Starting phenix.real_space_refine on Mon Mar 18 19:12:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/03_2024/6v3d_21033_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/03_2024/6v3d_21033.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/03_2024/6v3d_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_21033/03_2024/6v3d_21033_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/03_2024/6v3d_21033_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/03_2024/6v3d_21033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/03_2024/6v3d_21033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/03_2024/6v3d_21033_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3d_21033/03_2024/6v3d_21033_updated.pdb" } resolution = 2.95 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= -0.004 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 35.03, per 1000 atoms: 0.39 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: 36.74 Conformation dependent library (CDL) restraints added in 4.6 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: 43.79 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: 184.14 Time building geometry restraints manager: 39.70 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 1.155 1.451 -0.296 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C4 5MUAN1935 " pdb=" C5 5MUAN1935 " ideal model delta sigma weight residual 1.802 1.612 0.190 2.00e-02 2.50e+03 9.04e+01 bond pdb=" N1 5MUAN1935 " pdb=" C2 5MUAN1935 " ideal model delta sigma weight residual 1.436 1.562 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" N1 5MUAN1935 " pdb=" C6 5MUAN1935 " ideal model delta sigma weight residual 1.635 1.562 0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" N3 5MUAN1935 " pdb=" C4 5MUAN1935 " ideal model delta sigma weight residual 1.182 1.249 -0.067 2.00e-02 2.50e+03 1.13e+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' 6MZAN2026 " pdb=" N9 6MZAN2026 " pdb=" C8 6MZAN2026 " ideal model delta sigma weight residual 126.23 148.81 -22.58 3.00e+00 1.11e-01 5.67e+01 angle pdb=" C1' 2MGAN2441 " pdb=" N9 2MGAN2441 " pdb=" C8 2MGAN2441 " ideal model delta sigma weight residual 110.07 132.06 -21.99 3.00e+00 1.11e-01 5.37e+01 angle pdb=" C1' OMGAN2247 " pdb=" N9 OMGAN2247 " pdb=" C4 OMGAN2247 " ideal model delta sigma weight residual 108.29 130.24 -21.95 3.00e+00 1.11e-01 5.35e+01 angle pdb=" C1' OMGAN2247 " pdb=" N9 OMGAN2247 " pdb=" C8 OMGAN2247 " ideal model delta sigma weight residual 142.82 121.22 21.60 3.00e+00 1.11e-01 5.19e+01 angle pdb=" C1' 2MGAN2441 " pdb=" N9 2MGAN2441 " pdb=" C4 2MGAN2441 " ideal model delta sigma weight residual 138.70 119.77 18.93 3.00e+00 1.11e-01 3.98e+01 ... (remaining 145490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 54493 35.84 - 71.69: 6512 71.69 - 107.53: 762 107.53 - 143.37: 16 143.37 - 179.22: 29 Dihedral angle restraints: 61812 sinusoidal: 52997 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 61809 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 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: 9.460 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: 0.100 Extract box with map and model: 29.070 Check model and map are aligned: 0.990 Set scattering table: 0.650 Process input model: 370.620 Find NCS groups from input model: 1.570 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 424.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 0.296 96739 Z= 0.125 Angle : 0.477 22.582 145495 Z= 0.251 Chirality : 0.027 0.277 18708 Planarity : 0.014 0.622 7263 Dihedral : 22.904 179.218 56146 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % Rotamer: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.70 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 83 HIS 0.004 0.001 HIS I 95 PHE 0.008 0.001 PHE F 138 TYR 0.008 0.001 TYR R 75 ARG 0.004 0.000 ARG F 115 *********************** 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 : 6.151 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: 0 26 MET cc_start: 0.8538 (ttm) cc_final: 0.8235 (ttm) REVERT: C 181 MET cc_start: 0.6462 (mpp) cc_final: 0.5955 (mtm) REVERT: D 184 ASP cc_start: 0.7264 (t70) cc_final: 0.6949 (t0) REVERT: E 123 PHE cc_start: 0.8756 (t80) cc_final: 0.8516 (t80) REVERT: F 47 LYS cc_start: 0.6598 (mttm) cc_final: 0.6002 (mmtt) REVERT: F 51 ASP cc_start: 0.8062 (t70) cc_final: 0.7761 (p0) REVERT: F 120 LYS cc_start: 0.6834 (tptt) cc_final: 0.6618 (mmmt) REVERT: G 119 GLU cc_start: 0.7502 (tp30) cc_final: 0.7276 (tm-30) REVERT: G 164 TYR cc_start: 0.8695 (m-80) cc_final: 0.8489 (m-80) REVERT: I 67 ASN cc_start: 0.8836 (t0) cc_final: 0.8591 (t0) REVERT: M 1 MET cc_start: 0.8800 (mtm) cc_final: 0.8566 (mtp) REVERT: M 20 MET cc_start: 0.8088 (ttp) cc_final: 0.7851 (ttp) REVERT: N 30 ASN cc_start: 0.8718 (t0) cc_final: 0.8376 (t0) REVERT: N 58 SER cc_start: 0.8464 (m) cc_final: 0.8105 (m) REVERT: N 107 ASP cc_start: 0.8515 (p0) cc_final: 0.8181 (p0) REVERT: P 49 ASP cc_start: 0.7767 (m-30) cc_final: 0.7498 (m-30) REVERT: Q 97 LYS cc_start: 0.8825 (tptm) cc_final: 0.7864 (tmtm) REVERT: T 79 ASP cc_start: 0.7907 (t70) cc_final: 0.7123 (t0) REVERT: U 56 GLU cc_start: 0.8221 (pt0) cc_final: 0.7729 (pt0) outliers start: 1 outliers final: 5 residues processed: 837 average time/residue: 1.8800 time to fit residues: 2072.6236 Evaluate side-chains 620 