Starting phenix.real_space_refine (version: dev) on Fri Dec 16 11:45:59 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/12_2022/6v3d_21033_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/12_2022/6v3d_21033.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/12_2022/6v3d_21033_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/12_2022/6v3d_21033_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/12_2022/6v3d_21033_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/12_2022/6v3d_21033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/12_2022/6v3d_21033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/12_2022/6v3d_21033_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/12_2022/6v3d_21033_updated.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.087 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 537 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "0 ARG 6": "NH1" <-> "NH2" Residue "0 ARG 40": "NH1" <-> "NH2" Residue "1 ARG 3": "NH1" <-> "NH2" Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 ARG 33": "NH1" <-> "NH2" Residue "1 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 7": "NH1" <-> "NH2" Residue "2 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 23": "NH1" <-> "NH2" Residue "2 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 58": "NH1" <-> "NH2" Residue "3 ARG 18": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "3 ARG 32": "NH1" <-> "NH2" Residue "3 ARG 36": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "D ARG 8": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E ASP 139": "OD1" <-> "OD2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ASP 170": "OD1" <-> "OD2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F ARG 150": "NH1" <-> "NH2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "F GLU 165": "OE1" <-> "OE2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ASP 60": "OD1" <-> "OD2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "H ASP 2": "OD1" <-> "OD2" Residue "I ARG 27": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 31": "NH1" <-> "NH2" Residue "J ASP 37": "OD1" <-> "OD2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "J ARG 71": "NH1" <-> "NH2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "J ASP 80": "OD1" <-> "OD2" Residue "J ARG 104": "NH1" <-> "NH2" Residue "J GLU 105": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K ARG 19": "NH1" <-> "NH2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K ARG 111": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "K GLU 138": "OE1" <-> "OE2" Residue "K GLU 145": "OE1" <-> "OE2" Residue "K GLU 146": "OE1" <-> "OE2" Residue "L ARG 16": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 52": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 107": "OE1" <-> "OE2" Residue "L ASP 112": "OD1" <-> "OD2" Residue "L ARG 115": "NH1" <-> "NH2" Residue "L PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N ARG 34": "NH1" <-> "NH2" Residue "N ASP 56": "OD1" <-> "OD2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "N ARG 93": "NH1" <-> "NH2" Residue "N ASP 107": "OD1" <-> "OD2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "O ARG 91": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 97": "NH1" <-> "NH2" Residue "O ARG 112": "NH1" <-> "NH2" Residue "O GLU 115": "OE1" <-> "OE2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 12": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 70": "NH1" <-> "NH2" Residue "P ARG 78": "NH1" <-> "NH2" Residue "P ASP 102": "OD1" <-> "OD2" Residue "Q TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q ASP 45": "OD1" <-> "OD2" Residue "Q ARG 68": "NH1" <-> "NH2" Residue "Q ARG 73": "NH1" <-> "NH2" Residue "Q ARG 78": "NH1" <-> "NH2" Residue "Q ARG 79": "NH1" <-> "NH2" Residue "Q PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 8": "NH1" <-> "NH2" Residue "R ARG 25": "NH1" <-> "NH2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "R ASP 65": "OD1" <-> "OD2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "R ARG 95": "NH1" <-> "NH2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S ARG 76": "NH1" <-> "NH2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 31": "NH1" <-> "NH2" Residue "T GLU 35": "OE1" <-> "OE2" Residue "T GLU 53": "OE1" <-> "OE2" Residue "U ARG 11": "NH1" <-> "NH2" Residue "U ARG 22": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U GLU 56": "OE1" <-> "OE2" Residue "V TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 30": "OE1" <-> "OE2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W ARG 48": "NH1" <-> "NH2" Residue "X GLU 20": "OE1" <-> "OE2" Residue "X ARG 27": "NH1" <-> "NH2" Residue "X ARG 29": "NH1" <-> "NH2" Residue "X ARG 52": "NH1" <-> "NH2" Residue "X GLU 59": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 30": "NH1" <-> "NH2" Residue "Z ARG 7": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 16": "NH1" <-> "NH2" Residue "Z ARG 17": "NH1" <-> "NH2" Residue "Z ARG 39": "NH1" <-> "NH2" Residue "Z ASP 45": "OD1" <-> "OD2" Residue "Z PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 51": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 89040 Number of models: 1 Model: "" Number of chains: 45 Chain: "0" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 427 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "AN" Number of atoms: 62023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2892, 62023 Classifications: {'RNA': 2892} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 257, 'rna2p_pyr': 144, 'rna3p': 12, 'rna3p_pur': 1391, 'rna3p_pyr': 