Starting phenix.real_space_refine (version: dev) on Fri Dec 16 20:49:47 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl3_12216/12_2022/7bl3_12216.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl3_12216/12_2022/7bl3_12216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl3_12216/12_2022/7bl3_12216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl3_12216/12_2022/7bl3_12216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl3_12216/12_2022/7bl3_12216.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl3_12216/12_2022/7bl3_12216.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.034 sd= 0.805 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "9P ASP 5": "OD1" <-> "OD2" Residue "9P TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9P ASP 50": "OD1" <-> "OD2" Residue "9P TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9P ARG 129": "NH1" <-> "NH2" Residue "9P ARG 136": "NH1" <-> "NH2" Residue "9P PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9P ARG 177": "NH1" <-> "NH2" Residue "9P ARG 230": "NH1" <-> "NH2" Residue "9P ARG 239": "NH1" <-> "NH2" Residue "9P ASP 272": "OD1" <-> "OD2" Residue "9P GLU 307": "OE1" <-> "OE2" Residue "9P TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ASP 103": "OD1" <-> "OD2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ASP 14": "OD1" <-> "OD2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O GLU 84": "OE1" <-> "OE2" Residue "O ASP 93": "OD1" <-> "OD2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 110": "OE1" <-> "OE2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 45": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "R TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ASP 22": "OD1" <-> "OD2" Residue "S TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S ASP 62": "OD1" <-> "OD2" Residue "S ASP 68": "OD1" <-> "OD2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 5": "OE1" <-> "OE2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "U PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 100": "OE1" <-> "OE2" Residue "V PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 43": "OD1" <-> "OD2" Residue "V ASP 45": "OD1" <-> "OD2" Residue "V GLU 55": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 60": "OD1" <-> "OD2" Residue "W GLU 66": "OE1" <-> "OE2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 42": "OE1" <-> "OE2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ASP 39": "OD1" <-> "OD2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ASP 30": "OD1" <-> "OD2" Residue "0 GLU 35": "OE1" <-> "OE2" Residue "0 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "I PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "6 PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 15": "OD1" <-> "OD2" Residue "6 ASP 21": "OD1" <-> "OD2" Residue "6 ARG 96": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 162": "OD1" <-> "OD2" Residue "F PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 92831 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 62301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2902, 62301 Classifications: {'RNA': 2902} Modifications used: {'rna2p_pur': 272, 'rna2p_pyr': 149, 'rna3p_pur': 1403, 'rna3p_pyr': 1078} Link IDs: {'rna2p': 421, 'rna3p': 2480} Chain breaks: 2 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2548 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "9P" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2582 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain: "b" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 364 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "P" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "6" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 144} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" 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: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 39.19, per 1000 atoms: 0.42 Number of scatterers: 92831 At special positions: 0 Unit cell: (207.08, 226.92, 272.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 92 16.00 P 3020 15.00 Mg 1 11.99 O 26059 8.00 N 17217 7.00 C 46441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 18 " - pdb=" SG CYS b 40 " distance=2.03 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: 40.35 Conformation dependent library (CDL) restraints added in 3.7 seconds 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6570 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 48 sheets defined 28.3% alpha, 18.5% beta 989 base pairs and 1529 stacking pairs defined. Time for finding SS restraints: 29.29 Creating SS restraints... Processing helix chain '9P' and resid 56 through 60 removed outlier: 3.851A pdb=" N ARG9P 60 " --> pdb=" O ILE9P 57 " (cutoff:3.500A) Processing helix chain '9P' and resid 126 through 131 Processing helix chain '9P' and resid 171 through 177 removed outlier: 3.685A pdb=" N ILE9P 176 " --> pdb=" O LYS9P 172 " (cutoff:3.500A) Processing helix chain '9P' and resid 228 through 235 removed outlier: 4.305A pdb=" N PHE9P 231 " --> pdb=" O GLY9P 228 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS9P 233 " --> pdb=" O ARG9P 230 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS9P 234 " --> pdb=" O PHE9P 231 " (cutoff:3.500A) Processing helix chain '9P' and resid 255 through 257 No H-bonds generated for 'chain '9P' and resid 255 through 257' Processing helix chain '9P' and resid 258 through 268 removed outlier: 4.078A pdb=" N ILE9P 262 " --> pdb=" O ASN9P 258 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER9P 264 " --> pdb=" O ARG9P 260 " (cutoff:3.500A) Processing helix chain '9P' and resid 271 through 276 removed outlier: 4.074A pdb=" N THR9P 