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 615 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain W residue 59 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 506 optimal weight: 0.8980 chunk 454 optimal weight: 5.9990 chunk 252 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 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: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN 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 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 15 GLN O 59 ASN O 78 GLN P 11 HIS R 57 ASN R 60 HIS R 61 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: 0.8668 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 96739 Z= 0.323 Angle : 0.651 14.635 145495 Z= 0.337 Chirality : 0.037 0.308 18708 Planarity : 0.005 0.127 7263 Dihedral : 23.244 179.109 50112 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.53 % Favored : 96.41 % Rotamer: Outliers : 5.67 % Allowed : 17.18 % Favored : 77.15 % 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: -1.10 (0.14), residues: 3061 helix: 0.57 (0.18), residues: 780 sheet: -0.47 (0.19), residues: 698 loop : -1.54 (0.13), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 83 HIS 0.008 0.001 HIS C 53 PHE 0.015 0.002 PHE F 77 TYR 0.017 0.002 TYR F 128 ARG 0.008 0.001 ARG O 92 *********************** 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 769 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 626 time to evaluate : 3.730 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: 0 1 MET cc_start: 0.5955 (OUTLIER) cc_final: 0.5545 (tmm) REVERT: 0 26 MET cc_start: 0.8676 (ttm) cc_final: 0.8317 (ttm) REVERT: D 139 ASN cc_start: 0.8870 (t0) cc_final: 0.8536 (t0) REVERT: D 170 ASP cc_start: 0.8263 (t0) cc_final: 0.7850 (t0) REVERT: E 50 ASP cc_start: 0.8794 (m-30) cc_final: 0.8562 (m-30) REVERT: F 8 TYR cc_start: 0.7375 (t80) cc_final: 0.7087 (t80) REVERT: F 51 ASP cc_start: 0.8287 (t70) cc_final: 0.7830 (p0) REVERT: F 95 GLN cc_start: 0.7622 (tm-30) cc_final: 0.7405 (tp-100) REVERT: I 60 GLU cc_start: 0.8570 (pm20) cc_final: 0.8259 (pm20) REVERT: I 61 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8108 (mp-120) REVERT: I 67 ASN cc_start: 0.8930 (t0) cc_final: 0.8673 (t0) REVERT: I 76 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7958 (ptp90) REVERT: I 95 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.7740 (p-80) REVERT: M 20 MET cc_start: 0.8282 (ttp) cc_final: 0.8034 (ttp) REVERT: M 30 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7582 (tm-30) REVERT: N 30 ASN cc_start: 0.8676 (t0) cc_final: 0.8375 (t0) REVERT: N 44 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.7893 (p0) REVERT: N 76 LEU cc_start: 0.9430 (tp) cc_final: 0.8643 (tp) REVERT: N 107 ASP cc_start: 0.8581 (p0) cc_final: 0.8229 (p0) REVERT: O 97 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7670 (mtp85) REVERT: S 29 GLN cc_start: 0.8287 (mm110) cc_final: 0.8025 (mp10) REVERT: S 47 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7454 (mm-30) REVERT: S 73 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9023 (tt) REVERT: T 79 ASP cc_start: 0.8039 (t70) cc_final: 0.7238 (t0) REVERT: U 66 GLU cc_start: 0.8225 (tp30) cc_final: 0.7841 (tp30) REVERT: U 74 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: Y 29 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7180 (mmm160) REVERT: Z 51 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7525 (ttm110) outliers start: 143 outliers final: 65 residues processed: 677 average time/residue: 1.7516 time to fit residues: 1595.5341 Evaluate side-chains 658 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 583 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 1 MET Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 20 THR Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 128 TYR Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 30 GLU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 43 LEU Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 68 ARG Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 75 ARG Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain T residue 100 SER Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 74 GLU Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 49 THR Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Y residue 29 ARG Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 36 THR 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: 0.6980 chunk 371 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 545 optimal weight: 1.9990 chunk 589 optimal weight: 2.9990 chunk 486 optimal weight: 6.9990 chunk 541 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 chunk 437 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 137 HIS E 114 GLN F 135 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN I 63 GLN N 39 GLN R 61 ASN S 20 GLN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 ASN V 29 GLN ** W 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 96739 Z= 0.147 Angle : 0.534 13.379 145495 Z= 0.282 Chirality : 0.031 0.278 18708 Planarity : 0.005 0.123 7263 Dihedral : 23.209 179.697 50106 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.07 % Favored : 96.83 % Rotamer: Outliers : 3.85 % Allowed : 20.90 % Favored : 75.25 % 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: -0.65 (0.15), residues: 3061 helix: 1.00 (0.19), residues: 792 sheet: -0.23 (0.20), residues: 689 loop : -1.28 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 83 HIS 0.003 0.001 HIS N 35 PHE 0.016 0.001 PHE M 102 TYR 0.017 0.001 TYR G 164 ARG 0.007 0.000 ARG P 12 *********************** 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 738 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 641 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 25 GLN cc_start: 0.7973 (mt0) cc_final: 0.7570 (mt0) REVERT: D 139 ASN cc_start: 0.8754 (t0) cc_final: 0.8360 (t0) REVERT: D 170 ASP cc_start: 0.8095 (t0) cc_final: 0.7700 (t0) REVERT: E 50 ASP cc_start: 0.8758 (m-30) cc_final: 0.8539 (m-30) REVERT: F 51 ASP cc_start: 0.8270 (t70) cc_final: 0.8010 (p0) REVERT: F 95 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7254 (tp-100) REVERT: F 128 TYR cc_start: 0.7841 (t80) cc_final: 0.7534 (OUTLIER) REVERT: F 150 ARG cc_start: 0.5530 (OUTLIER) cc_final: 0.4970 (mmm160) REVERT: G 23 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6383 (tm-30) REVERT: H 8 ARG cc_start: 0.6717 (ptm-80) cc_final: 0.5947 (ttp-110) REVERT: I 60 GLU cc_start: 0.8461 (pm20) cc_final: 0.8237 (pm20) REVERT: I 61 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8102 (mp-120) REVERT: I 67 ASN cc_start: 0.8857 (t0) cc_final: 0.8611 (t0) REVERT: I 95 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7262 (p-80) REVERT: J 53 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8213 (mttt) REVERT: J 109 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7662 (mm-30) REVERT: K 7 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7707 (mt-10) REVERT: L 5 LYS cc_start: 0.8384 (mppt) cc_final: 0.7996 (mppt) REVERT: L 31 SER cc_start: 0.8928 (t) cc_final: 0.8691 (p) REVERT: L 130 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8589 (p) REVERT: M 20 MET cc_start: 0.8213 (ttp) cc_final: 0.7960 (ttp) REVERT: N 30 ASN cc_start: 0.8660 (t0) cc_final: 0.8393 (t0) REVERT: N 44 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7882 (p0) REVERT: N 76 LEU cc_start: 0.9377 (tp) cc_final: 0.9019 (tp) REVERT: P 49 ASP cc_start: 0.8014 (m-30) cc_final: 0.7784 (m-30) REVERT: P 97 ASP cc_start: 0.8094 (t70) cc_final: 0.7715 (t0) REVERT: S 47 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7452 (mm-30) REVERT: T 79 ASP cc_start: 0.8008 (t70) cc_final: 0.7274 (t0) REVERT: U 66 GLU cc_start: 0.8183 (tp30) cc_final: 0.7827 (tp30) REVERT: U 74 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: X 5 ASP cc_start: 0.8452 (t70) cc_final: 0.8206 (t70) REVERT: X 28 LEU cc_start: 0.9361 (mt) cc_final: 0.9119 (mp) REVERT: Y 29 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.7206 (mmm160) REVERT: Z 47 PHE cc_start: 0.8310 (m-80) cc_final: 0.7926 (m-80) REVERT: Z 52 GLN cc_start: 0.7809 (tp40) cc_final: 0.7560 (tp-100) outliers start: 97 outliers final: 44 residues processed: 666 average time/residue: 1.7461 time to fit residues: 1572.0388 Evaluate side-chains 647 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 595 time to evaluate : 3.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 37 ASP Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 100 SER Chi-restraints excluded: chain U residue 74 GLU Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Y residue 29 ARG Chi-restraints excluded: chain Z residue 33 THR 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: 8.9990 chunk 283 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 366 optimal weight: 7.9990 chunk 547 optimal weight: 10.0000 chunk 579 optimal weight: 7.9990 chunk 286 optimal weight: 7.9990 chunk 519 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN H 11 ASN ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN N 39 GLN O 9 GLN Q 43 ASN R 61 ASN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 67 ASN U 88 ASN W 20 HIS X 22 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.073 96739 Z= 0.595 Angle : 0.827 13.914 145495 Z= 0.417 Chirality : 0.047 0.342 18708 Planarity : 0.007 0.141 7263 Dihedral : 23.415 178.777 50104 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 6.47 % Allowed : 21.18 % Favored : 72.35 % 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: -1.04 (0.14), residues: 3061 helix: 0.52 (0.18), residues: 782 sheet: -0.37 (0.20), residues: 680 loop : -1.47 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 213 HIS 0.009 0.002 HIS I 95 PHE 0.023 0.003 PHE I 101 TYR 0.042 0.002 TYR F 8 ARG 0.007 0.001 ARG I 27 *********************** 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 746 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 583 time to evaluate : 3.