Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 13:58:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn5_11310/04_2023/6zn5_11310.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn5_11310/04_2023/6zn5_11310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn5_11310/04_2023/6zn5_11310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn5_11310/04_2023/6zn5_11310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn5_11310/04_2023/6zn5_11310.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zn5_11310/04_2023/6zn5_11310.pdb" } resolution = 3.2 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= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1671 5.49 5 S 202 5.16 5 C 43583 2.51 5 N 14582 2.21 5 O 19336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 13": "OE1" <-> "OE2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C ASP 108": "OD1" <-> "OD2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 175": "OE1" <-> "OE2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 209": "OD1" <-> "OD2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "E PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F GLU 38": "OE1" <-> "OE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "F GLU 61": "OE1" <-> "OE2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ASP 193": "OD1" <-> "OD2" Residue "F ASP 206": "OD1" <-> "OD2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F ASP 215": "OD1" <-> "OD2" Residue "F GLU 216": "OE1" <-> "OE2" Residue "G ASP 19": "OD1" <-> "OD2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G ASP 39": "OD1" <-> "OD2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ASP 151": "OD1" <-> "OD2" Residue "G TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 204": "OE1" <-> "OE2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "G GLU 219": "OE1" <-> "OE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 31": "OE1" <-> "OE2" Residue "H GLU 50": "OE1" <-> "OE2" Residue "H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 149": "OD1" <-> "OD2" Residue "H ASP 159": "OD1" <-> "OD2" Residue "H GLU 167": "OE1" <-> "OE2" Residue "H GLU 171": "OE1" <-> "OE2" Residue "I GLU 133": "OE1" <-> "OE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I ASP 150": "OD1" <-> "OD2" Residue "I GLU 151": "OE1" <-> "OE2" Residue "I GLU 164": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 26": "OD1" <-> "OD2" Residue "K ASP 27": "OD1" <-> "OD2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "K GLU 123": "OE1" <-> "OE2" Residue "K ASP 124": "OD1" <-> "OD2" Residue "K GLU 160": "OE1" <-> "OE2" Residue "K GLU 195": "OE1" <-> "OE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "M GLU 18": "OE1" <-> "OE2" Residue "M ASP 26": "OD1" <-> "OD2" Residue "M ASP 37": "OD1" <-> "OD2" Residue "M GLU 74": "OE1" <-> "OE2" Residue "N ASP 83": "OD1" <-> "OD2" Residue "N GLU 142": "OE1" <-> "OE2" Residue "O ASP 13": "OD1" <-> "OD2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "O GLU 71": "OE1" <-> "OE2" Residue "O ASP 80": "OD1" <-> "OD2" Residue "O GLU 87": "OE1" <-> "OE2" Residue "O ASP 95": "OD1" <-> "OD2" Residue "O GLU 97": "OE1" <-> "OE2" Residue "P ASP 80": "OD1" <-> "OD2" Residue "P ASP 131": "OD1" <-> "OD2" Residue "Q ASP 21": "OD1" <-> "OD2" Residue "Q ASP 23": "OD1" <-> "OD2" Residue "Q GLU 31": "OE1" <-> "OE2" Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q GLU 74": "OE1" <-> "OE2" Residue "Q TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 118": "OE1" <-> "OE2" Residue "R GLU 40": "OE1" <-> "OE2" Residue "R GLU 43": "OE1" <-> "OE2" Residue "R GLU 53": "OE1" <-> "OE2" Residue "R GLU 61": "OE1" <-> "OE2" Residue "R PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 75": "OE1" <-> "OE2" Residue "S GLU 77": "OE1" <-> "OE2" Residue "S GLU 87": "OE1" <-> "OE2" Residue "S ASP 101": "OD1" <-> "OD2" Residue "S ASP 110": "OD1" <-> "OD2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 21": "OD1" <-> "OD2" Residue "T ASP 51": "OD1" <-> "OD2" Residue "T GLU 58": "OE1" <-> "OE2" Residue "T ASP 89": "OD1" <-> "OD2" Residue "T TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 104": "OD1" <-> "OD2" Residue "U ASP 8": "OD1" <-> "OD2" Residue "U GLU 13": "OE1" <-> "OE2" Residue "U ASP 49": "OD1" <-> "OD2" Residue "U TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 130": "OD1" <-> "OD2" Residue "V PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 90": "OD1" <-> "OD2" Residue "V GLU 96": "OE1" <-> "OE2" Residue "V GLU 111": "OE1" <-> "OE2" Residue "W GLU 114": "OE1" <-> "OE2" Residue "W PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "X PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 3": "OD1" <-> "OD2" Residue "Y ASP 53": "OD1" <-> "OD2" Residue "Y PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 76": "OD1" <-> "OD2" Residue "a ASP 56": "OD1" <-> "OD2" Residue "b GLU 14": "OE1" <-> "OE2" Residue "b TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "c PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 62": "OE1" <-> "OE2" Residue "e GLU 23": "OE1" <-> "OE2" Residue "e ARG 31": "NH1" <-> "NH2" Residue "f PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 49": "OD1" <-> "OD2" Residue "f PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 110": "OE1" <-> "OE2" Residue "g GLU 125": "OE1" <-> "OE2" Residue "j GLU 49": "OE1" <-> "OE2" Residue "j ASP 68": "OD1" <-> "OD2" Residue "j ASP 74": "OD1" <-> "OD2" Residue "j ASP 126": "OD1" <-> "OD2" Residue "j ASP 220": "OD1" <-> "OD2" Residue "j GLU 223": "OE1" <-> "OE2" Residue "j ASP 234": "OD1" <-> "OD2" Residue "j ASP 260": "OD1" <-> "OD2" Residue "j ASP 268": "OD1" <-> "OD2" Residue "j GLU 269": "OE1" <-> "OE2" Residue "j GLU 282": "OE1" <-> "OE2" Residue "j ASP 294": "OD1" <-> "OD2" Residue "i ASP 152": "OD1" <-> "OD2" Residue "u GLU 66": "OE1" <-> "OE2" Residue "u ARG 73": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "u ARG 128": "NH1" <-> "NH2" Residue "u ARG 132": "NH1" <-> "NH2" Residue "u ARG 139": "NH1" <-> "NH2" Residue "u ASP 142": "OD1" <-> "OD2" Residue "u ASP 148": "OD1" <-> "OD2" Residue "u ASP 154": "OD1" <-> "OD2" Residue "u ARG 204": "NH1" <-> "NH2" Residue "u ARG 214": "NH1" <-> "NH2" Residue "u ASP 224": "OD1" <-> "OD2" Residue "u GLU 228": "OE1" <-> "OE2" Residue "u ARG 249": "NH1" <-> "NH2" Residue "u ASP 259": "OD1" <-> "OD2" Residue "u TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 287": "NH1" <-> "NH2" Residue "u PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ASP 362": "OD1" <-> "OD2" Residue "u GLU 465": "OE1" <-> "OE2" Residue "u GLU 468": "OE1" <-> "OE2" Residue "u GLU 478": "OE1" <-> "OE2" Residue "u GLU 481": "OE1" <-> "OE2" Residue "u ASP 486": "OD1" <-> "OD2" Residue "u ARG 492": "NH1" <-> "NH2" Residue "u ASP 493": "OD1" <-> "OD2" Residue "u ARG 499": "NH1" <-> "NH2" Residue "u ARG 537": "NH1" <-> "NH2" Residue "u GLU 545": "OE1" <-> "OE2" Residue "u GLU 553": "OE1" <-> "OE2" Residue "u GLU 588": "OE1" <-> "OE2" Residue "u ARG 599": "NH1" <-> "NH2" Residue "u GLU 613": "OE1" <-> "OE2" Residue "u ARG 624": "NH1" <-> "NH2" Residue "u ASP 636": "OD1" <-> "OD2" Residue "u ARG 642": "NH1" <-> "NH2" Residue "u ASP 647": "OD1" <-> "OD2" Residue "u ASP 688": "OD1" <-> "OD2" Residue "u ARG 720": "NH1" <-> "NH2" Residue "u ARG 732": "NH1" <-> "NH2" Residue "u ARG 737": "NH1" <-> "NH2" Residue "u GLU 743": "OE1" <-> "OE2" Residue "u PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 79377 Number of models: 1 Model: "" Number of chains: 39 Chain: "B" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 12, 'TRANS': 193} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1682 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "F" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1748 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1862 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1501 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 9, 'TRANS': 176} Chain: "I" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1682 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "J" Number of atoms: 1499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1499 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "K" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1495 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "L" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1229 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain: "M" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 800 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 953 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "P" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1006 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 984 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "R" Number of atoms: 1109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1109 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "S" Number of atoms: 1066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1066 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1184 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain: "U" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1122 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "V" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 803 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Y" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1014 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "Z" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 625 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "a" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 574 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "b" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 640 