275 " --> pdb=" O GLN9P 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS9P 276 " --> pdb=" O ASP9P 272 " (cutoff:3.500A) No H-bonds generated for 'chain '9P' and resid 271 through 276' Processing helix chain '9P' and resid 289 through 305 removed outlier: 4.273A pdb=" N GLU9P 295 " --> pdb=" O VAL9P 291 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU9P 304 " --> pdb=" O ILE9P 300 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY9P 305 " --> pdb=" O ALA9P 301 " (cutoff:3.500A) Processing helix chain '9P' and resid 321 through 334 removed outlier: 3.504A pdb=" N ASP9P 327 " --> pdb=" O ASP9P 323 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL9P 328 " --> pdb=" O LEU9P 324 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET9P 329 " --> pdb=" O CYS9P 325 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU9P 334 " --> pdb=" O THR9P 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 14 removed outlier: 4.244A pdb=" N HIS C 14 " --> pdb=" O GLY C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.364A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.224A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.508A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.619A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.572A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 removed outlier: 3.539A pdb=" N SER E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.646A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.734A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 removed outlier: 4.199A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.726A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 60 through 80 removed outlier: 3.696A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 151 removed outlier: 3.774A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.651A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 98 through 109 removed outlier: 3.570A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 4.004A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.525A pdb=" N ARG L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 56 through 61' Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.838A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 3.876A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 removed outlier: 3.555A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'N' and resid 82 through 88 removed outlier: 3.503A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 22 removed outlier: 4.390A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 4.148A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 114 removed outlier: 3.628A pdb=" N LEU O 106 " --> pdb=" O ARG O 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.849A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 29 removed outlier: 3.564A pdb=" N SER Q 28 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.111A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE Q 56 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.713A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.654A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.715A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 41 through 60 removed outlier: 3.543A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 3 through 10 removed outlier: 4.085A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 4.402A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER T 27 " --> pdb=" O ALA T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.529A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 19 Processing helix chain 'V' and resid 20 through 23 Processing helix chain 'V' and resid 44 through 52 removed outlier: 3.706A pdb=" N MET V 48 " --> pdb=" O HIS V 44 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 57 Processing helix chain 'X' and resid 52 through 62 Processing helix chain 'X' and resid 62 through 73 removed outlier: 3.541A pdb=" N GLU X 69 " --> pdb=" O THR X 65 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU X 70 " --> pdb=" O VAL X 66 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.660A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 34 removed outlier: 3.528A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 55 removed outlier: 4.103A pdb=" N GLN Y 45 " --> pdb=" O HIS Y 41 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 26 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.576A pdb=" N ALA Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 14 removed outlier: 3.549A pdb=" N ARG 0 12 " --> pdb=" O THR 0 8 " (cutoff:3.500A) Processing helix chain '0' and resid 15 through 19 removed outlier: 4.055A pdb=" N HIS 0 18 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.261A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 removed outlier: 3.695A pdb=" N ALA 2 36 " --> pdb=" O ALA 2 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 39 removed outlier: 4.019A pdb=" N CYS I 38 " --> pdb=" O MET I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 removed outlier: 3.644A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 126 removed outlier: 3.545A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 132 removed outlier: 4.336A pdb=" N THR I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 111 removed outlier: 3.723A pdb=" N LEU K 107 " --> pdb=" O THR K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 118 removed outlier: 3.854A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 12 removed outlier: 3.995A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN P 9 " --> pdb=" O LYS P 5 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 100 Processing helix chain 'P' and resid 104 through 108 