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 25 GLN cc_start: 0.8242 (mt0) cc_final: 0.7945 (mt0) REVERT: D 131 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7682 (mtp180) REVERT: D 139 ASN cc_start: 0.8898 (t0) cc_final: 0.8611 (t0) REVERT: D 170 ASP cc_start: 0.8414 (t0) cc_final: 0.8051 (t0) REVERT: E 50 ASP cc_start: 0.8839 (m-30) cc_final: 0.8616 (m-30) REVERT: F 95 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7296 (tp-100) REVERT: G 23 GLN cc_start: 0.7282 (OUTLIER) cc_final: 0.6305 (tm-30) REVERT: G 63 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8335 (mtm) REVERT: H 8 ARG cc_start: 0.6999 (ptm-80) cc_final: 0.6252 (ttp-110) REVERT: I 31 GLU cc_start: 0.8116 (tp30) cc_final: 0.7891 (tp30) REVERT: I 36 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8833 (mp) REVERT: I 60 GLU cc_start: 0.8532 (pm20) cc_final: 0.8202 (pm20) REVERT: I 61 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8154 (mp-120) REVERT: I 67 ASN cc_start: 0.8975 (t0) cc_final: 0.8702 (t0) REVERT: I 76 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7956 (ptp90) REVERT: I 95 HIS cc_start: 0.8790 (OUTLIER) cc_final: 0.7975 (p-80) REVERT: I 129 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: N 30 ASN cc_start: 0.8644 (t0) cc_final: 0.8365 (t0) REVERT: N 107 ASP cc_start: 0.8837 (t0) cc_final: 0.8286 (t0) REVERT: O 97 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7901 (mtp85) REVERT: P 97 ASP cc_start: 0.8237 (t70) cc_final: 0.7882 (t0) REVERT: Q 18 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: S 47 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7595 (mm-30) REVERT: T 25 LEU cc_start: 0.9239 (pt) cc_final: 0.9028 (pp) REVERT: T 79 ASP cc_start: 0.8094 (t70) cc_final: 0.7336 (t0) REVERT: U 7 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8547 (p0) REVERT: U 68 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8552 (mmmm) REVERT: U 77 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8622 (ttmm) REVERT: X 41 HIS cc_start: 0.7448 (OUTLIER) cc_final: 0.7107 (p90) REVERT: Y 29 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7386 (mmm160) outliers start: 163 outliers final: 86 residues processed: 649 average time/residue: 1.7807 time to fit residues: 1562.0170 Evaluate side-chains 659 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 560 time to evaluate : 3.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 20 THR Chi-restraints excluded: chain 0 residue 43 VAL Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 22 MET Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 3 residue 6 SER Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain S residue 68 ARG Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 75 ARG Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 48 ARG Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 87 LYS Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 11 LYS Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain W residue 33 LEU Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 41 HIS Chi-restraints excluded: chain X residue 49 THR Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Y residue 29 ARG Chi-restraints excluded: chain Y residue 34 THR Chi-restraints excluded: chain Z residue 33 THR 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: 0.9990 chunk 8 optimal weight: 0.7980 chunk 431 optimal weight: 0.4980 chunk 239 optimal weight: 5.9990 chunk 494 optimal weight: 0.9980 chunk 400 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 520 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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** D 33 ASN E 114 GLN F 37 ASN G 19 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN I 63 GLN J 3 GLN K 125 GLN N 39 GLN Q 43 ASN Q 82 HIS ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8603 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.136 96739 Z= 0.134 Angle : 0.558 12.855 145495 Z= 0.293 Chirality : 0.031 0.315 18708 Planarity : 0.005 0.122 7263 Dihedral : 23.261 179.547 50104 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.60 % Rotamer: Outliers : 3.89 % Allowed : 25.23 % Favored : 70.88 % 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: -0.49 (0.15), residues: 3061 helix: 1.13 (0.19), residues: 790 sheet: -0.12 (0.20), residues: 695 loop : -1.19 (0.14), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 62 HIS 0.004 0.001 HIS N 35 PHE 0.018 0.001 PHE M 102 TYR 0.034 0.001 TYR F 128 ARG 0.011 0.000 ARG 0 24 *********************** 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 718 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 620 time to evaluate : 3.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: D 139 ASN cc_start: 0.8713 (t0) cc_final: 0.8330 (t0) REVERT: D 170 ASP cc_start: 0.8235 (t0) cc_final: 0.7817 (t0) REVERT: E 50 ASP cc_start: 0.8765 (m-30) cc_final: 0.8563 (m-30) REVERT: F 37 ASN cc_start: 0.6775 (OUTLIER) cc_final: 0.6458 (p0) REVERT: F 51 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6869 (p0) REVERT: F 87 CYS cc_start: 0.7569 (m) cc_final: 0.7225 (t) REVERT: G 35 PHE cc_start: 0.8324 (t80) cc_final: 0.8110 (t80) REVERT: G 63 MET cc_start: 0.8406 (ttp) cc_final: 0.8118 (mtm) REVERT: H 8 ARG cc_start: 0.6812 (ptm-80) cc_final: 0.6124 (ttp-110) REVERT: I 67 ASN cc_start: 0.8835 (t0) cc_final: 0.8586 (t0) REVERT: L 29 PHE cc_start: 0.8740 (m-10) cc_final: 0.8536 (m-10) REVERT: L 31 SER cc_start: 0.8804 (t) cc_final: 0.8583 (p) REVERT: N 30 ASN cc_start: 0.8595 (t0) cc_final: 0.8378 (t0) REVERT: N 44 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7911 (p0) REVERT: N 72 LYS cc_start: 0.9215 (mttm) cc_final: 0.8997 (mttm) REVERT: P 97 ASP cc_start: 0.8065 (t70) cc_final: 0.7781 (t0) REVERT: P 100 MET cc_start: 0.8632 (ttt) cc_final: 0.8409 (ttp) REVERT: S 47 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7458 (mm-30) REVERT: T 79 ASP cc_start: 0.7878 (t70) cc_final: 0.7209 (t0) REVERT: V 68 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8449 (ttpp) outliers start: 98 outliers