1085} Link IDs: {'rna2p': 404, 'rna3p': 2487} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 54, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 101} Chain: "C" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2096 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1572 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "E" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1419 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain: "F" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1381 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1318 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 458 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "I" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1125 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1089 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1087 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 857 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "O" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "P" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "S" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "T" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 749 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "U" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 598 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "W" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 498 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "Y" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 463 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "Z" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 106 Unusual residues: {' MG': 105, ' NA': 1} Classifications: {'undetermined': 106} Link IDs: {None: 105} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AN" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 218 Classifications: {'water': 218} Link IDs: {None: 217} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 67.999 45.098 159.521 1.00103.99 S ATOM 1398 SG CYS 3 14 71.092 46.060 157.997 1.00100.21 S ATOM 1503 SG CYS 3 27 69.669 43.006 156.570 1.00104.23 S Time building chain proxies: 38.69, per 1000 atoms: 0.43 Number of scatterers: 89040 At special positions: 0 Unit cell: (184.072, 234.08, 239.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 77 16.00 P 3006 15.00 Mg 106 11.99 Na 1 11.00 O 25450 8.00 N 16475 7.00 C 43924 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: 37.61 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5666 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 46 sheets defined 25.3% alpha, 18.8% beta 927 base pairs and 1521 stacking pairs defined. Time for finding SS restraints: 37.85 Creating SS restraints... Processing helix chain '1' and resid 9 through 15 Processing helix chain '1' and resid 18 through 23 Processing helix chain '1' and resid 25 through 37 Processing helix chain '2' and resid 8 through 13 Processing helix chain '2' and resid 32 through 34 No H-bonds generated for 'chain '2' and resid 32 through 34' Processing helix chain '2' and resid 37 through 42 Processing helix chain '2' and resid 54 through 60 Processing helix chain '3' and resid 31 through 33 No H-bonds generated for 'chain '3' and resid 31 through 33' Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'D' and resid 41 through 44 No H-bonds generated for 'chain 'D' and resid 41 through 44' Processing helix chain 'D' and resid 63 through 72 Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 124 through 128 Processing helix chain 'E' and resid 24 through 38 removed outlier: 3.702A pdb=" N GLY E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 113 Processing helix chain 'E' and resid 130 through 138 Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 189 through 198 Processing helix chain 'F' and resid 8 through 19 Processing helix chain 'F' and resid 48 through 60 removed outlier: 3.952A pdb=" N GLY F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 105 removed outlier: 3.717A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU F 98 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE F 99 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'G' and resid 3 through 6 No H-bonds generated for 'chain 'G' and resid 3 through 6' Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'H' and resid 23 through 28 Processing helix chain 'H' and resid 30 through 33 No H-bonds generated for 'chain 'H' and resid 30 through 33' Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'H' and resid 51 through 55 Processing helix chain 'I' and resid 25 through 37 Processing helix chain 'I' and resid 59 through 61 No H-bonds generated for 'chain 'I' and resid 59 through 61' Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 89 through 95 Processing helix chain 'I' and resid 97 through 108 removed outlier: 3.882A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 121 removed outlier: 3.668A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 106 No H-bonds generated for 'chain 'J' and resid 104 through 106' Processing helix chain 'J' and resid 112 through 117 Processing helix chain 'K' and resid 53 through 55 No H-bonds generated for 'chain 'K' and resid 53 through 55' Processing helix chain 'K' and resid 59 through 62 No H-bonds generated for 'chain 'K' and resid 59 through 62' Processing helix chain 'K' and resid 72 through 75 Processing helix chain 'K' and resid 82 through 85 Processing helix chain 'K' and resid 94 through 99 Processing helix chain 'K' and resid 131 through 139 Processing helix