removed outlier: 4.072A pdb=" N ARG P 108 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain '6' and resid 4 through 17 removed outlier: 3.591A pdb=" N ASP 6 8 " --> pdb=" O LYS 6 4 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS 6 13 " --> pdb=" O PHE 6 9 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU 6 17 " --> pdb=" O LYS 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 61 removed outlier: 3.505A pdb=" N ASP 6 53 " --> pdb=" O MET 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 92 through 96 removed outlier: 3.608A pdb=" N ARG 6 96 " --> pdb=" O GLU 6 92 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 92 through 96' Processing helix chain 'H' and resid 22 through 27 Processing helix chain 'H' and resid 42 through 71 removed outlier: 3.701A pdb=" N GLU H 48 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 10 through 20 removed outlier: 3.742A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 73 through 77 removed outlier: 3.538A pdb=" N PHE F 76 " --> pdb=" O VAL F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.894A pdb=" N ALA F 170 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '9P' and resid 64 through 66 removed outlier: 9.028A pdb=" N PHE9P 65 " --> pdb=" O SER9P 8 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU9P 10 " --> pdb=" O PHE9P 65 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR9P 94 " --> pdb=" O ASP9P 107 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASP9P 107 " --> pdb=" O THR9P 94 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL9P 96 " --> pdb=" O MET9P 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '9P' and resid 22 through 23 Processing sheet with id=AA3, first strand: chain '9P' and resid 87 through 91 removed outlier: 6.516A pdb=" N TRP9P 46 " --> pdb=" O ILE9P 88 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL9P 90 " --> pdb=" O TRP9P 46 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU9P 48 " --> pdb=" O VAL9P 90 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL9P 45 " --> pdb=" O VAL9P 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '9P' and resid 165 through 166 removed outlier: 3.936A pdb=" N LEU9P 165 " --> pdb=" O LEU9P 242 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU9P 244 " --> pdb=" O LEU9P 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '9P' and resid 197 through 199 Processing sheet with id=AA6, first strand: chain 'b' and resid 21 through 25 removed outlier: 3.959A pdb=" N LEU b 32 " --> pdb=" O THR b 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.575A pdb=" N TYR C 61 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 104 removed outlier: 3.530A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.061A pdb=" N VAL C 164 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 169 through 175 removed outlier: 5.040A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.016A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 48 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AB5, first strand: chain 'E' and resid 2 through 3 removed outlier: 3.629A pdb=" N LEU E 12 " --> pdb=" O LEU E 3 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.796A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 17 through 18 Processing sheet with id=AB8, first strand: chain 'G' and resid 40 through 43 removed outlier: 3.749A pdb=" N LYS G 43 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 120 through 123 Processing sheet with id=AC1, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.554A pdb=" N ARG G 94 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 102 " --> pdb=" O HIS G 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.353A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AC4, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AC5, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.483A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 47 through 51 removed outlier: 4.162A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR O 36 " --> pdb=" O HIS O 29 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN O 38 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.642A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA R 42 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE R 41 " --> pdb=" O VAL R 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 19 through 23 removed outlier: 3.657A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 72 through 75 Processing sheet with id=AD1, first strand: chain 'S' and resid 2 through 10 removed outlier: 3.622A pdb=" N HIS S 9 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS S 98 " --> pdb=" O SER S 81 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER S 81 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 86 through 87 Processing sheet with id=AD3, first strand: chain 'T' and resid 11 through 14 removed outlier: 3.931A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.470A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN U 73 " --> pdb=" O LYS U 78 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS U 78 " --> pdb=" O ASN U 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AD6, first strand: chain 'U' and resid 82 through 85 removed outlier: 3.518A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 2 through 8 removed outlier: 7.985A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU V 7 " --> pdb=" O GLU V 41 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU V 86 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ARG V 79 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN V 75 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE V 2 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL V 64 