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "c" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "d" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "e" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 422 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 52} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "f" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "g" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2440 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 10, 'TRANS': 303} Chain: "2" Number of atoms: 35677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1671, 35677 Classifications: {'RNA': 1671} Modifications used: {'rna2p_pur': 129, 'rna2p_pyr': 116, 'rna3p_pur': 757, 'rna3p_pyr': 669} Link IDs: {'rna2p': 244, 'rna3p': 1426} Chain breaks: 10 Chain: "i" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 239 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 1, 'TRANS': 27} Chain: "u" Number of atoms: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4954 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 573} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33519 SG CYS c 23 88.665 165.391 108.742 1.00 43.08 S ATOM 33923 SG CYS c 74 91.183 162.020 107.478 1.00 37.96 S ATOM 35218 SG CYS f 21 156.980 156.404 70.554 1.00 7.97 S ATOM 35242 SG CYS f 24 153.910 153.207 71.005 1.00 11.79 S Time building chain proxies: 32.42, per 1000 atoms: 0.41 Number of scatterers: 79377 At special positions: 0 Unit cell: (216.036, 244.629, 205.446, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 202 16.00 P 1671 15.00 O 19336 8.00 N 14582 7.00 C 43583 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.57 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 201 " pdb="ZN ZN c 201 " - pdb=" SG CYS c 74 " pdb="ZN ZN c 201 " - pdb=" SG CYS c 23 " pdb=" ZN f 201 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 21 " pdb="ZN ZN f 201 " - pdb=" SG CYS f 24 " 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10174 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 68 sheets defined 31.9% alpha, 18.0% beta 504 base pairs and 929 stacking pairs defined. Time for finding SS restraints: 21.39 Creating SS restraints... Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.703A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 50 through 67 removed outlier: 3.620A pdb=" N THR B 54 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 83 Processing helix chain 'B' and resid 84 through 89 removed outlier: 3.760A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.649A pdb=" N GLY B 172 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.701A pdb=" N PHE B 203 " --> pdb=" O ASP B 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 removed outlier: 3.642A pdb=" N SER C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 23 through 26' Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.985A pdb=" N CYS C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 175 removed outlier: 3.650A pdb=" N ARG C 165 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 171 " --> pdb=" O LYS C 167 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR C 173 " --> pdb=" O MET C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 189 removed outlier: 3.507A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 186 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.598A pdb=" N LYS C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 removed outlier: 3.864A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.558A pdb=" N ASP D 72 " --> pdb=" O ARG D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 84 Processing helix chain 'D' and resid 90 through 98 removed outlier: 4.399A pdb=" N ILE D 94 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 102 Processing helix chain 'D' and resid 146 through 161 Processing helix chain 'D' and resid 207 through 218 removed outlier: 3.792A pdb=" N LYS D 212 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU D 213 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 244 removed outlier: 4.030A pdb=" N ASP D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 250 removed outlier: 3.827A pdb=" N TYR D 248 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR D 250 " --> pdb=" O THR D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.813A pdb=" N TRP D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS D 257 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'E' and resid 15 through 19 Processing helix chain 'E' and resid 44 through 50 Processing helix chain 'E' and resid 59 through 66 Processing helix chain 'E' and resid 247 through 259 removed outlier: 3.750A pdb=" N ARG E 255 " --> pdb=" O GLU E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 262 No H-bonds generated for 'chain 'E' and resid 260 through 262' Processing helix chain 'F' and resid 6 through 30 removed outlier: 3.518A pdb=" N PHE F 11 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY F 15 " --> pdb=" O PHE F 11 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS F 18 " --> pdb=" O ASP F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 58 removed outlier: 3.607A pdb=" N ASN F 57 " --> pdb=" O ARG F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 78 removed outlier: 3.842A pdb=" N GLU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N PHE F 77 " --> pdb=" O VAL F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 111 removed outlier: 3.531A pdb=" N GLN F 101 " --> pdb=" O CYS F 97 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU F 103 " --> pdb=" O ILE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 129 removed outlier: 3.587A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 28 removed outlier: 3.705A pdb=" N TYR G 28 " --> pdb=" O ARG G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.890A pdb=" N ARG G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 156 Processing helix chain 'G' and resid 181 through 228 removed outlier: 3.535A pdb=" N LYS G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN G 202 " --> pdb=" O ARG G 198 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA G 206 " --> pdb=" O ASN G 202 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA G 207 " --> pdb=" O LYS G 203 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU G 208 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 29 removed outlier: 3.917A pdb=" N GLY H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE H 23 " --> pdb=" O PHE H 19 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU H 29 " --> pdb=" O GLN H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 removed outlier: 4.047A pdb=" N SER H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 41 removed outlier: 3.928A pdb=" N ARG H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 68 through 74 removed outlier: 4.027A pdb=" N LYS H 74 " --> pdb=" O LYS H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.688A pdb=" N ARG H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 127 through 134 removed outlier: 3.739A pdb=" N ASP H 132 " --> pdb=" O ALA H 128 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL H 134 " --> pdb=" O LEU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 181 Processing helix chain 'I' and resid 25 through 27 No H-bonds generated for 'chain 'I' and resid 25 through 27' Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 88 through 93 removed outlier: 3.661A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 130 through 138 removed outlier: 3.650A pdb=" N GLU I 135 " --> pdb=" O PRO I 131 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE I 136 " --> pdb=" O GLU I 132 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 153 removed outlier: 3.797A pdb=" N ASP I 150 " --> pdb=" O GLN I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 169 removed outlier: 3.615A pdb=" N GLU I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN I 168 " --> pdb=" O GLU I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 192 through 206 removed outlier: 3.868A pdb=" N ARG I 200 " --> pdb=" O GLU I 196 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS I 206 " --> pdb=" O ILE I 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 36 removed outlier: 3.670A pdb=" N TYR J 35 " --> pdb=" O LEU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 45 through 61 Processing helix chain 'J' and resid 67 through 84 removed outlier: 3.543A pdb=" N ASN J 75 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 107 removed outlier: 3.862A pdb=" N PHE J 105 " --> pdb=" O LYS J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 117 Processing helix chain 'J' and resid 122 through 132 removed outlier: 3.753A pdb=" N ARG J 127 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL J 128 " --> pdb=" O HIS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 180 removed outlier: 4.025A pdb=" N ARG J 175 " --> pdb=" O GLY J 171 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS J 176 " --> pdb=" O ARG J 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 18 through 22 Processing helix chain 'K' and resid 55 through 59 removed outlier: 3.610A pdb=" N ALA K 58 " --> pdb=" O ARG K 55 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS K 59 " --> pdb=" O TYR K 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 55 through 59' Processing helix chain 'K' and resid 61 through 66 removed outlier: 3.617A pdb=" N CYS K 66 " --> pdb=" O LYS K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 77 removed outlier: 3.859A pdb=" N MET K 77 " --> pdb=" O THR K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 83 removed outlier: 6.165A pdb=" N ARG K 81 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASN K 83 " --> pdb=" O GLY K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 105 removed outlier: 3.789A pdb=" N THR K 89 " --> pdb=" O LYS K 85 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG K 91 