final: 46 residues processed: 661 average time/residue: 1.7457 time to fit residues: 1593.4999 Evaluate side-chains 624 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 573 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 117 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Z residue 33 THR 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: 7.9990 chunk 114 optimal weight: 6.9990 chunk 340 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 580 optimal weight: 0.9990 chunk 481 optimal weight: 0.0970 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: 3.1784 ------------------------------------------------------------------------------- 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 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN H 11 ASN I 63 GLN N 39 GLN Q 86 GLN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 96739 Z= 0.274 Angle : 0.608 12.744 145495 Z= 0.317 Chirality : 0.035 0.288 18708 Planarity : 0.005 0.129 7263 Dihedral : 23.215 178.707 50102 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 4.76 % Allowed : 25.66 % Favored : 69.58 % 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: -0.52 (0.15), residues: 3061 helix: 1.13 (0.19), residues: 787 sheet: -0.15 (0.20), residues: 689 loop : -1.21 (0.14), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 83 HIS 0.005 0.001 HIS R 102 PHE 0.017 0.001 PHE M 102 TYR 0.034 0.002 TYR F 128 ARG 0.008 0.000 ARG 0 24 *********************** 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 710 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 590 time to evaluate : 3.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 25 GLN cc_start: 0.8204 (mt0) cc_final: 0.7820 (mt0) REVERT: 2 48 MET cc_start: 0.8024 (mmt) cc_final: 0.7817 (mmm) REVERT: C 117 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: D 139 ASN cc_start: 0.8843 (t0) cc_final: 0.8500 (t0) REVERT: D 170 ASP cc_start: 0.8300 (t0) cc_final: 0.7844 (OUTLIER) REVERT: E 50 ASP cc_start: 0.8812 (m-30) cc_final: 0.8595 (m-30) REVERT: F 51 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.6992 (p0) REVERT: F 87 CYS cc_start: 0.7628 (m) cc_final: 0.7338 (t) REVERT: F 135 GLN cc_start: 0.5372 (OUTLIER) cc_final: 0.4786 (mm-40) REVERT: G 63 MET cc_start: 0.8501 (ttp) cc_final: 0.8110 (mtm) REVERT: H 8 ARG cc_start: 0.6825 (ptm-80) cc_final: 0.6075 (ttp-110) REVERT: I 60 GLU cc_start: 0.8523 (pm20) cc_final: 0.8078 (pm20) REVERT: I 61 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8011 (mp-120) REVERT: I 67 ASN cc_start: 0.8899 (t0) cc_final: 0.8670 (t0) REVERT: I 95 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7560 (p-80) REVERT: L 29 PHE cc_start: 0.8797 (m-10) cc_final: 0.8566 (m-10) REVERT: N 30 ASN cc_start: 0.8615 (t0) cc_final: 0.8398 (t0) REVERT: N 44 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8149 (p0) REVERT: N 76 LEU cc_start: 0.9310 (tp) cc_final: 0.8924 (tt) REVERT: Q 87 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8755 (tt0) REVERT: S 29 GLN cc_start: 0.8203 (mm110) cc_final: 0.7820 (mp10) REVERT: S 47 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7470 (mm-30) REVERT: T 79 ASP cc_start: 0.7893 (t70) cc_final: 0.7186 (t0) REVERT: W 11 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7416 (ptp90) REVERT: W 58 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8978 (mp) outliers start: 120 outliers final: 75 residues processed: 645 average time/residue: 1.7307 time to fit residues: 1514.1472 Evaluate side-chains 659 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 576 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 53 ASP Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 117 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 87 GLN Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 48 ARG Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 74 GLU Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 36 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 559 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 330 optimal weight: 3.9990 chunk 423 optimal weight: 7.9990 chunk 328 optimal weight: 4.9990 chunk 488 optimal weight: 0.0570 chunk 324 optimal weight: 0.9980 chunk 578 optimal weight: 2.9990 chunk 361 optimal weight: 5.9990 chunk 352 optimal weight: 2.9990 chunk 266 optimal weight: 8.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- 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** E 114 GLN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN G 23 GLN G 106 ASN H 11 ASN I 63 GLN N 39 GLN Q 86 GLN S 20 GLN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 96739 Z= 0.204 Angle : 0.583 12.805 145495 Z= 0.306 Chirality : 0.034 0.291 18708 Planarity : 0.005 0.125 7263 Dihedral : 23.217 178.799 50102 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.18 % Rotamer: Outliers : 4.64 % Allowed : 26.10 % Favored : 69.26 % 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: -0.49 (0.15), residues: 3061 helix: 1.19 (0.19), residues: 786 sheet: -0.15 (0.20), residues: 695 loop : -1.19 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 83 HIS 0.005 0.001 HIS M 31 PHE 0.022 0.001 PHE M 102 TYR 0.035 0.001 TYR F 128 ARG 0.019 0.000 ARG O 112 *********************** 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 705 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 