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 18 through 19 removed outlier: 6.961A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY W 48 " --> pdb=" O PHE W 56 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'W' and resid 26 through 27 removed outlier: 3.590A pdb=" N GLY W 61 " --> pdb=" O VAL W 27 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 12 through 15 removed outlier: 3.658A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.641A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 35 through 38 removed outlier: 3.676A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU Z 57 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AE5, first strand: chain '1' and resid 19 through 24 removed outlier: 3.647A pdb=" N VAL 1 11 " --> pdb=" O LYS 1 49 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.933A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 70 through 71 removed outlier: 3.828A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE P 58 " --> pdb=" O PHE P 73 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG P 38 " --> pdb=" O VAL P 31 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '6' and resid 20 through 24 removed outlier: 3.845A pdb=" N GLN 6 20 " --> pdb=" O THR 6 41 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR 6 41 " --> pdb=" O GLN 6 20 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE 6 22 " --> pdb=" O ILE 6 39 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE 6 39 " --> pdb=" O ILE 6 22 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA 6 24 " --> pdb=" O MET 6 37 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N MET 6 37 " --> pdb=" O ALA 6 24 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS 6 36 " --> pdb=" O ILE 6 86 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N HIS 6 88 " --> pdb=" O CYS 6 36 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE 6 38 " --> pdb=" O HIS 6 88 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET 6 90 " --> pdb=" O ILE 6 38 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS 6 40 " --> pdb=" O MET 6 90 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL 6 87 " --> pdb=" O VAL 6 80 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL 6 80 " --> pdb=" O VAL 6 87 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AF1, first strand: chain 'H' and resid 77 through 82 removed outlier: 6.532A pdb=" N VAL H 78 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL H 147 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE H 80 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER H 131 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 89 through 94 removed outlier: 7.243A pdb=" N ARG H 123 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 66 through 67 removed outlier: 3.689A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR F 154 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN F 36 " --> pdb=" O ASP F 152 " (cutoff:3.500A) 839 hydrogen bonds defined for protein. 2298 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2507 hydrogen bonds 3952 hydrogen bond angles 0 basepair planarities 989 basepair parallelities 1529 stacking parallelities Total time for adding SS restraints: 142.49 Time building geometry restraints manager: 43.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 7487 1.29 - 1.42: 44665 1.42 - 1.56: 42602 1.56 - 1.69: 6039 1.69 - 1.82: 164 Bond restraints: 100957 Sorted by residual: bond pdb=" CG PRO G 111 " pdb=" CD PRO G 111 " ideal model delta sigma weight residual 1.503 1.161 0.342 3.40e-02 8.65e+02 1.01e+02 bond pdb=" N PRO G 111 " pdb=" CD PRO G 111 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" CB PRO G 111 " pdb=" CG PRO G 111 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.88e+00 bond pdb=" C THR D 151 " pdb=" N PRO D 152 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.20e-02 6.94e+03 3.92e+00 bond pdb=" N PHE9P 191 " pdb=" CA PHE9P 191 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.77e+00 ... (remaining 100952 not shown) Histogram of bond angle deviations from ideal: 83.65 - 93.74: 2 93.74 - 103.83: 7962 103.83 - 113.92: 73508 113.92 - 124.01: 56413 124.01 - 134.10: 13437 Bond angle restraints: 151322 Sorted by residual: angle pdb=" N PRO G 111 " pdb=" CD PRO G 111 " pdb=" CG PRO G 111 " ideal model delta sigma weight residual 103.20 83.65 19.55 1.50e+00 4.44e-01 1.70e+02 angle pdb=" CA PRO G 111 " pdb=" N PRO G 111 " pdb=" CD PRO G 111 " ideal model delta sigma weight residual 112.00 98.37 13.63 1.40e+00 5.10e-01 9.48e+01 angle pdb=" CA PRO G 111 " pdb=" CB PRO G 111 " pdb=" CG PRO G 111 " ideal model delta sigma weight residual 104.50 90.12 14.38 1.90e+00 2.77e-01 5.73e+01 angle pdb=" N GLY D 147 " pdb=" CA GLY D 147 " pdb=" C GLY D 147 " ideal model delta sigma weight residual 110.29 117.33 -7.04 1.28e+00 6.10e-01 3.03e+01 angle pdb=" N VAL C 203 " pdb=" CA VAL C 203 " pdb=" C VAL C 203 " ideal model delta sigma weight residual 113.53 108.28 5.25 9.80e-01 1.04e+00 2.87e+01 ... (remaining 151317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 51913 35.88 - 71.76: 1635 71.76 - 107.64: 148 107.64 - 143.52: 6 143.52 - 179.41: 13 Dihedral angle restraints: 53715 sinusoidal: 43498 harmonic: 10217 Sorted by residual: dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 60.41 139.59 1 1.50e+01 4.44e-03 7.52e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual -128.00 51.41 -179.41 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C A 323 " pdb=" C1' C A 323 " pdb=" N1 C A 323 " pdb=" C2 C A 323 " ideal model delta sinusoidal sigma weight residual -128.00 50.05 -178.05 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 53712 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 