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU K 98 " --> pdb=" O LYS K 94 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE K 99 " --> pdb=" O HIS K 95 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N HIS K 101 " --> pdb=" O PHE K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 120 removed outlier: 3.983A pdb=" N GLY K 120 " --> pdb=" O ILE K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 161 removed outlier: 3.558A pdb=" N TRP K 152 " --> pdb=" O ASN K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 178 removed outlier: 3.580A pdb=" N GLU K 176 " --> pdb=" O CYS K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 202 removed outlier: 3.747A pdb=" N GLU K 195 " --> pdb=" O LYS K 191 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA K 200 " --> pdb=" O LEU K 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 28 Processing helix chain 'L' and resid 47 through 53 Processing helix chain 'M' and resid 4 through 19 removed outlier: 3.949A pdb=" N ALA M 10 " --> pdb=" O LYS M 6 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR M 12 " --> pdb=" O ARG M 8 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU M 14 " --> pdb=" O ALA M 10 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU M 15 " --> pdb=" O ILE M 11 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE M 16 " --> pdb=" O TYR M 12 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS M 17 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU M 18 " --> pdb=" O LEU M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 56 removed outlier: 3.531A pdb=" N VAL M 45 " --> pdb=" O PRO M 41 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER M 54 " --> pdb=" O GLN M 50 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG M 55 " --> pdb=" O SER M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 83 removed outlier: 4.044A pdb=" N GLN M 77 " --> pdb=" O ASN M 73 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR M 78 " --> pdb=" O GLU M 74 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR M 82 " --> pdb=" O TYR M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 95 removed outlier: 3.894A pdb=" N LEU M 94 " --> pdb=" O PRO M 91 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG M 95 " --> pdb=" O ALA M 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 91 through 95' Processing helix chain 'N' and resid 29 through 43 Processing helix chain 'N' and resid 46 through 57 removed outlier: 3.644A pdb=" N GLY N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 Processing helix chain 'N' and resid 71 through 79 removed outlier: 3.777A pdb=" N SER N 77 " --> pdb=" O ARG N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 105 removed outlier: 3.529A pdb=" N ALA N 97 " --> pdb=" O LYS N 93 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 132 removed outlier: 3.727A pdb=" N PHE N 113 " --> pdb=" O LYS N 109 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE N 116 " --> pdb=" O LYS N 112 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU N 117 " --> pdb=" O PHE N 113 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE N 118 " --> pdb=" O ARG N 114 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG N 124 " --> pdb=" O SER N 120 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR N 128 " --> pdb=" O ARG N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 148 removed outlier: 4.442A pdb=" N SER N 147 " --> pdb=" O SER N 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 17 through 27 removed outlier: 4.116A pdb=" N VAL O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE O 27 " --> pdb=" O LYS O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 43 removed outlier: 3.713A pdb=" N LEU O 42 " --> pdb=" O ALA O 38 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP O 43 " --> pdb=" O ALA O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 58 through 72 removed outlier: 3.765A pdb=" N VAL O 62 " --> pdb=" O GLU O 58 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS O 63 " --> pdb=" O PRO O 59 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU O 64 " --> pdb=" O MET O 60 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL O 65 " --> pdb=" O TYR O 61 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA O 67 " --> pdb=" O LYS O 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA O 70 " --> pdb=" O GLU O 66 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS O 72 " --> pdb=" O LEU O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 130 removed outlier: 3.672A pdb=" N CYS O 130 " --> pdb=" O GLU O 126 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 70 removed outlier: 3.859A pdb=" N GLU P 68 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER P 69 " --> pdb=" O ARG P 66 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER P 70 " --> pdb=" O ASP P 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 65 through 70' Processing helix chain 'P' and resid 76 through 88 removed outlier: 3.779A pdb=" N ASP P 80 " --> pdb=" O LEU P 76 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA P 82 " --> pdb=" O ALA P 78 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN P 83 " --> pdb=" O GLN P 79 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG P 84 " --> pdb=" O ASP P 80 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS P 85 " --> pdb=" O VAL P 81 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS P 86 " --> pdb=" O ALA P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 112 through 121 removed outlier: 3.542A pdb=" N LEU P 119 " --> pdb=" O ALA P 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 removed outlier: 3.862A pdb=" N ASP Q 27 " --> pdb=" O ASP Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 34 removed outlier: 3.847A pdb=" N MET Q 34 " --> pdb=" O TYR Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 48 Processing helix chain 'Q' and resid 50 through 65 removed outlier: 3.949A pdb=" N SER Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU Q 56 " --> pdb=" O LYS Q 52 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU Q 57 " --> pdb=" O GLN Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 90 removed outlier: 4.180A pdb=" N VAL Q 90 " --> pdb=" O PRO Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 119 removed outlier: 3.678A pdb=" N GLU Q 118 " --> pdb=" O TYR Q 115 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE Q 119 " --> pdb=" O LEU Q 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 115 through 119' Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'R' and resid 47 through 59 Proline residue: R 54 - end of helix removed outlier: 4.022A pdb=" N LEU R 58 " --> pdb=" O PRO R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 100 removed outlier: 3.882A pdb=" N GLN R 86 " --> pdb=" O TYR R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.629A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 27 through 38 removed outlier: 4.071A pdb=" N GLU S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 46 through 58 Processing helix chain 'S' and resid 58 through 63 removed outlier: 3.896A pdb=" N GLN S 62 " --> pdb=" O MET S 58 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG S 63 " --> pdb=" O LYS S 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 58 through 63' Processing helix chain 'S' and resid 73 through 83 removed outlier: 3.752A pdb=" N GLU S 77 " --> pdb=" O LEU S 73 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU S 79 " --> pdb=" O GLU S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 109 removed outlier: 3.724A pdb=" N LYS S 103 " --> pdb=" O ASP S 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 33 Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.622A pdb=" N ALA T 41 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS T 42 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 removed outlier: 3.797A pdb=" N VAL T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE T 68 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE T 70 " --> pdb=" O ARG T 66 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N MET T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN T 73 " --> pdb=" O THR T 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 78 removed outlier: 3.940A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 84 removed outlier: 3.574A pdb=" N PHE T 83 " --> pdb=" O PRO T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 117 removed outlier: 4.759A pdb=" N ASP T 104 " --> pdb=" O ALA T 100 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASN T 105 " --> pdb=" O ASN T 101 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N GLU T 109 " --> pdb=" O ASN T 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 121 through 127 Processing helix chain 'U' and resid 5 through 9 removed outlier: 3.704A pdb=" N VAL U 9 " --> pdb=" O VAL U 6 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 26 removed outlier: 4.083A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY U 26 " --> pdb=" O LEU U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 3.885A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA U 61 " --> pdb=" O ALA U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 103 through 108 Processing helix chain 'U' and resid 124 through 140 removed outlier: 4.080A pdb=" N ASP U 130 " --> pdb=" O GLN U 126 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU U 131 " --> pdb=" O GLY U 127 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP U 132 " --> pdb=" O GLN U 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 45 Processing helix chain 'V' and resid 94 through 102 removed outlier: 4.011A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS V 99 " --> pdb=" O SER V 95 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLN V 100 " --> pdb=" O GLU V 96 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE V 101 " --> pdb=" O ILE V 97 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR V 102 " --> pdb=" O VAL V 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 94 through 102' Processing helix chain 'W' and resid 5 through 10 removed outlier: 3.578A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 11 through 20 removed outlier: 3.632A pdb=" N ALA W 17 " --> pdb=" O SER W 13 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU W 18 " --> pdb=" O ILE W 14 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG W 20 " --> pdb=" O ASN W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 44 removed outlier: 3.795A pdb=" N VAL W 35 " --> pdb=" O SER W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 84 No H-bonds generated for 'chain 'W' and resid 82 through 84' Processing helix chain 'W' and resid 85 through 93 removed outlier: 3.875A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 119 removed outlier: 3.616A pdb=" N ALA W 116 " --> pdb=" O ASP W 112 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG W 118 " --> pdb=" O GLU W 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 21 removed outlier: 3.547A pdb=" N ARG X 18 " --> pdb=" O ARG X 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 29 Processing helix chain 'X' and resid 90 through 94 removed outlier: 3.738A pdb=" N PHE X 93 " --> pdb=" O CYS X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 135 Processing helix chain 'Y' and resid 36 through 48 removed outlier: 3.900A pdb=" N GLU Y 42 " --> pdb=" O THR Y 38 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS Y 43 " --> pdb=" O GLU Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 80 through 85 Processing helix chain 'Y' and resid 87 through 95 removed outlier: 3.628A pdb=" N ALA Y 92 " --> pdb=" O HIS Y 89 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG Y 93 " --> pdb=" O ARG Y 90 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY Y 95 " --> pdb=" O ALA Y 92 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 114 removed outlier: 3.529A pdb=" N ARG Y 107 " --> pdb=" O SER Y 103 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET Y 114 " --> pdb=" O ARG Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 117 No H-bonds generated for 'chain 'Y' and resid 115 through 117' Processing helix chain 'Y' and resid 118 through 123 removed outlier: 3.727A pdb=" N ALA Y 121 " --> pdb=" O ARG Y 118 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS Y 122 " --> pdb=" O GLY Y 119 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA Y 123 " --> pdb=" O THR Y 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 118 through 123' Processing helix chain 'Z' and resid 56 through 63 Processing helix chain 'Z' and resid 65 through 74 removed outlier: 3.767A pdb=" N ARG Z 71 " --> pdb=" O ASP Z 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 61 removed outlier: 3.847A pdb=" N ASP a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS a 60 " --> pdb=" O ASP a 56 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU a 61 " --> pdb=" O LYS a 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 65 removed outlier: 3.939A pdb=" N TYR a 65 " --> pdb=" O VAL a 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 62 through 65' Processing helix chain 'a' and resid 69 through 77 removed outlier: 3.833A pdb=" N SER a 74 " --> pdb=" O PRO a 70 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 87 Processing helix chain 'a' and resid 88 through 91 Processing helix chain 'b' and resid 11 through 18 removed outlier: 3.523A pdb=" N LYS b 16 " --> pdb=" O PRO b 12 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS b 18 " --> pdb=" O GLU b 14 " (cutoff:3.500A) Processing helix chain 'c' and resid 46 through 48 No H-bonds generated for 'chain 'c' and resid 46 through 48' Processing helix chain 'c' and resid 49 through 56 removed outlier: 3.788A pdb=" N SER c 54 " --> pdb=" O VAL c 50 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA c 56 " --> pdb=" O ASP c 52 " (cutoff:3.500A) Processing helix chain 'c' and resid 75 through 81 removed outlier: 3.792A pdb=" N ILE c 79 " --> pdb=" O VAL c 75 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS c 80 " --> pdb=" O SER c 76 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 16 Processing helix chain 'e' and resid 30 through 42 removed outlier: 3.589A pdb=" N ARG e 41 " --> pdb=" O GLN e 37 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 19 removed outlier: 3.533A pdb=" N SER f 18 " --> pdb=" O GLY f 15 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG f 19 " --> pdb=" O GLN f 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 15 through 19' Processing helix chain 'f' and resid 32 through 36 Processing helix chain 'f' and resid 40 through 46 removed outlier: 3.877A pdb=" N ARG f 44 " --> pdb=" O ARG f 40 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN f 45 " --> pdb=" O GLN f 41 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR f 46 " --> pdb=" O CYS f 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 40 through 46' Processing helix chain 'f' and resid 46 through 51 Processing helix chain 'g' and resid 101 through 106 Processing helix chain 'i' and resid 153 through 161 Processing helix chain 'i' and resid 162 through 164 No H-bonds generated for 'chain 'i' and resid 162 through 164' Processing helix chain 'i' and resid 165 through 179 removed outlier: 3.550A pdb=" N GLY i 179 " --> pdb=" O ARG i 175 " (cutoff:3.500A) Processing helix chain 'u' and resid 50 through 68 removed outlier: 3.533A pdb=" N ARG u 54 " --> pdb=" O ARG u 50 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG u 56 " --> pdb=" O ASP u 52 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU u 60 " --> pdb=" O ARG u 56 " (cutoff:3.500A) Processing helix chain 'u' and resid 71 through 75 removed outlier: 3.692A pdb=" N LEU u 75 " --> pdb=" O LYS u 72 " (cutoff:3.500A) Processing helix chain 'u' and resid 96 through 101 removed outlier: 3.516A pdb=" N MET u 100 " --> pdb=" O LEU u 96 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN u 101 " --> pdb=" O PRO u 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 96 through 101' Processing helix chain 'u' and resid 142 through 148 removed outlier: 3.635A pdb=" N ASP u 148 " --> pdb=" O HIS u 144 " (cutoff:3.500A) Processing helix chain 'u' and resid 167 through 181 removed outlier: 3.613A pdb=" N ASP u 171 " --> pdb=" O ASP u 167 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR u 172 " --> pdb=" O SER u 168 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS u 173 " --> pdb=" O THR u 169 " (cutoff:3.500A) Processing helix chain 'u' and resid 225 through 238 removed outlier: 4.102A pdb=" N MET u 231 " --> pdb=" O GLN u 227 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU u 232 " --> pdb=" O GLU u 228 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG u 234 " --> pdb=" O GLY u 230 " (cutoff:3.500A) Processing helix chain 'u' and resid 465 through 475 removed outlier: 3.706A pdb=" N GLU u 473 " --> pdb=" O ALA u 469 " (cutoff:3.500A) Processing helix chain 'u' and resid 495 through 500 Processing helix chain 'u' and resid 523 through 527 removed outlier: 4.018A pdb=" N ILE u 527 " --> pdb=" O TYR u 524 " (cutoff:3.500A) Processing helix chain 'u' and resid 532 through 546 removed outlier: 3.608A pdb=" N SER u 539 " --> pdb=" O ASN u 535 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE u 540 " --> pdb=" O THR u 536 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU u 543 " --> pdb=" O SER u 539 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL u 544 " --> pdb=" O ILE u 540 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU u 545 " --> pdb=" O PHE u 541 " (cutoff:3.500A) Processing helix chain 'u' and resid 567 through 576 removed outlier: 4.222A pdb=" N GLU u 571 " --> pdb=" O VAL u 567 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N CYS u 572 " --> pdb=" O SER u 568 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE u 573 " --> pdb=" O VAL u 569 " (cutoff:3.500A) Processing helix chain 'u' and resid 720 through 726 removed outlier: 4.293A pdb=" N LEU u 724 " --> pdb=" O ARG u 720 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP u 725 " --> pdb=" O GLU u 721 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.878A pdb=" N LYS B 40 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.600A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA B 146 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.241A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 33 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 97 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS C 85 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N MET C 103 " --> pdb=" O LYS C 83 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LYS C 83 " --> pdb=" O MET C 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.241A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 33 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 14.204A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.577A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.920A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG C 136 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA C 123 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 103 through 116 removed outlier: 6.550A pdb=" N PHE D 127 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE D 109 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LYS D 125 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG D 123 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN D 113 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ARG D 121 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLN D 115 " --> pdb=" O GLY D 119 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLY D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 187 Processing sheet with id=AA7, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AA8, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AA9, first strand: chain 'E' and resid 138 through 141 removed outlier: 6.754A pdb=" N HIS E 138 " --> pdb=" O ILE E 129 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE E 129 " --> pdb=" O HIS E 138 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL E 140 " --> pdb=" O ARG E 127 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 217 through 221 removed outlier: 6.109A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS E 230 " --> pdb=" O LYS E 233 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 233 " --> pdb=" O LYS E 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 34 through 41 removed outlier: 4.003A pdb=" N GLY F 36 " --> pdb=" O LEU F 51 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR F 46 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N TYR F 87 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE F 48 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLU F 89 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE F 50 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 152 through 155 removed outlier: 3.757A pdb=" N GLY F 133 " --> pdb=" O MET F 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 209 through 210 removed outlier: 3.713A pdb=" N SER F 209 " --> pdb=" O ILE S 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 223 through 225 removed outlier: 6.655A pdb=" N VAL j 176 " --> pdb=" O LYS j 185 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 12 through 17 removed outlier: 5.823A pdb=" N LEU G 106 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP G 57 " --> pdb=" O LEU G 106 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ASN G 110 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 72 through 77 Processing sheet with id=AB8, first strand: chain 'G' and resid 160 through 162 removed outlier: 3.630A pdb=" N ARG G 170 " --> pdb=" O LEU G 162 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 47 through 52 removed outlier: 3.705A pdb=" N ALA H 47 " --> pdb=" O PHE H 63 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL H 93 " --> pdb=" O ILE H 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 185 through 188 removed outlier: 4.217A pdb=" N GLY H 141 " --> pdb=" O HIS H 157 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE W 50 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 3 through 4 removed outlier: 3.868A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.372A pdb=" N ARG I 42 " --> pdb=" O LEU I 58 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 72 through 77 removed outlier: 3.632A pdb=" N GLY I 63 " --> pdb=" O THR I 76 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N GLY I 187 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASN I 64 " --> pdb=" O GLY I 187 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N VAL I 189 " --> pdb=" O ASN I 64 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER I 66 " --> pdb=" O VAL I 189 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR I 83 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU I 103 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL I 81 " --> pdb=" O LEU I 103 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 140 through 141 Processing sheet with id=AC6, first strand: chain 'K' and resid 125 through 126 Processing sheet with id=AC7, first strand: chain 'K' and resid 129 through 130 Processing sheet with id=AC8, first strand: chain 'K' and resid 140 through 141 removed outlier: 3.580A pdb=" N LYS d 47 " --> pdb=" O ASP K 140 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG d 31 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N VAL d 17 " --> pdb=" O ARG d 31 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU d 33 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N THR d 15 " --> pdb=" O GLU d 33 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 72 through 79 removed outlier: 18.218A pdb=" N ILE L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 15.569A pdb=" N LEU L 93 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 9.219A pdb=" N SER L 74 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP L 91 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL L 87 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N PHE L 140 " --> pdb=" O ASN L 108 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER L 110 " --> pdb=" O PHE L 140 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL L 142 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N HIS L 112 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N LYS L 144 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 21 through 22 Processing sheet with id=AD2, first strand: chain 'O' and resid 31 through 33 removed outlier: 3.740A pdb=" N VAL O 110 " --> pdb=" O ALA O 32 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL O 109 " --> pdb=" O VAL O 51 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU O 49 " --> pdb=" O VAL O 111 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N CYS O 50 " --> pdb=" O ILE O 77 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL O 79 " --> pdb=" O CYS O 50 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU O 52 " --> pdb=" O VAL O 79 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 93 through 94 Processing sheet with id=AD4, first strand: chain 'P' and resid 52 through 55 removed outlier: 7.380A pdb=" N VAL P 44 " --> pdb=" O ILE P 53 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE P 95 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE P 129 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU P 97 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP P 131 " --> pdb=" O LEU P 97 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 76 through 78 removed outlier: 6.340A pdb=" N VAL Q 76 " --> pdb=" O GLY Q 95 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR Q 97 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N THR Q 78 " --> pdb=" O TYR Q 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 9 through 15 removed outlier: 3.522A pdb=" N LYS R 73 " --> pdb=" O THR R 20 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS R 26 " --> pdb=" O ASP R 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 96 through 98 removed outlier: 6.011A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'T' and resid 13 through 15 removed outlier: 3.775A pdb=" N LEU T 13 " --> pdb=" O ILE T 20 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 81 through 85 removed outlier: 5.143A pdb=" N ASN U 85 " --> pdb=" O PRO U 89 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE2, first strand: chain 'V' and resid 54 through 63 removed outlier: 5.747A pdb=" N ARG V 55 " --> pdb=" O LEU V 88 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU V 88 " --> pdb=" O ARG V 55 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS V 86 " --> pdb=" O PRO V 57 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS V 59 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 72 through 74 Processing sheet with id=AE4, first strand: chain 'W' and resid 72 through 74 removed outlier: 6.087A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 56 through 58 removed outlier: 6.747A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU X 99 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL X 125 " --> pdb=" O GLU X 99 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 56 through 58 removed outlier: 4.489A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 6 through 9 removed outlier: 3.729A pdb=" N THR Y 6 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 6 through 9 removed outlier: 3.729A pdb=" N THR Y 6 " --> pdb=" O LEU Y 28 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N PHE Y 72 " --> pdb=" O GLY Y 59 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLY Y 59 " --> pdb=" O PHE Y 72 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET Y 74 " --> pdb=" O VAL Y 57 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL Y 57 " --> pdb=" O MET Y 74 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR Y 76 " --> pdb=" O ILE Y 55 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE Y 55 " --> pdb=" O TYR Y 76 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 32 through 39 removed outlier: 5.168A pdb=" N GLN Z 49 " --> pdb=" O GLU Z 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'a' and resid 97 through 102 removed outlier: 4.878A pdb=" N LEU a 99 " --> pdb=" O THR a 110 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR a 110 " --> pdb=" O LEU a 99 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 44 through 47 removed outlier: 3.625A pdb=" N THR b 44 " --> pdb=" O VAL b 35 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL b 35 " --> pdb=" O THR b 44 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL b 46 " --> pdb=" O MET b 33 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b' and resid 54 through 55 removed outlier: 3.737A pdb=" N VAL b 54 " --> pdb=" O CYS b 64 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N CYS b 64 " --> pdb=" O VAL b 54 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'c' and resid 20 through 21 Processing sheet with id=AF5, first strand: chain 'c' and resid 36 through 39 Processing sheet with id=AF6, first strand: chain 'c' and resid 42 through 43 removed outlier: 3.761A pdb=" N ARG c 42 " --> pdb=" O LEU c 67 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'f' and resid 30 through 31 Processing sheet with id=AF8, first strand: chain 'g' and resid 133 through 134 Processing sheet with id=AF9, first strand: chain 'j' and resid 3 through 11 removed outlier: 6.022A pdb=" N MET j 5 " --> pdb=" O THR j 