chain 'L' and resid 44 through 57 Processing helix chain 'L' and resid 111 through 124 removed outlier: 4.027A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 31 Processing helix chain 'M' and resid 38 through 56 removed outlier: 3.993A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 3.519A pdb=" N LYS M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 70 Processing helix chain 'M' and resid 73 through 86 removed outlier: 4.870A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 4 through 22 removed outlier: 4.171A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 84 Processing helix chain 'N' and resid 101 through 111 Processing helix chain 'O' and resid 6 through 15 removed outlier: 4.065A pdb=" N SER O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 104 Processing helix chain 'O' and resid 109 through 111 No H-bonds generated for 'chain 'O' and resid 109 through 111' Processing helix chain 'P' and resid 8 through 21 removed outlier: 3.603A pdb=" N ALA P 21 " --> pdb=" O ILE P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 29 Processing helix chain 'P' and resid 32 through 71 removed outlier: 3.884A pdb=" N GLN P 37 " --> pdb=" O ARG P 33 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 85 Processing helix chain 'P' and resid 92 through 101 Processing helix chain 'P' and resid 103 through 117 Processing helix chain 'R' and resid 14 through 21 removed outlier: 3.970A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 37 Processing helix chain 'R' and resid 43 through 60 Processing helix chain 'R' and resid 89 through 91 No H-bonds generated for 'chain 'R' and resid 89 through 91' Processing helix chain 'S' and resid 5 through 9 Processing helix chain 'S' and resid 17 through 25 Processing helix chain 'S' and resid 39 through 50 Processing helix chain 'U' and resid 18 through 26 Processing helix chain 'U' and resid 48 through 56 Processing helix chain 'U' and resid 59 through 62 No H-bonds generated for 'chain 'U' and resid 59 through 62' Processing helix chain 'W' and resid 53 through 62 Processing helix chain 'W' and resid 64 through 74 removed outlier: 3.912A pdb=" N GLN W 74 " --> pdb=" O ASP W 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 6 No H-bonds generated for 'chain 'X' and resid 3 through 6' Processing helix chain 'X' and resid 11 through 34 Processing helix chain 'X' and resid 42 through 62 Processing helix chain 'Y' and resid 17 through 25 Processing helix chain 'Y' and resid 41 through 49 removed outlier: 3.638A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 19 removed outlier: 4.889A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '0' and resid 16 through 21 Processing sheet with id= B, first strand: chain '2' and resid 22 through 24 Processing sheet with id= C, first strand: chain '3' and resid 2 through 4 Processing sheet with id= D, first strand: chain '3' and resid 14 through 19 Processing sheet with id= E, first strand: chain 'C' and resid 34 through 37 removed outlier: 4.050A pdb=" N LYS C 37 " --> pdb=" O GLN C 60 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN C 60 " --> pdb=" O LYS C 37 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.790A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL C 78 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= H, first strand: chain 'C' and resid 181 through 185 removed outlier: 3.594A pdb=" N GLY C 166 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ARG C 175 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N LEU C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 172 through 179 removed outlier: 5.640A pdb=" N VAL D 110 " --> pdb=" O GLY D 177 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG D 14 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL D 23 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LYS D 193 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE D 180 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.256A pdb=" N THR D 52 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE D 35 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 118 through 122 removed outlier: 6.055A pdb=" N LEU D 168 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE D 121 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY D 166 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 117 through 120 removed outlier: 6.382A pdb=" N VAL E 185 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL E 120 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N MET E 187 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ASP E 167 " --> pdb=" O ILE E 147 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR E 149 " --> pdb=" O ASP E 167 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL E 169 " --> pdb=" O THR E 149 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 87 through 92 removed outlier: 6.583A pdb=" N THR F 157 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE F 34 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N THR F 155 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU F 36 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP F 153 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 16 through 18 Processing sheet with id= O, first strand: chain 'G' and resid 41 through 44 Processing sheet with id= P, first strand: chain 'G' and resid 87 through 90 Processing sheet with id= Q, first strand: chain 'G' and resid 95 through 99 Processing sheet with id= R, first strand: chain 'G' and resid 121 through 124 Processing sheet with id= S, first strand: chain 'I' and resid 15 through 19 removed outlier: 6.494A pdb=" N TYR I 53 " --> pdb=" O PHE I 16 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL I 18 " --> pdb=" O TYR I 53 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE I 55 " --> pdb=" O VAL I 18 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 73 through 77 Processing sheet with id= U, first strand: chain 'J' and resid 7 through 9 removed outlier: 6.824A pdb=" N LYS J 40 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL J 24 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE J 38 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN J 59 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA J 83 " --> pdb=" O VAL J 63 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 76 through 80 removed outlier: 6.792A pdb=" N ARG K 109 " --> pdb=" O ALA K 77 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL K 79 " --> pdb=" O ARG K 109 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG K 111 " --> pdb=" O VAL K 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'L' and resid 129 through 133 removed outlier: 3.609A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA L 36 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE L 102 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 40 through 43 removed outlier: 6.927A pdb=" N ILE L 74 " --> pdb=" O GLU L 91 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TRP L 93 " --> pdb=" O LYS L 72 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS L 72 " --> pdb=" O TRP L 93 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'M' and resid 33 through 37 Processing sheet with id= Z, first strand: chain 'N' and resid 90 through 92 removed outlier: 3.680A pdb=" N VAL N 29 " --> pdb=" O ASP N 92 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA N 50 " --> pdb=" O VAL N 40 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'O' and resid 86 through 91 removed outlier: 3.699A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE O 67 " --> pdb=" O GLU O 47 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR O 63 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS O 53 " --> pdb=" O ALA O 61 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA O 61 " --> pdb=" O LYS O 53 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Q' and resid 10 through 15 removed outlier: 3.943A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N GLN Q 6 " --> pdb=" O VAL Q 38 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL Q 38 " --> pdb=" O GLN Q 6 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 19 through 22 removed outlier: 3.705A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Q' and resid 32 through 35 removed outlier: 6.397A pdb=" N GLU Q 62 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE Q 98 " --> pdb=" O GLU Q 62 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Q' and resid 72 through 78 removed outlier: 4.164A pdb=" N TYR Q 83 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'R' and resid 3 through 7 removed outlier: 6.343A pdb=" N GLY R 108 " --> pdb=" O VAL R 71 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL R 71 " --> pdb=" O GLY R 108 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'R' and resid 82 through 87 Processing sheet with id= AH, first strand: chain 'S' and resid 28 through 33 removed outlier: 4.235A pdb=" N LYS S 80 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS S 56 " --> pdb=" O THR S 85 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'S' and resid 66 through 69 Processing sheet with id= AJ, first strand: chain 'T' and resid 21 through 23 Processing sheet with id= AK, first strand: chain 'T' and resid 39 through 44 Processing sheet with id= AL, first strand: chain 'T' and resid 81 through 83 Processing sheet with id= AM, first strand: chain 'T' and resid 24 through 28 removed outlier: 6.655A pdb=" N LYS T 33 " --> pdb=" O LEU T 25 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL T 27 " --> pdb=" O ARG T 31 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG T 31 " --> pdb=" O VAL T 27 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'U' and resid 5 through 7 removed outlier: 6.821A pdb=" N GLU U 66 " --> pdb=" O LEU U 6 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP U 94 " --> pdb=" O GLN U 79 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU U 81 " --> pdb=" O HIS U 92 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS U 92 " --> pdb=" O LEU U 81 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ALA U 93 " --> pdb=" O LEU U 29 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N PHE U 95 " --> pdb=" O PRO U 31 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE U 33 " --> pdb=" O PHE U 95 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ARG U 97 " --> pdb=" O ILE U 33 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N TYR U 35 " --> pdb=" O ARG U 97 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'V' and resid 45 through 47 removed outlier: 7.050A pdb=" N ARG V 78 " --> pdb=" O HIS V 46 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'V' and resid 51 through 53 Processing sheet with id= AQ, first strand: chain 'W' and resid 13 through 18 Processing sheet with id= AR, first strand: chain 'W' and resid 34 through 40 Processing sheet with id= AS, first strand: chain 'Y' and resid 34 through 38 removed outlier: 3.764A pdb=" N LYS Y 5 " --> pdb=" O GLU Y 57 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Z' and resid 27 through 29 757 hydrogen bonds defined for protein. 