588 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 117 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8001 (mt0) REVERT: D 139 ASN cc_start: 0.8749 (t0) cc_final: 0.8379 (t0) REVERT: D 170 ASP cc_start: 0.8245 (t0) cc_final: 0.7800 (t0) REVERT: E 50 ASP cc_start: 0.8803 (m-30) cc_final: 0.8591 (m-30) REVERT: F 51 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7072 (p0) REVERT: F 87 CYS cc_start: 0.7558 (m) cc_final: 0.7288 (t) REVERT: F 135 GLN cc_start: 0.5455 (OUTLIER) cc_final: 0.4860 (mm-40) REVERT: G 63 MET cc_start: 0.8467 (ttp) cc_final: 0.8135 (mtm) REVERT: H 8 ARG cc_start: 0.6677 (ptm-80) cc_final: 0.5964 (ttp-110) REVERT: I 31 GLU cc_start: 0.8041 (tp30) cc_final: 0.7785 (tp30) REVERT: I 60 GLU cc_start: 0.8524 (pm20) cc_final: 0.8107 (pm20) REVERT: I 61 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7994 (mp-120) REVERT: I 67 ASN cc_start: 0.8885 (t0) cc_final: 0.8638 (t0) REVERT: I 95 HIS cc_start: 0.8128 (OUTLIER) cc_final: 0.7401 (p-80) REVERT: N 44 ASP cc_start: 0.8422 (OUTLIER) cc_final: 0.8185 (p0) REVERT: O 97 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.7966 (mtp85) REVERT: P 100 MET cc_start: 0.8676 (ttt) cc_final: 0.8438 (ttp) REVERT: Q 87 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8761 (tt0) REVERT: S 29 GLN cc_start: 0.8215 (mm110) cc_final: 0.7858 (mp10) REVERT: S 47 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7379 (mm-30) REVERT: T 79 ASP cc_start: 0.7877 (t70) cc_final: 0.7215 (t0) REVERT: U 56 GLU cc_start: 0.8192 (pt0) cc_final: 0.7990 (pt0) REVERT: V 68 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8483 (ttpp) REVERT: W 58 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8967 (mp) outliers start: 117 outliers final: 84 residues processed: 644 average time/residue: 1.7843 time to fit residues: 1566.3556 Evaluate side-chains 674 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 580 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 53 ASP Chi-restraints excluded: chain 3 residue 6 SER Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 117 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 87 GLN Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 48 ARG Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Z residue 33 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 357 optimal weight: 4.9990 chunk 230 optimal weight: 50.0000 chunk 345 optimal weight: 0.7980 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: 10.0000 chunk 285 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 454 optimal weight: 0.4980 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN C 120 ASN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN F 37 ASN G 19 GLN G 23 GLN G 106 ASN H 11 ASN I 63 GLN N 39 GLN O 9 GLN Q 86 GLN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 96739 Z= 0.312 Angle : 0.644 13.393 145495 Z= 0.334 Chirality : 0.037 0.289 18708 Planarity : 0.006 0.131 7263 Dihedral : 23.241 178.651 50102 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.48 % Favored : 95.46 % Rotamer: Outliers : 4.80 % Allowed : 26.66 % Favored : 68.54 % 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: 1.07 (0.19), residues: 786 sheet: -0.20 (0.20), residues: 696 loop : -1.27 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 83 HIS 0.005 0.001 HIS I 95 PHE 0.034 0.002 PHE G 35 TYR 0.037 0.002 TYR F 128 ARG 0.012 0.000 ARG 0 24 *********************** 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 703 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 582 time to evaluate : 3.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 21 LYS cc_start: 0.8464 (ttpt) cc_final: 0.8250 (ptmm) REVERT: C 117 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8088 (mt0) REVERT: D 139 ASN cc_start: 0.8870 (t0) cc_final: 0.8551 (t0) REVERT: D 170 ASP cc_start: 0.8307 (t0) cc_final: 0.7874 (t0) REVERT: F 37 ASN cc_start: 0.7278 (OUTLIER) cc_final: 0.6924 (p0) REVERT: F 51 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7142 (p0) REVERT: F 87 CYS cc_start: 0.7551 (m) cc_final: 0.7246 (t) REVERT: F 135 GLN cc_start: 0.5922 (OUTLIER) cc_final: 0.5052 (tp-100) REVERT: G 23 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: G 35 PHE cc_start: 0.8296 (t80) cc_final: 0.8018 (t80) REVERT: G 63 MET cc_start: 0.8505 (ttp) cc_final: 0.8120 (mtm) REVERT: H 8 ARG cc_start: 0.6650 (ptm-80) cc_final: 0.5972 (ttp-110) REVERT: I 31 GLU cc_start: 0.8051 (tp30) cc_final: 0.7827 (tp30) REVERT: I 60 GLU cc_start: 0.8440 (pm20) cc_final: 0.7997 (pm20) REVERT: I 61 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8002 (mp-120) REVERT: I 67 ASN cc_start: 0.8926 (t0) cc_final: 0.8674 (t0) REVERT: I 76 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7637 (ptp90) REVERT: I 95 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.7742 (p-80) REVERT: N 44 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8112 (p0) REVERT: N 56 ASP cc_start: 0.7731 (p0) cc_final: 0.7498 (p0) REVERT: O 97 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8147 (mtp85) REVERT: Q 87 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8723 (tt0) REVERT: S 29 GLN cc_start: 0.8263 (mm110) cc_final: 0.7901 (mp10) REVERT: T 79 ASP cc_start: 0.7839 (t70) cc_final: 0.7181 (t0) REVERT: U 7 ASN cc_start: 0.8765 (p0) cc_final: 0.8565 (p0) REVERT: U 68 LYS cc_start: 0.8844 (mmmm) cc_final: 0.8513 (mmmm) REVERT: U 77 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8572 (mttt) REVERT: U 96 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8915 (tttt) REVERT: V 68 LYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8508 (ttpp) REVERT: W 58 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8991 (mp) outliers start: 121 outliers final: 83 residues processed: 642 average time/residue: 1.7485 time to fit residues: 1523.8467 Evaluate side-chains 666 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 569 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 2 residue 6 THR Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 53 ASP Chi-restraints excluded: chain 3 residue 6 SER Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 117 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 58 SER Chi-restraints excluded: chain N residue 61 SER Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain Q residue 18 GLU Chi-restraints excluded: chain Q residue 87 GLN Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 48 ARG Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 96 LYS Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 11 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 36 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 526 optimal weight: 0.0060 chunk 554 optimal weight: 7.9990 chunk 505 optimal weight: 7.9990 chunk 538 optimal weight: 0.9990 chunk 553 optimal weight: 5.9990 chunk 324 optimal weight: 0.3980 chunk 234 optimal weight: 50.0000 chunk 423 optimal weight: 0.0270 chunk 165 optimal weight: 30.0000 chunk 486 optimal weight: 5.9990 chunk 509 optimal weight: 3.9990 overall best weight: 1.0858 ------------------------------------------------------------------------------- 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** E 114 GLN ** G 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN I 63 GLN N 39 GLN Q 86 GLN ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 88 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 96739 Z= 0.144 Angle : 0.591 13.122 145495 Z= 0.311 Chirality : 0.033 0.295 18708 Planarity : 0.005 0.120 7263 Dihedral : 23.273 179.019 50102 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 3.33 % Allowed : 28.36 % Favored : 68.31 % 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: -0.50 (0.15), residues: 3061 helix: 1.18 (0.19), residues: 783 sheet: -0.14 (0.20), residues: 711 loop : -1.21 (0.14), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 83 HIS 0.004 0.001 HIS M 31 PHE 0.027 0.001 PHE M 102 TYR 0.027 0.001 TYR F 128 ARG 0.014 0.000 ARG O 112 *********************** 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 669 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 585 time to evaluate : 5.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 25 GLN cc_start: 0.8265 (mt0) cc_final: 0.7893 (mt0) REVERT: C 117 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: D 139 ASN cc_start: 0.8759 (t0) cc_final: 0.8411 (t0) REVERT: D 170 ASP cc_start: 0.8202 (t0) cc_final: 0.7795 (t0) REVERT: F 51 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7127 (p0) REVERT: F 87 CYS cc_start: 0.7632 (m) cc_final: 0.7058 (t) REVERT: F 135 GLN cc_start: 0.5911 (OUTLIER) cc_final: 0.5057 (tp-100) REVERT: G 23 GLN cc_start: 0.7653 (tt0) cc_final: 0.7291 (tm-30) REVERT: G 63 MET cc_start: 0.8412 (ttp) cc_final: 0.8122 (mtm) REVERT: H 8 ARG cc_start: 0.6732 (ptm-80) cc_final: 0.6089 (ttp-110) REVERT: I 31 GLU cc_start: 0.7990 (tp30) cc_final: 0.7734 (tp30) REVERT: I 60 GLU cc_start: 0.8510 (pm20) cc_final: 0.8212 (pm20) REVERT: I 61 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8095 (mp-120) REVERT: I 95 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7535 (p-80) REVERT: N 44 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8113 (p0) REVERT: O 112 ARG cc_start: 0.7885 (mmm160) cc_final: 0.7310 (mtp85) REVERT: P 100 MET cc_start: 0.8653 (ttt) cc_final: 0.8417 (ttp) REVERT: S 29 GLN cc_start: 0.8153 (mm110) cc_final: 0.7822 (mp10) REVERT: T 79 ASP cc_start: 0.7878 (t70) cc_final: 0.7260 (t0) REVERT: U 77 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8539 (mttt) REVERT: U 96 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8910 (tttt) REVERT: V 68 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8458 (ttpp) REVERT: W 58 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8965 (mp) outliers start: 84 outliers final: 57 residues processed: 629 average time/residue: 1.7597 time to fit residues: 1500.4679 Evaluate side-chains 639 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 573 time to evaluate : 3.