313 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR j 313 " --> pdb=" O MET j 5 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU j 7 " --> pdb=" O GLN j 311 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN j 311 " --> pdb=" O LEU j 7 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLY j 9 " --> pdb=" O VAL j 309 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL j 307 " --> pdb=" O LEU j 11 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'j' and resid 20 through 23 removed outlier: 3.624A pdb=" N GLN j 20 " --> pdb=" O ALA j 34 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE j 31 " --> pdb=" O TRP j 43 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER j 33 " --> pdb=" O ILE j 41 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE j 41 " --> pdb=" O SER j 33 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE j 40 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA j 58 " --> pdb=" O ILE j 40 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET j 42 " --> pdb=" O GLN j 56 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'j' and resid 66 through 71 removed outlier: 3.820A pdb=" N ASP j 68 " --> pdb=" O GLY j 81 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA j 78 " --> pdb=" O TRP j 90 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP j 90 " --> pdb=" O ALA j 78 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER j 82 " --> pdb=" O THR j 86 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR j 86 " --> pdb=" O SER j 82 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ASP j 91 " --> pdb=" O THR j 97 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N THR j 97 " --> pdb=" O ASP j 91 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'j' and resid 108 through 113 removed outlier: 3.624A pdb=" N VAL j 121 " --> pdb=" O ALA j 112 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE j 129 " --> pdb=" O THR j 141 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR j 141 " --> pdb=" O ILE j 129 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU j 131 " --> pdb=" O LYS j 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'j' and resid 195 through 200 removed outlier: 6.928A pdb=" N GLY j 210 " --> pdb=" O ASN j 196 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL j 198 " --> pdb=" O ALA j 208 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA j 208 " --> pdb=" O VAL j 198 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL j 200 " --> pdb=" O LEU j 206 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU j 206 " --> pdb=" O VAL j 200 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'j' and resid 239 through 242 removed outlier: 3.852A pdb=" N SER j 242 " --> pdb=" O TRP j 247 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP j 247 " --> pdb=" O SER j 242 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE j 256 " --> pdb=" O GLU j 269 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU j 269 " --> pdb=" O ILE j 256 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ILE j 258 " --> pdb=" O VAL j 267 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'u' and resid 110 through 112 removed outlier: 3.969A pdb=" N CYS u 126 " --> pdb=" O HIS u 131 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS u 131 " --> pdb=" O CYS u 126 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN u 84 " --> pdb=" O THR u 155 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU u 157 " --> pdb=" O GLN u 84 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU u 86 " --> pdb=" O LEU u 157 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU u 159 " --> pdb=" O LEU u 86 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL u 88 " --> pdb=" O LEU u 159 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'u' and resid 188 through 189 Processing sheet with id=AG8, first strand: chain 'u' and resid 257 through 264 removed outlier: 3.512A pdb=" N ALA u 257 " --> pdb=" O SER u 275 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER u 263 " --> pdb=" O VAL u 269 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU u 272 " --> pdb=" O VAL u 562 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY u 276 " --> pdb=" O VAL u 558 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL u 558 " --> pdb=" O GLY u 276 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N LYS u 300 " --> pdb=" O ALA u 347 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ALA u 347 " --> pdb=" O LYS u 300 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE u 302 " --> pdb=" O MET u 345 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET u 345 " --> pdb=" O ILE u 302 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA u 304 " --> pdb=" O VAL u 343 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL u 343 " --> pdb=" O ALA u 304 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'u' and resid 257 through 264 removed outlier: 3.512A pdb=" N ALA u 257 " --> pdb=" O SER u 275 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER u 263 " --> pdb=" O VAL u 269 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'u' and resid 296 through 297 Processing sheet with id=AH2, first strand: chain 'u' and resid 623 through 625 removed outlier: 6.749A pdb=" N VAL u 665 " --> pdb=" O THR u 681 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR u 681 " --> pdb=" O VAL u 665 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU u 667 " --> pdb=" O ILE u 679 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'u' and resid 637 through 639 removed outlier: 6.246A pdb=" N HIS u 638 " --> pdb=" O ILE u 694 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ARG u 696 " --> pdb=" O HIS u 638 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'u' and resid 702 through 706 removed outlier: 6.776A pdb=" N VAL u 712 " --> pdb=" O PHE u 704 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'u' and resid 731 through 732 removed outlier: 5.523A pdb=" N ILE u 741 " --> pdb=" O SER u 754 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N SER u 754 " --> pdb=" O ILE u 741 " (cutoff:3.500A) 1337 hydrogen bonds defined for protein. 3702 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1252 hydrogen bonds 1996 hydrogen bond angles 0 basepair planarities 504 basepair parallelities 929 stacking parallelities Total time for adding SS restraints: 60.31 Time building geometry restraints manager: 33.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 10237 1.31 - 1.44: 31524 1.44 - 1.57: 38982 1.57 - 1.69: 3319 1.69 - 1.82: 312 Bond restraints: 84374 Sorted by residual: bond pdb=" CB PRO D 210 " pdb=" CG PRO D 210 " ideal model delta sigma weight residual 1.492 1.317 0.175 5.00e-02 4.00e+02 1.23e+01 bond pdb=" CB VAL F 168 " pdb=" CG1 VAL F 168 " ideal model delta sigma weight residual 1.521 1.415 0.106 3.30e-02 9.18e+02 1.02e+01 bond pdb=" CB VAL W 25 " pdb=" CG1 VAL W 25 " ideal model delta sigma weight residual 1.521 1.419 0.102 3.30e-02 9.18e+02 9.54e+00 bond pdb=" CG1 ILE J 144 " pdb=" CD1 ILE J 144 " ideal model delta sigma weight residual 1.513 1.393 0.120 3.90e-02 6.57e+02 9.48e+00 bond pdb=" CB PRO F 163 " pdb=" CG PRO F 163 " ideal model delta sigma weight residual 1.492 1.345 0.147 5.00e-02 4.00e+02 8.66e+00 ... (remaining 84369 not shown) Histogram of bond angle deviations from ideal: 96.16 - 104.59: 7923 104.59 - 113.02: 48960 113.02 - 121.45: 43854 121.45 - 129.88: 20019 129.88 - 138.31: 1162 Bond angle restraints: 121918 Sorted by residual: angle pdb=" C SER f 9 " pdb=" N HIS f 10 " pdb=" CA HIS f 10 " ideal model delta sigma weight residual 120.51 129.42 -8.91 1.45e+00 4.76e-01 3.77e+01 angle pdb=" C LYS e 27 " pdb=" N LYS e 28 " pdb=" CA LYS e 28 " ideal model delta sigma weight residual 121.54 132.99 -11.45 1.91e+00 2.74e-01 3.59e+01 angle pdb=" O3' C 2 382 " pdb=" C3' C 2 382 " pdb=" C2' C 2 382 " ideal model delta sigma weight residual 113.70 122.51 -8.81 1.50e+00 4.44e-01 3.45e+01 angle pdb=" C4' C 21373 " pdb=" C3' C 21373 " pdb=" O3' C 21373 " ideal model delta sigma weight residual 113.00 121.73 -8.73 1.50e+00 4.44e-01 3.39e+01 angle pdb=" CA GLN J 132 " pdb=" CB GLN J 132 " pdb=" CG GLN J 132 " ideal model delta sigma weight residual 114.10 125.14 -11.04 2.00e+00 2.50e-01 3.05e+01 ... (remaining 121913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 45416 35.79 - 71.59: 1888 71.59 - 107.38: 133 107.38 - 143.18: 28 143.18 - 178.97: 39 Dihedral angle restraints: 47504 sinusoidal: 31742 harmonic: 15762 Sorted by residual: dihedral pdb=" CA LEU f 6 " pdb=" C LEU f 6 " pdb=" N TYR f 7 " pdb=" CA TYR f 7 " ideal model delta harmonic sigma weight residual -180.00 -122.59 -57.41 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" CA ALA K 40 " pdb=" C ALA K 40 " pdb=" N VAL K 41 " pdb=" CA VAL K 41 " ideal model delta harmonic sigma weight residual -180.00 -133.22 -46.78 0 5.00e+00 4.00e-02 8.75e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual 200.00 21.99 178.01 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 47501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 13925 0.115 - 0.229: 954 0.229 - 0.344: 69 0.344 - 0.458: 13 0.458 - 0.573: 4 Chirality restraints: 14965 Sorted by residual: chirality pdb=" C3' C 21373 " pdb=" C4' C 21373 " pdb=" O3' C 21373 " pdb=" C2' C 21373 " both_signs ideal model delta sigma weight residual False -2.48 -1.90 -0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" C3' C 2 382 " pdb=" C4' C 2 382 " pdb=" O3' C 2 382 " pdb=" C2' C 2 382 " both_signs ideal model delta sigma weight residual False -2.48 -1.91 -0.57 2.00e-01 2.50e+01 8.12e+00 chirality pdb=" C3' G 2 114 " pdb=" C4' G 2 114 " pdb=" O3' G 2 114 " pdb=" C2' G 2 114 " both_signs ideal model delta sigma weight residual False -2.74 -2.27 -0.48 2.00e-01 2.50e+01 5.73e+00 ... (remaining 14962 not