2136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2315 hydrogen bonds 3604 hydrogen bond angles 0 basepair planarities 927 basepair parallelities 1521 stacking parallelities Total time for adding SS restraints: 172.33 Time building geometry restraints manager: 40.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 7464 1.30 - 1.43: 44379 1.43 - 1.56: 38745 1.56 - 1.69: 6014 1.69 - 1.81: 137 Bond restraints: 96739 Sorted by residual: bond pdb=" C5 5MUAN1935 " pdb=" C6 5MUAN1935 " ideal model delta sigma weight residual 1.150 1.451 -0.301 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C4 5MUAN1935 " pdb=" C5 5MUAN1935 " ideal model delta sigma weight residual 1.805 1.612 0.193 2.00e-02 2.50e+03 9.33e+01 bond pdb=" N1 5MUAN1935 " pdb=" C2 5MUAN1935 " ideal model delta sigma weight residual 1.432 1.562 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" N1 5MUAN1935 " pdb=" C6 5MUAN1935 " ideal model delta sigma weight residual 1.638 1.562 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" N3 5MUAN1935 " pdb=" C4 5MUAN1935 " ideal model delta sigma weight residual 1.179 1.249 -0.070 2.00e-02 2.50e+03 1.23e+01 ... (remaining 96734 not shown) Histogram of bond angle deviations from ideal: 99.74 - 109.55: 41318 109.55 - 119.37: 57426 119.37 - 129.18: 44233 129.18 - 139.00: 2516 139.00 - 148.81: 2 Bond angle restraints: 145495 Sorted by residual: angle pdb=" C1' 2MAAN2499 " pdb=" N9 2MAAN2499 " pdb=" C4 2MAAN2499 " ideal model delta sigma weight residual 103.49 139.13 -35.64 3.00e+00 1.11e-01 1.41e+02 angle pdb=" C1' 2MAAN2499 " pdb=" N9 2MAAN2499 " pdb=" C8 2MAAN2499 " ideal model delta sigma weight residual 144.94 109.89 35.05 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C1' 6MZAN2026 " pdb=" N9 6MZAN2026 " pdb=" C8 6MZAN2026 " ideal model delta sigma weight residual 118.16 148.81 -30.65 3.00e+00 1.11e-01 1.04e+02 angle pdb=" C1' 6MZAN2026 " pdb=" N9 6MZAN2026 " pdb=" C4 6MZAN2026 " ideal model delta sigma weight residual 131.42 103.24 28.18 3.00e+00 1.11e-01 8.82e+01 angle pdb=" C5 6MZAN2026 " pdb=" C6 6MZAN2026 " pdb=" N6 6MZAN2026 " ideal model delta sigma weight residual 112.30 133.11 -20.81 3.00e+00 1.11e-01 4.81e+01 ... (remaining 145490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 49449 35.84 - 71.69: 1589 71.69 - 107.53: 119 107.53 - 143.37: 16 143.37 - 179.22: 29 Dihedral angle restraints: 51202 sinusoidal: 42387 harmonic: 8815 Sorted by residual: dihedral pdb=" CA ARG 3 36 " pdb=" C ARG 3 36 " pdb=" N GLN 3 37 " pdb=" CA GLN 3 37 " ideal model delta harmonic sigma weight residual -180.00 -126.07 -53.93 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" O4' UAN2880 " pdb=" C1' UAN2880 " pdb=" N1 UAN2880 " pdb=" C2 UAN2880 " ideal model delta sinusoidal sigma weight residual 200.00 23.38 176.62 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' CAN 912 " pdb=" C1' CAN 912 " pdb=" N1 CAN 912 " pdb=" C2 CAN 912 " ideal model delta sinusoidal sigma weight residual -160.00 9.57 -169.57 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 51199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 17624 0.055 - 0.111: 967 0.111 - 0.166: 107 0.166 - 0.222: 8 0.222 - 0.277: 2 Chirality restraints: 18708 Sorted by residual: chirality pdb=" C1' AAN 980 " pdb=" O4' AAN 980 " pdb=" C2' AAN 980 " pdb=" N9 AAN 980 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C1* PSUAN1913 " pdb=" O4* PSUAN1913 " pdb=" C2* PSUAN1913 " pdb=" C5 PSUAN1913 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" P GAN 369 " pdb=" OP1 GAN 369 " pdb=" OP2 GAN 369 " pdb=" O5' GAN 369 " both_signs ideal model delta sigma weight residual True 2.41 -2.60 -0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 18705 not shown) Planarity restraints: 7263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MGAN2065 " 0.064 2.00e-02 2.50e+03 6.22e-01 8.72e+03 pdb=" C4' 7MGAN2065 " 0.461 2.00e-02 2.50e+03 pdb=" O4' 7MGAN2065 " 0.731 2.00e-02 2.50e+03 pdb=" C3' 7MGAN2065 " -0.593 2.00e-02 2.50e+03 pdb=" O3' 7MGAN2065 " -0.644 2.00e-02 2.50e+03 pdb=" C2' 7MGAN2065 " -0.194 2.00e-02 2.50e+03 pdb=" O2' 7MGAN2065 " 0.963 2.00e-02 2.50e+03 pdb=" C1' 7MGAN2065 " 0.195 2.00e-02 2.50e+03 pdb=" N9 7MGAN2065 " -0.983 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGAN2441 " 0.045 2.00e-02 2.50e+03 5.90e-01 7.84e+03 pdb=" C4' 2MGAN2441 " 0.440 2.00e-02 2.50e+03 pdb=" O4' 2MGAN2441 " 0.663 2.00e-02 2.50e+03 pdb=" C3' 2MGAN2441 " -0.594 2.00e-02 2.50e+03 pdb=" O3' 2MGAN2441 " -0.601 2.00e-02 2.50e+03 pdb=" C2' 2MGAN2441 " -0.201 2.00e-02 2.50e+03 pdb=" O2' 2MGAN2441 " 0.937 2.00e-02 2.50e+03 pdb=" C1' 2MGAN2441 " 0.217 2.00e-02 2.50e+03 pdb=" N9 2MGAN2441 " -0.906 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGAN2247 " 0.032 2.00e-02 2.50e+03 5.67e-01 7.22e+03 pdb=" C4' OMGAN2247 " 0.429 2.00e-02 2.50e+03 pdb=" O4' OMGAN2247 " 0.619 2.00e-02 2.50e+03 pdb=" C3' OMGAN2247 " -0.590 2.00e-02 2.50e+03 pdb=" O3' OMGAN2247 " -0.562 2.00e-02 2.50e+03 pdb=" C2' OMGAN2247 " -0.210 2.00e-02 2.50e+03 pdb=" O2' OMGAN2247 " 0.909 2.00e-02 2.50e+03 pdb=" C1' OMGAN2247 " 0.230 2.00e-02 2.50e+03 pdb=" N9 OMGAN2247 " -0.857 2.00e-02 2.50e+03 ... (remaining 7260 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 249 2.34 - 2.98: 39643 2.98 - 3.62: 138979 3.62 - 4.26: 255779 4.26 - 4.90: 348133 Nonbonded interactions: 782783 Sorted by model distance: nonbonded pdb=" N3 AAN1029 " pdb="MG MGAN3098 " model vdw 1.698 2.250 nonbonded pdb=" N7 AAN 68 " pdb="MG MGAN3018 " model vdw 1.895 2.250 nonbonded pdb=" N7 AAN2430 " pdb="MG MGAN3037 " model vdw 1.895 2.250 nonbonded pdb=" N7 GAN2049 " pdb="MG MGAN3027 " model vdw 1.896 2.250 nonbonded pdb=" N7 GAN 626 " pdb="MG MGAN3056 " model vdw 1.896 2.250 ... (remaining 782778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3006 5.49 5 Mg 106 5.21 5 S 77 5.16 5 Na 1 4.78 5 C 43924 2.51 5 N 16475 2.21 5 O 25450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.420 Construct map_model_manager: 0.090 Extract box with map and model: 31.900 Check model and map are aligned: 1.160 Convert atoms to be neutral: 0.600 Process input model: 360.630 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:10.