 114 ASN 9 59 ASN ** a 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 69 ASN c 79 ASN e 19 GLN e 20 ASN f 16 GLN f 44 GLN h 34 HIS i 46 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.7916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 133935 Z= 0.436 Angle : 0.751 12.535 197022 Z= 0.381 Chirality : 0.043 0.345 24773 Planarity : 0.006 0.140 12011 Dihedral : 22.255 179.782 55388 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.57 % Allowed : 6.35 % Favored : 93.08 % Rotamer: Outliers : 2.21 % Allowed : 29.06 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.10), residues: 6124 helix: 1.14 (0.11), residues: 2206 sheet: -1.24 (0.17), residues: 869 loop : -1.29 (0.11), residues: 3049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 5 242 HIS 0.011 0.002 HIS U 147 PHE 0.048 0.003 PHE J 231 TYR 0.041 0.003 TYR X 110 ARG 0.016 0.001 ARG 5 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1495 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1374 time to evaluate : 6.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 121 outliers final: 80 residues processed: 1438 average time/residue: 1.1783 time to fit residues: 2868.7159 Evaluate side-chains 1408 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1328 time to evaluate : 6.163 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.8951 time to fit residues: 144.3009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 834 optimal weight: 0.9990 chunk 879 optimal weight: 1.9990 chunk 802 optimal weight: 10.0000 chunk 855 optimal weight: 0.8980 chunk 878 optimal weight: 0.2980 chunk 514 optimal weight: 5.9990 chunk 372 optimal weight: 5.9990 chunk 671 optimal weight: 0.9990 chunk 262 optimal weight: 8.9990 chunk 772 optimal weight: 6.9990 chunk 808 optimal weight: 8.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN E 181 ASN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS E 260 GLN F 285 HIS F 362 GLN ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 ASN J 252 GLN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 ASN ** O 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 HIS P 154 ASN P 159 HIS Q 73 ASN Q 84 ASN ** Q 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN R 68 HIS S 43 ASN U 7 ASN ** U 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 28 ASN X 114 HIS 1 78 ASN 3 3 ASN 3 115 GLN ** 4 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 70 ASN 9 59 ASN a 11 ASN a 69 ASN ** e 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 ASN f 16 GLN f 44 GLN i 22 HIS i 46 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.8054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 133935 Z= 0.162 Angle : 0.615 11.843 197022 Z= 0.314 Chirality : 0.035 0.259 24773 Planarity : 0.005 0.140 12011 Dihedral : 22.212 179.505 55388 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.32 % Favored : 94.15 % Rotamer: Outliers : 1.19 % Allowed : 29.84 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 6124 helix: 1.40 (0.11), residues: 2214 sheet: -1.16 (0.17), residues: 846 loop : -1.15 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 5 242 HIS 0.012 0.001 HIS X 114 PHE 0.025 0.002 PHE F 257 TYR 0.032 0.002 TYR X 110 ARG 0.018 0.001 ARG H 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1494 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1429 time to evaluate : 6.212 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 outliers start: 65 outliers final: 35 residues processed: 1458 average time/residue: 1.2252 time to fit residues: 2986.0240 Evaluate side-chains 1393 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1358 time to evaluate : 6.140 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.9695 time to fit residues: 69.8496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 852 optimal weight: 10.0000 chunk 561 optimal weight: 20.0000 chunk 904 optimal weight: 0.7980 chunk 551 optimal weight: 8.9990 chunk 428 optimal weight: 10.0000 chunk 628 optimal weight: 0.5980 chunk 948 optimal weight: 0.7980 chunk 872 optimal weight: 2.9990 chunk 755 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 583 optimal weight: 7.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS F 285 HIS ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 GLN ** M 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 35 ASN ** O 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 159 HIS ** Q 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 HIS U 7 ASN ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 32 GLN 1 78 ASN ** 3 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 106 GLN 3 115 GLN ** 4 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 27 GLN 7 114 ASN 8 70 ASN 9 59 ASN ** a 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 14 ASN ** e 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 44 GLN h 34 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.8110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 133935 Z= 0.227 Angle : 0.625 12.491 197022 Z= 0.319 Chirality : 0.037 0.300 24773 Planarity : 0.005 0.141 12011 Dihedral : 22.127 179.642 55388 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.81 % Favored : 93.70 % Rotamer: Outliers : 0.69 % Allowed : 31.14 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.11), residues: 6124 helix: 1.34 (0.11), residues: 2211 sheet: -1.14 (0.17), residues: 860 loop : -1.14 (0.11), residues: 3053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP 5 242 HIS 0.010 0.001 HIS D 118 PHE 0.048 0.002 PHE J 231 TYR 0.032 0.002 TYR X 102 ARG 0.014 0.001 ARG 5 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12248 Ramachandran restraints generated. 6124 Oldfield, 0 Emsley, 6124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1403 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 1365 time to evaluate : 6.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 20 residues processed: 1381 average time/residue: 1.2033 time to fit residues: 2824.9429 Evaluate side-chains 1350 residues out of total 5511 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1330 time to evaluate : 6.158 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.9351 time to fit residues: 42.5335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 952 random chunks: chunk 463 optimal weight: 0.9980 chunk 599 optimal weight: 5.9990 chunk 804 optimal weight: 0.7980 chunk 231 optimal weight: 40.0000 chunk 696 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 756 optimal weight: 7.9990 chunk 316 optimal weight: 10.0000 chunk 776 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS G 95 ASN ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 ASN L 18 GLN M 35 ASN ** O 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 154 ASN P 159 HIS ** Q 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN R 59 GLN R 68 HIS U 7 ASN ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 ASN 1 78 ASN 2 79 GLN 3 3 ASN 3 106 GLN 3 115 GLN ** 4 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 27 GLN 7 114 ASN 8 70 ASN 9 59 ASN ** a 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 20 ASN f 16 GLN f 44 GLN h 34 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.141620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.117709 restraints weight = 178245.410| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 0.95 r_work: 0.3152 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.8193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 133935 Z= 0.294 Angle : 0.662 22.931 197022 Z= 0.337 Chirality : 0.039 0.436 24773 Planarity : 0.006 0.184 12011 Dihedral : 22.123 179.766 55388 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.22 % Favored : 93.29 % Rotamer: Outliers : 0.95 % Allowed : 31.14 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.11), residues: 6124 helix: 1.23 (0.11), residues: 2210 sheet: -1.15 (0.17), residues: 848 loop : -1.19 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP P 11 HIS 0.010 0.001 HIS D 118 PHE 0.039 0.002 PHE J 231 TYR 0.038 0.002 TYR X 102 ARG 0.015 0.001 ARG 5 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44568.33 seconds wall clock time: 772 minutes 46.15 seconds (46366.15 seconds total)