shown) Planarity restraints: 9288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 21692 " -0.060 2.00e-02 2.50e+03 3.16e-02 2.25e+01 pdb=" N1 U 21692 " 0.066 2.00e-02 2.50e+03 pdb=" C2 U 21692 " 0.010 2.00e-02 2.50e+03 pdb=" O2 U 21692 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U 21692 " -0.006 2.00e-02 2.50e+03 pdb=" C4 U 21692 " -0.022 2.00e-02 2.50e+03 pdb=" O4 U 21692 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U 21692 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U 21692 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 21474 " 0.057 2.00e-02 2.50e+03 2.52e-02 1.74e+01 pdb=" N9 A 21474 " -0.047 2.00e-02 2.50e+03 pdb=" C8 A 21474 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A 21474 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A 21474 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 21474 " 0.014 2.00e-02 2.50e+03 pdb=" N6 A 21474 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A 21474 " 0.010 2.00e-02 2.50e+03 pdb=" C2 A 21474 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A 21474 " -0.010 2.00e-02 2.50e+03 pdb=" C4 A 21474 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 102 " 0.047 2.00e-02 2.50e+03 2.32e-02 1.48e+01 pdb=" N9 A 2 102 " -0.055 2.00e-02 2.50e+03 pdb=" C8 A 2 102 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A 2 102 " 0.011 2.00e-02 2.50e+03 pdb=" C5 A 2 102 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A 2 102 " -0.000 2.00e-02 2.50e+03 pdb=" N6 A 2 102 " 0.012 2.00e-02 2.50e+03 pdb=" N1 A 2 102 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A 2 102 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 2 102 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A 2 102 " -0.019 2.00e-02 2.50e+03 ... (remaining 9285 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 4537 2.68 - 3.23: 64729 3.23 - 3.79: 146377 3.79 - 4.34: 194506 4.34 - 4.90: 279227 Nonbonded interactions: 689376 Sorted by model distance: nonbonded pdb=" OE1 GLU g 125 " pdb="ZN ZN g 500 " model vdw 2.124 2.230 nonbonded pdb=" O6 G 21722 " pdb=" O2 U 21812 " model vdw 2.209 3.040 nonbonded pdb=" O SER D 190 " pdb=" OG SER D 190 " model vdw 2.211 2.440 nonbonded pdb=" OP2 A 21291 " pdb=" O2' G 21302 " model vdw 2.229 2.440 nonbonded pdb=" OE2 GLU V 33 " pdb=" O2' G 21447 " model vdw 2.234 2.440 ... (remaining 689371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.100 Extract box with map and model: 14.540 Check model and map are aligned: 0.880 Set scattering table: 0.520 Process input model: 219.010 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 242.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 : 0.011 0.175 84374 Z= 0.711 Angle : 1.158 16.457 121918 Z= 0.578 Chirality : 0.064 0.573 14965 Planarity : 0.007 0.079 9288 Dihedral : 17.494 178.970 37330 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.94 % Favored : 92.93 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.09), residues: 5402 helix: -3.88 (0.08), residues: 1520 sheet: -2.19 (0.14), residues: 1029 loop : -2.48 (0.10), residues: 2853 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1036 time to evaluate : 4.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 1055 average time/residue: 0.8525 time to fit residues: 1453.0862 Evaluate side-chains 854 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 845 time to evaluate : 4.913 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5533 time to fit residues: 15.7589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 701 random chunks: chunk 591 optimal weight: 0.6980 chunk 531 optimal weight: 0.6980 chunk 294 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 358 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 549 optimal weight: 20.0000 chunk 212 optimal weight: 2.9990 chunk 334 optimal weight: 0.0020 chunk 408 optimal weight: 2.9990 chunk 636 optimal weight: 20.0000 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN B 36 GLN C 95 ASN C 99 ASN C 149 GLN C 157 GLN C 179 ASN C 208 HIS ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN E 8 HIS E 50 ASN E 98 ASN E 179 ASN E 197 ASN G 81 HIS G 110 ASN ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 GLN H 163 GLN I 116 HIS I 138 ASN J 177 ASN L 18 GLN ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 58 HIS N 90 HIS N 105 ASN P 79 GLN Q 41 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 HIS S 118 GLN T 11 HIS T 19 ASN ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 ASN V 85 HIS V 92 HIS X 97 ASN X 127 ASN Y 89 HIS Y 124 ASN a 45 ASN a 64 ASN a 103 HIS c 8 ASN d 45 ASN f 28 HIS g 135 HIS j 14 HIS j 51 ASN ** j 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 196 ASN j 272 GLN ** j 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 74 GLN u 121 ASN u 180 GLN ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 519 ASN u 587 HIS u 631 GLN u 632 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.076 84374 Z= 0.155 Angle : 0.629 10.255 121918 Z= 0.325 Chirality : 0.040 0.359 14965 Planarity : 0.005 0.063 9288 Dihedral : 16.508 178.939 26086 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.08 (0.10), residues: 5402 helix: -2.39 (0.11), residues: 1580 sheet: -1.72 (0.15), residues: 1032 loop : -1.89 (0.10), residues: 2790 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 932 time to evaluate : 5.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 42 residues processed: 976 average time/residue: 0.8316 time to fit residues: 1340.8374 Evaluate side-chains 875 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 833 time to evaluate : 4.879 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.5726 time to fit residues: 52.3480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 701 random chunks: chunk 353 optimal weight: 0.0970 chunk 197 optimal weight: 5.9990 chunk 529 optimal weight: 4.9990 chunk 433 optimal weight: 1.9990 chunk 175 optimal weight: 0.3980 chunk 637 optimal weight: 9.9990 chunk 688 optimal weight: 0.0030 chunk 567 optimal weight: 5.9990 chunk 632 optimal weight: 20.0000 chunk 217 optimal weight: 4.9990 chunk 511 optimal weight: 6.9990 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 208 HIS D 272 HIS ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN K 149 GLN ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN Q 35 GLN S 118 GLN ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 GLN W 91 ASN X 97 ASN Y 124 ASN b 65 GLN c 8 ASN d 29 GLN j 51 ASN ** j 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 587 HIS u 631 GLN u 673 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 84374 Z= 0.181 Angle : 0.600 9.731 121918 Z= 0.309 Chirality : 0.039 0.344 14965 Planarity : 0.004 0.060 9288 Dihedral : 16.275 179.307 26086 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.18 % Favored : 94.78 % Rotamer Outliers : 1.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.11), residues: 5402 helix: -1.44 (0.12), residues: 1583 sheet: -1.41 (0.15), residues: 1038 loop : -1.65 (0.11), residues: 2781 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 862 time to evaluate : 4.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 47 residues processed: 918 average time/residue: 0.7965 time to fit residues: 1223.8126 Evaluate side-chains 865 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 818 time to evaluate : 4.915 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.5970 time to fit residues: 59.3278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 701 random chunks: chunk 630 optimal weight: 10.0000 chunk 479 optimal weight: 7.9990 chunk 330 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 304 optimal weight: 7.9990 chunk 428 optimal weight: 2.9990 chunk 640 optimal weight: 0.2980 chunk 677 optimal weight: 10.0000 chunk 334 optimal weight: 20.0000 chunk 606 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN E 209 HIS F 4 GLN F 174 HIS ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 HIS L 11 GLN ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS P 113 GLN Q 35 GLN ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS X 73 GLN X 97 ASN X 127 ASN Y 124 ASN d 29 GLN j 117 ASN j 191 HIS ** j 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 83 HIS u 120 GLN ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 587 HIS u 631 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 84374 Z= 0.378 Angle : 0.705 10.657 121918 Z= 0.359 Chirality : 0.045 0.338 14965 Planarity : 0.005 0.075 9288 Dihedral : 16.397 179.539 26086 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.78 % Favored : 94.21 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.11), residues: 5402 helix: -1.11 (0.13), residues: 1581 sheet: -1.32 (0.15), residues: 1027 loop : -1.61 (0.11), residues: 2794 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 845 time to evaluate : 5.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 109 outliers final: 66 residues processed: 909 average time/residue: 0.8523 time to fit residues: 1298.6851 Evaluate side-chains 869 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 803 time to evaluate : 5.427 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.6248 time to fit residues: 85.9025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 701 random chunks: chunk 564 optimal weight: 10.0000 chunk 384 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 504 optimal weight: 3.9990 chunk 279 optimal weight: 10.0000 chunk 578 optimal weight: 6.9990 chunk 468 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 345 optimal weight: 9.9990 chunk 608 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN G 186 GLN ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 HIS N 105 ASN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS X 97 ASN X 127 ASN Y 124 ASN Z 21 ASN d 29 GLN ** j 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 84374 Z= 0.339 Angle : 0.678 11.055 121918 Z= 0.346 Chirality : 0.043 0.332 14965 Planarity : 0.005 0.069 9288 Dihedral : 16.384 178.911 26086 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.87 % Favored : 94.11 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.11), residues: 5402 helix: -0.89 (0.13), residues: 1579 sheet: -1.19 (0.16), residues: 1017 loop : -1.54 (0.11), residues: 2806 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 841 time to evaluate : 4.