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 418.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 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 : 0.002 0.301 96739 Z= 0.125 Angle : 0.492 35.639 145495 Z= 0.254 Chirality : 0.027 0.277 18708 Planarity : 0.014 0.622 7263 Dihedral : 14.476 179.218 45536 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 3061 helix: -0.46 (0.17), residues: 795 sheet: -0.79 (0.19), residues: 660 loop : -1.94 (0.13), residues: 1606 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 837 time to evaluate : 4.500 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: 1 outliers final: 5 residues processed: 837 average time/residue: 1.7878 time to fit residues: 1988.5520 Evaluate side-chains 617 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 612 time to evaluate : 3.910 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 4 average time/residue: 0.6743 time to fit residues: 8.9399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 506 optimal weight: 0.0770 chunk 454 optimal weight: 5.9990 chunk 252 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 242 optimal weight: 7.9990 chunk 470 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 285 optimal weight: 7.9990 chunk 350 optimal weight: 3.9990 chunk 544 optimal weight: 0.2980 overall best weight: 3.6744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN ** 3 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 HIS C 58 HIS C 60 GLN C 90 HIS C 117 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS C 243 GLN D 50 GLN D 108 GLN D 139 ASN D 143 HIS E 61 GLN E 96 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 143 GLN ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN I 67 ASN I 77 HIS I 135 GLN K 40 GLN K 56 GLN K 125 GLN L 3 GLN M 5 ASN M 91 ASN N 39 GLN O 9 GLN O 15 GLN O 59 ASN O 78 GLN P 11 HIS R 57 ASN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 GLN T 67 ASN U 7 ASN U 16 GLN U 79 GLN U 84 HIS X 22 GLN Y 14 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 96739 Z= 0.316 Angle : 0.629 13.513 145495 Z= 0.325 Chirality : 0.036 0.293 18708 Planarity : 0.005 0.132 7263 Dihedral : 14.805 178.939 39492 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.28 % Rotamer Outliers : 5.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.14), residues: 3061 helix: 0.54 (0.18), residues: 783 sheet: -0.47 (0.20), residues: 683 loop : -1.53 (0.13), residues: 1595 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 624 time to evaluate : 4.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 70 residues processed: 672 average time/residue: 1.6552 time to fit residues: 1512.7315 Evaluate side-chains 653 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 583 time to evaluate : 3.961 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 26 residues processed: 49 average time/residue: 0.8612 time to fit residues: 74.5038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 302 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 453 optimal weight: 0.8980 chunk 371 optimal weight: 6.9990 chunk 150 optimal weight: 6.9990 chunk 545 optimal weight: 1.9990 chunk 589 optimal weight: 0.9980 chunk 486 optimal weight: 6.9990 chunk 541 optimal weight: 0.5980 chunk 186 optimal weight: 7.9990 chunk 437 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN E 114 GLN F 95 GLN F 135 GLN G 64 GLN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN I 63 GLN I 95 HIS Q 43 ASN S 20 GLN T 67 ASN V 29 GLN X 22 GLN X 41 HIS X 61 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 96739 Z= 0.126 Angle : 0.520 12.502 145495 Z= 0.275 Chirality : 0.030 0.277 18708 Planarity : 0.004 0.121 7263 Dihedral : 14.680 179.758 39492 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer Outliers : 3.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3061 helix: 1.02 (0.19), residues: 787 sheet: -0.23 (0.20), residues: 686 loop : -1.28 (0.14), residues: 1588 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 623 time to evaluate : 4.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 53 residues processed: 652 average time/residue: 1.6599 time to fit residues: 1474.3079 Evaluate side-chains 639 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 586 time to evaluate : 3.960 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 22 residues processed: 34 average time/residue: 0.7373 time to fit residues: 48.6818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 539 optimal weight: 6.9990 chunk 410 optimal weight: 4.9990 chunk 283 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 547 optimal weight: 6.9990 chunk 579 optimal weight: 6.9990 chunk 286 optimal weight: 7.9990 chunk 519 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN F 37 ASN G 106 ASN H 11 ASN ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN P 101 HIS Q 43 ASN R 60 HIS R 61 ASN T 67 ASN U 7 ASN U 88 ASN ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.082 96739 Z= 0.544 Angle : 0.785 13.308 145495 Z= 0.399 Chirality : 0.045 0.332 18708 Planarity : 0.006 0.140 7263 Dihedral : 15.347 179.295 39492 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.28 % Favored : 95.66 % Rotamer Outliers : 5.