18202 0.054 - 0.108: 1031 0.108 - 0.162: 142 0.162 - 0.215: 14 0.215 - 0.269: 5 Chirality restraints: 19394 Sorted by residual: chirality pdb=" CA THR D 151 " pdb=" N THR D 151 " pdb=" C THR D 151 " pdb=" CB THR D 151 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ARG T 3 " pdb=" N ARG T 3 " pdb=" C ARG T 3 " pdb=" CB ARG T 3 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE N 113 " pdb=" CA ILE N 113 " pdb=" CG1 ILE N 113 " pdb=" CG2 ILE N 113 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 19391 not shown) Planarity restraints: 7943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE9P 29 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO9P 30 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO9P 30 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO9P 30 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Z 16 " -0.067 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO Z 17 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO Z 17 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO Z 17 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 110 " -0.071 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO G 111 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO G 111 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO G 111 " -0.053 5.00e-02 4.00e+02 ... (remaining 7940 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 3480 2.65 - 3.21: 80059 3.21 - 3.78: 187333 3.78 - 4.34: 243004 4.34 - 4.90: 323768 Nonbonded interactions: 837644 Sorted by model distance: nonbonded pdb=" OG1 THR O 31 " pdb=" O HIS O 34 " model vdw 2.089 2.440 nonbonded pdb=" O PRO9P 190 " pdb=" OG1 THR9P 192 " model vdw 2.103 2.440 nonbonded pdb=" N6 A A1287 " pdb=" O2' G A1649 " model vdw 2.105 2.520 nonbonded pdb=" OP2 A A2530 " pdb=" NZ LYS G 174 " model vdw 2.110 2.520 nonbonded pdb=" O2 C A1800 " pdb=" O6 G A1817 " model vdw 2.130 2.432 ... (remaining 837639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3020 5.49 5 Mg 1 5.21 5 S 92 5.16 5 C 46441 2.51 5 N 17217 2.21 5 O 26059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 11.180 Check model and map are aligned: 1.080 Convert atoms to be neutral: 0.600 Process input model: 316.180 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 334.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 0.342 100957 Z= 0.144 Angle : 0.481 19.552 151322 Z= 0.261 Chirality : 0.027 0.269 19394 Planarity : 0.004 0.108 7943 Dihedral : 14.108 179.406 47142 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3554 helix: -0.40 (0.19), residues: 795 sheet: -0.01 (0.21), residues: 670 loop : -1.40 (0.13), residues: 2089 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 859 time to evaluate : 4.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 860 average time/residue: 0.8336 time to fit residues: 1230.9572 Evaluate side-chains 701 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 701 time to evaluate : 4.107 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 548 optimal weight: 6.9990 chunk 492 optimal weight: 9.9990 chunk 273 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 332 optimal weight: 20.0000 chunk 263 optimal weight: 10.0000 chunk 509 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 309 optimal weight: 20.0000 chunk 379 optimal weight: 4.9990 chunk 590 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9P 111 HIS 9P 123 HIS ** 9P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9P 205 ASN C 85 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN E 30 GLN J 136 GLN N 62 ASN O 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN R 91 GLN T 28 ASN ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN 0 3 GLN 0 18 HIS 1 18 HIS 2 13 ASN 6 88 HIS 6 91 GLN ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.126 100957 Z= 0.376 Angle : 0.680 15.448 151322 Z= 0.343 Chirality : 0.037 0.259 19394 Planarity : 0.006 0.076 7943 Dihedral : 13.972 179.222 40206 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.47 (0.14), residues: 3554 helix: -0.43 (0.18), residues: 855 sheet: -0.46 (0.19), residues: 727 loop : -1.42 (0.14), residues: 1972 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 801 time to evaluate : 4.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 77 residues processed: 839 average time/residue: 0.8843 time to fit residues: 1284.2862 Evaluate side-chains 789 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 712 time to evaluate : 4.154 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 0 residues processed: 77 average time/residue: 0.6997 time to fit residues: 107.5743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 328 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 491 optimal weight: 0.9990 chunk 401 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 591 optimal weight: 1.9990 chunk 638 optimal weight: 10.0000 chunk 526 optimal weight: 7.9990 chunk 586 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 474 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9P 143 ASN C 116 GLN C 162 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN E 115 GLN G 127 GLN ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN Q 36 GLN Q 43 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN 2 29 GLN P 2 ASN ** 6 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 88 HIS ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 100957 Z= 0.162 Angle : 0.519 16.883 151322 Z= 0.265 Chirality : 0.031 0.238 19394 Planarity : 0.004 0.063 7943 Dihedral : 13.824 178.436 40206 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 2.