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 0 residue 36 ASP Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 117 GLN Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 ASP Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 48 ARG Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain U residue 94 ASP Chi-restraints excluded: chain U residue 96 LYS Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Z residue 33 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 600 random chunks: chunk 537 optimal weight: 0.0050 chunk 353 optimal weight: 0.8980 chunk 569 optimal weight: 0.7980 chunk 347 optimal weight: 1.9990 chunk 270 optimal weight: 10.0000 chunk 396 optimal weight: 20.0000 chunk 597 optimal weight: 1.9990 chunk 550 optimal weight: 8.9990 chunk 475 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 367 optimal weight: 0.6980 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN H 11 ASN I 63 GLN I 67 ASN N 39 GLN Q 86 GLN S 29 GLN U 75 ASN U 88 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 96739 Z= 0.131 Angle : 0.549 12.601 145495 Z= 0.289 Chirality : 0.030 0.308 18708 Planarity : 0.005 0.122 7263 Dihedral : 23.208 179.972 50102 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.66 % Favored : 96.24 % Rotamer: Outliers : 2.70 % Allowed : 29.39 % Favored : 67.91 % 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: -0.33 (0.15), residues: 3061 helix: 1.31 (0.19), residues: 783 sheet: -0.04 (0.20), residues: 688 loop : -1.08 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 83 HIS 0.009 0.001 HIS 0 42 PHE 0.022 0.001 PHE M 102 TYR 0.029 0.001 TYR F 8 ARG 0.017 0.000 ARG O 112 ********************** 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 665 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 597 time to evaluate : 3.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 25 GLN cc_start: 0.8214 (mt0) cc_final: 0.7973 (mt0) REVERT: C 117 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7988 (mt0) REVERT: D 139 ASN cc_start: 0.8753 (t0) cc_final: 0.8369 (t0) REVERT: D 170 ASP cc_start: 0.8104 (t0) cc_final: 0.7656 (t0) REVERT: F 51 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7169 (p0) REVERT: F 170 MET cc_start: 0.7072 (tpt) cc_final: 0.6768 (tpt) REVERT: G 170 LEU cc_start: 0.8256 (tp) cc_final: 0.7629 (pt) REVERT: H 8 ARG cc_start: 0.6706 (ptm-80) cc_final: 0.6126 (ttp-110) REVERT: I 31 GLU cc_start: 0.7967 (tp30) cc_final: 0.7687 (tp30) REVERT: I 60 GLU cc_start: 0.8534 (pm20) cc_final: 0.8252 (pm20) REVERT: I 61 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8052 (mp-120) REVERT: K 1 MET cc_start: 0.6114 (tpp) cc_final: 0.5911 (tpp) REVERT: L 31 SER cc_start: 0.8808 (t) cc_final: 0.8594 (p) REVERT: N 56 ASP cc_start: 0.7788 (p0) cc_final: 0.7271 (p0) REVERT: N 58 SER cc_start: 0.8553 (m) cc_final: 0.8229 (p) REVERT: P 100 MET cc_start: 0.8650 (ttt) cc_final: 0.8418 (ttp) REVERT: T 79 ASP cc_start: 0.7894 (t70) cc_final: 0.7317 (t0) REVERT: U 68 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8394 (mmmm) REVERT: U 77 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8496 (mttt) REVERT: V 68 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8470 (ttpp) REVERT: W 54 LYS cc_start: 0.8500 (tttt) cc_final: 0.8226 (tttt) REVERT: W 58 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8902 (mp) outliers start: 68 outliers final: 43 residues processed: 629 average time/residue: 1.7326 time to fit residues: 1479.8177 Evaluate side-chains 618 residues out of total 2521 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 570 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 117 GLN Chi-restraints excluded: chain D residue 10 CYS Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 PHE Chi-restraints excluded: chain G residue 40 LEU Chi-restraints excluded: chain G residue 169 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain I residue 61 GLN Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 129 GLU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain K residue 85 SER Chi-restraints excluded: chain K residue 144 VAL Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain M residue 13 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 47 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 41 ILE Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain P residue 89 ILE Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 38 ASN Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain V residue 64 ASP Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain Z residue 33 THR 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: 2.9990 chunk 507 optimal weight: 0.6980 chunk 145 optimal weight: 7.9990 chunk 438 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 476 optimal weight: 0.7980 chunk 199 optimal weight: 7.9990 chunk 489 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 overall best weight: 2.4784 ------------------------------------------------------------------------------- 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** E 114 GLN F 37 ASN H 11 ASN I 63 GLN I 67 ASN ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN U 88 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.068497 restraints weight = 195432.489| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.12 r_work: 0.2860 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 96739 Z= 0.225 Angle : 0.580 12.769 145495 Z= 0.302 Chirality : 0.033 0.287 18708 Planarity : 0.005 0.126 7263 Dihedral : 23.158 179.371 50102 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 2.82 % Allowed : 29.55 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.38 (0.15), residues: 3061 helix: 1.25 (0.19), residues: 781 sheet: -0.00 (0.20), residues: 700 loop : -1.16 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 83 HIS 0.004 0.001 HIS R 102 PHE 0.022 0.001 PHE G 35 TYR 0.025 0.001 TYR F 8 ARG 0.016 0.000 ARG O 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25609.49 seconds wall clock time: 448 minutes 29.67 seconds (26909.67 seconds total)