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3061 helix: 0.50 (0.18), residues: 786 sheet: -0.37 (0.20), residues: 691 loop : -1.39 (0.14), residues: 1584 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 588 time to evaluate : 3.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 148 outliers final: 79 residues processed: 650 average time/residue: 1.6243 time to fit residues: 1439.3128 Evaluate side-chains 640 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 561 time to evaluate : 3.921 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 37 residues processed: 45 average time/residue: 0.8642 time to fit residues: 69.7443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 483 optimal weight: 0.9980 chunk 329 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 431 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 494 optimal weight: 8.9990 chunk 400 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 520 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN 3 20 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN E 114 GLN G 19 GLN H 11 ASN I 61 GLN I 63 GLN I 67 ASN I 95 HIS J 3 GLN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Q 43 ASN U 7 ASN U 75 ASN U 88 ASN ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 96739 Z= 0.174 Angle : 0.564 12.450 145495 Z= 0.298 Chirality : 0.033 0.304 18708 Planarity : 0.005 0.123 7263 Dihedral : 14.932 179.733 39492 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.15), residues: 3061 helix: 0.99 (0.19), residues: 784 sheet: -0.21 (0.20), residues: 707 loop : -1.23 (0.14), residues: 1570 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 607 time to evaluate : 4.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 58 residues processed: 657 average time/residue: 1.5794 time to fit residues: 1422.9828 Evaluate side-chains 636 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 578 time to evaluate : 3.927 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 37 residues processed: 22 average time/residue: 0.6893 time to fit residues: 31.8019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 195 optimal weight: 7.9990 chunk 522 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 340 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 580 optimal weight: 5.9990 chunk 481 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 192 optimal weight: 8.9990 chunk 304 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN 2 30 HIS C 120 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN G 19 GLN G 106 ASN H 11 ASN I 63 GLN O 9 GLN Q 86 GLN T 38 ASN U 7 ASN U 88 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.075 96739 Z= 0.482 Angle : 0.740 13.465 145495 Z= 0.378 Chirality : 0.043 0.313 18708 Planarity : 0.006 0.137 7263 Dihedral : 15.301 177.809 39492 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.84 % Favored : 95.10 % Rotamer Outliers : 5.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3061 helix: 0.60 (0.18), residues: 791 sheet: -0.29 (0.20), residues: 692 loop : -1.44 (0.14), residues: 1578 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 578 time to evaluate : 4.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 90 residues processed: 652 average time/residue: 1.6283 time to fit residues: 1449.7225 Evaluate side-chains 661 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 571 time to evaluate : 3.924 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 48 residues processed: 43 average time/residue: 0.8541 time to fit residues: 65.4478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 559 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 330 optimal weight: 5.9990 chunk 423 optimal weight: 9.9990 chunk 328 optimal weight: 5.9990 chunk 488 optimal weight: 6.9990 chunk 324 optimal weight: 0.7980 chunk 578 optimal weight: 6.9990 chunk 361 optimal weight: 0.9990 chunk 352 optimal weight: 0.9990 chunk 266 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN 3 20 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN I 61 GLN I 63 GLN I 95 HIS K 125 GLN N 39 GLN O 9 GLN T 67 ASN U 7 ASN U 88 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 96739 Z= 0.257 Angle : 0.613 12.485 145495 Z= 0.322 Chirality : 0.036 0.300 18708 Planarity : 0.005 0.126 7263 Dihedral : 15.084 178.559 39492 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.82 % Favored : 96.11 % Rotamer Outliers : 4.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.15), residues: 3061 helix: 0.87 (0.19), residues: 790 sheet: -0.29 (0.20), residues: 704 loop : -1.34 (0.14), residues: 1567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 582 time to evaluate : 4.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 79 residues processed: 643 average time/residue: 1.6299 time to fit residues: 1431.7328 Evaluate side-chains 651 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 572 time to evaluate : 4.038 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 49 residues processed: 32 average time/residue: 0.8094 time to fit residues: 48.6308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 357 optimal weight: 3.9990 chunk 230 optimal weight: 50.0000 chunk 345 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 367 optimal weight: 4.9990 chunk 393 optimal weight: 9.9990 chunk 285 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 454 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN 2 30 HIS 3 20 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN I 61 GLN I 63 GLN I 67 ASN N 99 HIS O 9 GLN Q 86 GLN U 88 ASN W 20 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.072 96739 Z= 0.430 Angle : 0.716 13.721 145495 Z= 0.369 Chirality : 0.041 0.300 18708 Planarity : 0.006 0.135 7263 Dihedral : 15.335 179.069 39492 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.13 % Favored : 94.77 % Rotamer Outliers : 4.