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.27 (0.14), residues: 3554 helix: -0.20 (0.18), residues: 862 sheet: -0.34 (0.20), residues: 708 loop : -1.32 (0.14), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 780 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 27 residues processed: 811 average time/residue: 0.8504 time to fit residues: 1191.1121 Evaluate side-chains 742 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 715 time to evaluate : 4.123 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.6909 time to fit residues: 39.1040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 584 optimal weight: 9.9990 chunk 444 optimal weight: 7.9990 chunk 306 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 282 optimal weight: 10.0000 chunk 397 optimal weight: 20.0000 chunk 593 optimal weight: 2.9990 chunk 628 optimal weight: 30.0000 chunk 310 optimal weight: 10.0000 chunk 562 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9P 54 ASN ** 9P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9P 123 HIS ** 9P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 49 GLN E 115 GLN J 58 ASN ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 87 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN I 106 GLN P 2 ASN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 HIS 6 54 HIS H 43 ASN H 133 GLN ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.111 100957 Z= 0.363 Angle : 0.691 15.773 151322 Z= 0.350 Chirality : 0.038 0.342 19394 Planarity : 0.006 0.065 7943 Dihedral : 14.359 178.792 40206 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.33 % Favored : 91.64 % Rotamer Outliers : 4.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.58 (0.14), residues: 3554 helix: -0.39 (0.18), residues: 874 sheet: -0.81 (0.19), residues: 748 loop : -1.45 (0.14), residues: 1932 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 747 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 86 residues processed: 799 average time/residue: 0.8338 time to fit residues: 1153.8549 Evaluate side-chains 782 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 696 time to evaluate : 4.122 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 0.7209 time to fit residues: 120.4511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 523 optimal weight: 8.9990 chunk 356 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 467 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 chunk 536 optimal weight: 9.9990 chunk 434 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 320 optimal weight: 5.9990 chunk 563 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN E 115 GLN J 58 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 70 GLN Q 71 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 80 HIS ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 100957 Z= 0.300 Angle : 0.626 16.906 151322 Z= 0.320 Chirality : 0.036 0.361 19394 Planarity : 0.005 0.064 7943 Dihedral : 14.314 177.233 40206 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.64 (0.14), residues: 3554 helix: -0.37 (0.18), residues: 868 sheet: -0.96 (0.19), residues: 740 loop : -1.46 (0.14), residues: 1946 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 735 time to evaluate : 4.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 53 residues processed: 789 average time/residue: 0.8510 time to fit residues: 1163.9204 Evaluate side-chains 747 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 694 time to evaluate : 4.119 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.6457 time to fit residues: 71.7182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 211 optimal weight: 50.0000 chunk 565 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 368 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 628 optimal weight: 30.0000 chunk 522 optimal weight: 5.9990 chunk 291 optimal weight: 40.0000 chunk 52 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 330 optimal weight: 8.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9P 123 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN E 115 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN J 58 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 HIS ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.100 100957 Z= 0.337 Angle : 0.675 15.843 151322 Z= 0.344 Chirality : 0.038 0.369 19394 Planarity : 0.005 0.068 7943 Dihedral : 14.550 177.113 40206 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer Outliers : 3.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.83 (0.14), residues: 3554 helix: -0.53 (0.18), residues: 879 sheet: -1.09 (0.18), residues: 721 loop : -1.58 (0.14), residues: 1954 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 732 time to evaluate : 4.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 63 residues processed: 785 average time/residue: 0.8841 time to fit residues: 1201.6780 Evaluate side-chains 760 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 697 time to evaluate : 4.176 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.7052 time to fit residues: 88.9438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 606 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 358 optimal weight: 7.9990 chunk 459 optimal weight: 9.9990 chunk 355 optimal weight: 8.9990 chunk 529 optimal weight: 8.9990 chunk 351 optimal weight: 10.0000 chunk 626 optimal weight: 0.3980 chunk 392 optimal weight: 7.9990 chunk 381 optimal weight: 6.9990 chunk 289 optimal weight: 40.0000 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN J 58 ASN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 80 HIS ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.098 100957 Z= 0.305 Angle : 0.645 15.731 151322 Z= 0.329 Chirality : 0.037 0.367 19394 Planarity : 0.005 0.059 7943 Dihedral : 14.556 177.347 40206 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.14), residues: 3554 helix: -0.53 (0.18), residues: 885 sheet: -1.19 (0.19), residues: 709 loop : -1.56 (0.14), residues: 1960 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 727 time to evaluate : 4.