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 56 residues processed: 898 average time/residue: 0.8251 time to fit residues: 1237.9273 Evaluate side-chains 864 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 808 time to evaluate : 4.917 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.5887 time to fit residues: 69.2600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 701 random chunks: chunk 227 optimal weight: 10.0000 chunk 610 optimal weight: 10.0000 chunk 133 optimal weight: 30.0000 chunk 397 optimal weight: 0.0020 chunk 167 optimal weight: 0.2980 chunk 678 optimal weight: 6.9990 chunk 563 optimal weight: 6.9990 chunk 314 optimal weight: 10.0000 chunk 56 optimal weight: 0.3980 chunk 224 optimal weight: 4.9990 chunk 356 optimal weight: 0.8980 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 56 ASN H 25 GLN ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 179 ASN M 32 HIS M 42 ASN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 ASN X 97 ASN Y 124 ASN d 29 GLN ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 587 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 84374 Z= 0.174 Angle : 0.584 11.620 121918 Z= 0.301 Chirality : 0.038 0.331 14965 Planarity : 0.004 0.060 9288 Dihedral : 16.177 178.863 26086 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.11 % Favored : 94.87 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.11), residues: 5402 helix: -0.51 (0.13), residues: 1579 sheet: -0.99 (0.16), residues: 1004 loop : -1.38 (0.11), residues: 2819 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 884 time to evaluate : 4.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 30 residues processed: 909 average time/residue: 0.8310 time to fit residues: 1258.2209 Evaluate side-chains 868 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 838 time to evaluate : 4.854 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.5877 time to fit residues: 39.7734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 701 random chunks: chunk 653 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 386 optimal weight: 0.7980 chunk 495 optimal weight: 10.0000 chunk 383 optimal weight: 6.9990 chunk 570 optimal weight: 8.9990 chunk 378 optimal weight: 7.9990 chunk 675 optimal weight: 9.9990 chunk 422 optimal weight: 30.0000 chunk 411 optimal weight: 20.0000 chunk 311 optimal weight: 1.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 179 ASN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS X 97 ASN Z 21 ASN b 65 GLN ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.096 84374 Z= 0.386 Angle : 0.703 11.874 121918 Z= 0.357 Chirality : 0.045 0.332 14965 Planarity : 0.005 0.079 9288 Dihedral : 16.314 179.626 26086 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.41 % Favored : 93.56 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.11), residues: 5402 helix: -0.59 (0.13), residues: 1584 sheet: -1.03 (0.16), residues: 995 loop : -1.44 (0.11), residues: 2823 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 841 time to evaluate : 4.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 47 residues processed: 892 average time/residue: 0.8154 time to fit residues: 1220.6173 Evaluate side-chains 853 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 806 time to evaluate : 4.815 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.5935 time to fit residues: 59.0346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 701 random chunks: chunk 417 optimal weight: 30.0000 chunk 269 optimal weight: 9.9990 chunk 403 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 429 optimal weight: 0.8980 chunk 460 optimal weight: 20.0000 chunk 334 optimal weight: 0.0070 chunk 62 optimal weight: 0.4980 chunk 531 optimal weight: 5.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 25 GLN ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 179 ASN ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN Q 53 GLN ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 ASN V 92 HIS X 97 ASN a 106 GLN b 65 GLN j 51 ASN ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 587 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 84374 Z= 0.135 Angle : 0.577 12.120 121918 Z= 0.296 Chirality : 0.038 0.325 14965 Planarity : 0.004 0.057 9288 Dihedral : 16.096 178.845 26086 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.11), residues: 5402 helix: -0.23 (0.13), residues: 1564 sheet: -0.86 (0.16), residues: 1003 loop : -1.24 (0.11), residues: 2835 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 867 time to evaluate : 4.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 15 residues processed: 884 average time/residue: 0.8579 time to fit residues: 1261.4606 Evaluate side-chains 839 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 824 time to evaluate : 4.952 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6000 time to fit residues: 23.3540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 701 random chunks: chunk 614 optimal weight: 9.9990 chunk 647 optimal weight: 0.3980 chunk 590 optimal weight: 6.9990 chunk 629 optimal weight: 20.0000 chunk 378 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 chunk 494 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 chunk 568 optimal weight: 5.9990 chunk 595 optimal weight: 10.0000 chunk 627 optimal weight: 20.0000 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 155 GLN ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN K 83 ASN ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 HIS X 31 HIS X 97 ASN Z 21 ASN b 65 GLN ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.099 84374 Z= 0.409 Angle : 0.726 12.722 121918 Z= 0.368 Chirality : 0.045 0.337 14965 Planarity : 0.005 0.084 9288 Dihedral : 16.265 179.475 26086 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.44 % Favored : 93.52 % Rotamer Outliers : 0.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.11), residues: 5402 helix: -0.45 (0.13), residues: 1576 sheet: -0.99 (0.16), residues: 995 loop : -1.35 (0.11), residues: 2831 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 828 time to evaluate : 5.763 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 outliers start: 37 outliers final: 23 residues processed: 841 average time/residue: 0.8361 time to fit residues: 1178.1875 Evaluate side-chains 831 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 808 time to evaluate : 5.017 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.6093 time to fit residues: 32.7517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 701 random chunks: chunk 413 optimal weight: 9.9990 chunk 665 optimal weight: 9.9990 chunk 406 optimal weight: 5.9990 chunk 315 optimal weight: 10.0000 chunk 462 optimal weight: 8.9990 chunk 698 optimal weight: 5.9990 chunk 642 optimal weight: 0.0020 chunk 556 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 429 optimal weight: 0.9990 chunk 340 optimal weight: 0.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 ASN V 92 HIS X 97 ASN b 65 GLN ** u 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 84374 Z= 0.203 Angle : 0.612 13.142 121918 Z= 0.314 Chirality : 0.039 0.317 14965 Planarity : 0.004 0.079 9288 Dihedral : 16.116 178.429 26086 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.98 % Favored : 95.00 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.11), residues: 5402 helix: -0.29 (0.13), residues: 1583 sheet: -0.84 (0.16), residues: 990 loop : -1.28 (0.11), residues: 2829 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10804 Ramachandran restraints generated. 5402 Oldfield, 0 Emsley, 5402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 832 time to evaluate : 4.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 837 average time/residue: 0.8520 time to fit residues: 1186.6071 Evaluate side-chains 830 residues out of total 4739 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 823 time to evaluate : 4.895 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.5742 time to fit residues: 13.9110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 701 random chunks: chunk 441 optimal weight: 0.8980 chunk 592 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 chunk 512 optimal weight: 6.9990 chunk 82 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 557 optimal weight: 20.0000 chunk 233 optimal weight: 4.9990 chunk 571 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 GLN ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 ASN b 65 GLN ** g 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 587 HIS u 641 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.152217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.129773 restraints weight = 125483.514| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 0.85 r_work: 0.3256 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 84374 Z= 0.180 Angle : 0.593 13.414 121918 Z= 0.303 Chirality : 0.038 0.318 14965 Planarity : 0.004 0.059 9288 Dihedral : 15.989 179.404 26086 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.11), residues: 5402 helix: -0.14 (0.13), residues: 1589 sheet: -0.69 (0.17), residues: 968 loop : -1.20 (0.11), residues: 2845 =============================================================================== Job complete usr+sys time: 19067.98 seconds wall clock time: 335 minutes 51.33 seconds (20151.33 seconds total)