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.14), residues: 3061 helix: 0.66 (0.19), residues: 791 sheet: -0.37 (0.20), residues: 689 loop : -1.49 (0.14), residues: 1581 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 583 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 83 residues processed: 648 average time/residue: 1.6197 time to fit residues: 1435.7986 Evaluate side-chains 663 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 580 time to evaluate : 3.928 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 54 residues processed: 33 average time/residue: 0.7508 time to fit residues: 48.1645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 526 optimal weight: 0.9980 chunk 554 optimal weight: 9.9990 chunk 505 optimal weight: 1.9990 chunk 538 optimal weight: 0.8980 chunk 553 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 234 optimal weight: 40.0000 chunk 423 optimal weight: 5.9990 chunk 165 optimal weight: 30.0000 chunk 486 optimal weight: 2.9990 chunk 509 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN 3 20 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN I 61 GLN I 63 GLN I 95 HIS N 39 GLN O 9 GLN Q 82 HIS Q 86 GLN U 7 ASN U 88 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 96739 Z= 0.169 Angle : 0.579 13.306 145495 Z= 0.305 Chirality : 0.033 0.307 18708 Planarity : 0.005 0.124 7263 Dihedral : 15.016 178.508 39492 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.18 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3061 helix: 1.00 (0.19), residues: 789 sheet: -0.24 (0.20), residues: 701 loop : -1.29 (0.14), residues: 1571 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 598 time to evaluate : 5.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 82 outliers final: 61 residues processed: 655 average time/residue: 1.6644 time to fit residues: 1497.7127 Evaluate side-chains 635 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 574 time to evaluate : 3.955 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 50 residues processed: 15 average time/residue: 0.7426 time to fit residues: 24.1445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 537 optimal weight: 0.4980 chunk 353 optimal weight: 7.9990 chunk 569 optimal weight: 0.0010 chunk 347 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 396 optimal weight: 30.0000 chunk 597 optimal weight: 3.9990 chunk 550 optimal weight: 8.9990 chunk 475 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 367 optimal weight: 4.9990 overall best weight: 2.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN G 106 ASN H 11 ASN I 61 GLN I 63 GLN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 ASN W 20 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 96739 Z= 0.228 Angle : 0.599 12.534 145495 Z= 0.314 Chirality : 0.034 0.292 18708 Planarity : 0.005 0.125 7263 Dihedral : 14.997 178.274 39492 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.44 % Favored : 95.46 % Rotamer Outliers : 2.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3061 helix: 0.98 (0.19), residues: 786 sheet: -0.20 (0.20), residues: 697 loop : -1.29 (0.14), residues: 1578 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6122 Ramachandran restraints generated. 3061 Oldfield, 0 Emsley, 3061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 584 time to evaluate : 4.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 60 residues processed: 636 average time/residue: 1.6437 time to fit residues: 1429.5385 Evaluate side-chains 637 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 577 time to evaluate : 3.950 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 48 residues processed: 15 average time/residue: 0.9512 time to fit residues: 26.8583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 291 optimal weight: 10.0000 chunk 378 optimal weight: 8.9990 chunk 507 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 438 optimal weight: 0.0770 chunk 70 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 476 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 489 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN 2 30 HIS 3 20 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN H 11 ASN I 63 GLN I 95 HIS O 9 GLN T 38 ASN U 7 ASN U 88 ASN W 20 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.065081 restraints weight = 195727.234| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 1.19 r_work: 0.2789 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 96739 Z= 0.392 Angle : 0.697 14.063 145495 Z= 0.360 Chirality : 0.040 0.299 18708 Planarity : 0.006 0.133 7263 Dihedral : 15.243 179.476 39492 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.20 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.15), residues: 3061 helix: 0.69 (0.19), residues: 793 sheet: -0.32 (0.20), residues: 679 loop : -1.38 (0.14), residues: 1589 =============================================================================== Job complete usr+sys time: 24232.86 seconds wall clock time: 424 minutes 18.60 seconds (25458.60 seconds total)