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 31 residues processed: 756 average time/residue: 0.8465 time to fit residues: 1101.0624 Evaluate side-chains 724 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 693 time to evaluate : 4.402 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.6676 time to fit residues: 43.7051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 387 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 374 optimal weight: 10.0000 chunk 188 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 398 optimal weight: 7.9990 chunk 426 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 492 optimal weight: 6.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9P 123 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN J 58 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 45 HIS 2 29 GLN ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.108 100957 Z= 0.312 Angle : 0.656 15.689 151322 Z= 0.335 Chirality : 0.038 0.416 19394 Planarity : 0.005 0.064 7943 Dihedral : 14.646 179.684 40206 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.88 (0.14), residues: 3554 helix: -0.54 (0.18), residues: 870 sheet: -1.24 (0.18), residues: 732 loop : -1.58 (0.14), residues: 1952 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 726 time to evaluate : 4.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 29 residues processed: 742 average time/residue: 0.8644 time to fit residues: 1102.7622 Evaluate side-chains 714 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 685 time to evaluate : 4.206 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.7053 time to fit residues: 42.9218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 569 optimal weight: 1.9990 chunk 600 optimal weight: 0.9990 chunk 547 optimal weight: 7.9990 chunk 583 optimal weight: 5.9990 chunk 351 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 458 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 chunk 527 optimal weight: 10.0000 chunk 552 optimal weight: 6.9990 chunk 581 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN J 58 ASN ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN Q 43 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 ASN 6 91 GLN ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.086 100957 Z= 0.180 Angle : 0.573 15.526 151322 Z= 0.294 Chirality : 0.033 0.351 19394 Planarity : 0.004 0.074 7943 Dihedral : 14.416 179.408 40206 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.14), residues: 3554 helix: -0.41 (0.18), residues: 863 sheet: -1.10 (0.18), residues: 722 loop : -1.46 (0.14), residues: 1969 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 721 time to evaluate : 4.154 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 13 residues processed: 728 average time/residue: 0.8978 time to fit residues: 1137.0066 Evaluate side-chains 712 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 699 time to evaluate : 4.159 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.6941 time to fit residues: 21.3983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 383 optimal weight: 7.9990 chunk 617 optimal weight: 5.9990 chunk 376 optimal weight: 10.0000 chunk 292 optimal weight: 40.0000 chunk 429 optimal weight: 10.0000 chunk 647 optimal weight: 7.9990 chunk 596 optimal weight: 6.9990 chunk 515 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 398 optimal weight: 5.9990 chunk 316 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN J 58 ASN ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 100957 Z= 0.289 Angle : 0.637 15.680 151322 Z= 0.324 Chirality : 0.036 0.354 19394 Planarity : 0.005 0.067 7943 Dihedral : 14.525 177.375 40206 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3554 helix: -0.45 (0.18), residues: 870 sheet: -1.28 (0.18), residues: 736 loop : -1.43 (0.14), residues: 1948 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 697 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 705 average time/residue: 0.8528 time to fit residues: 1041.0720 Evaluate side-chains 689 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 674 time to evaluate : 4.082 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6754 time to fit residues: 23.4473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 409 optimal weight: 0.0570 chunk 549 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 475 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 516 optimal weight: 3.9990 chunk 216 optimal weight: 50.0000 chunk 530 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN O 19 GLN ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.113060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.086560 restraints weight = 266395.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088530 restraints weight = 84514.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.089677 restraints weight = 45000.473| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.097 100957 Z= 0.242 Angle : 0.611 16.117 151322 Z= 0.312 Chirality : 0.035 0.348 19394 Planarity : 0.005 0.056 7943 Dihedral : 14.505 177.133 40206 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.14), residues: 3554 helix: -0.45 (0.18), residues: 868 sheet: -1.20 (0.18), residues: 756 loop : -1.42 (0.14), residues: 1930 =============================================================================== Job complete usr+sys time: 17630.04 seconds wall clock time: 314 minutes 34.28 seconds (18874.28 seconds total)