Starting phenix.real_space_refine on Thu Dec 14 14:57:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtv_32802/12_2023/7wtv_32802_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtv_32802/12_2023/7wtv_32802.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtv_32802/12_2023/7wtv_32802_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtv_32802/12_2023/7wtv_32802_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtv_32802/12_2023/7wtv_32802_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtv_32802/12_2023/7wtv_32802.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtv_32802/12_2023/7wtv_32802.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtv_32802/12_2023/7wtv_32802_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wtv_32802/12_2023/7wtv_32802_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 1 6.06 5 P 1574 5.49 5 S 238 5.16 5 C 47130 2.51 5 N 15360 2.21 5 O 19874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 77": "OE1" <-> "OE2" Residue "R GLU 79": "OE1" <-> "OE2" Residue "R ASP 82": "OD1" <-> "OD2" Residue "b GLU 14": "OE1" <-> "OE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "c ASP 37": "OD1" <-> "OD2" Residue "c GLU 52": "OE1" <-> "OE2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E ASP 59": "OD1" <-> "OD2" Residue "E ASP 79": "OD1" <-> "OD2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "F ASP 16": "OD1" <-> "OD2" Residue "F TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 98": "OE1" <-> "OE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "F GLU 123": "OE1" <-> "OE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 103": "OD1" <-> "OD2" Residue "G ASP 126": "OD1" <-> "OD2" Residue "G ASP 152": "OD1" <-> "OD2" Residue "G GLU 208": "OE1" <-> "OE2" Residue "Z PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 75": "OE1" <-> "OE2" Residue "Z GLU 90": "OE1" <-> "OE2" Residue "Y GLU 86": "OE1" <-> "OE2" Residue "Y GLU 98": "OE1" <-> "OE2" Residue "Y GLU 109": "OE1" <-> "OE2" Residue "x TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 117": "OE1" <-> "OE2" Residue "x PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 19": "OD1" <-> "OD2" Residue "X TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 21": "OD1" <-> "OD2" Residue "w GLU 70": "OE1" <-> "OE2" Residue "w PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 261": "OD1" <-> "OD2" Residue "w GLU 296": "OE1" <-> "OE2" Residue "w PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 399": "OE1" <-> "OE2" Residue "w GLU 403": "OE1" <-> "OE2" Residue "W GLU 18": "OE1" <-> "OE2" Residue "W GLU 87": "OE1" <-> "OE2" Residue "W PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 403": "OE1" <-> "OE2" Residue "u ASP 486": "OD1" <-> "OD2" Residue "u ASP 515": "OD1" <-> "OD2" Residue "u ASP 647": "OD1" <-> "OD2" Residue "u PHE 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 132": "OD1" <-> "OD2" Residue "S ASP 21": "OD1" <-> "OD2" Residue "S GLU 58": "OE1" <-> "OE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S GLU 63": "OE1" <-> "OE2" Residue "S ASP 81": "OD1" <-> "OD2" Residue "S TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 112": "OE1" <-> "OE2" Residue "Q TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 102": "OE1" <-> "OE2" Residue "P ASP 21": "OD1" <-> "OD2" Residue "P GLU 66": "OE1" <-> "OE2" Residue "P PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 106": "OE1" <-> "OE2" Residue "O TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 31": "OD1" <-> "OD2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N ASP 110": "OD1" <-> "OD2" Residue "L GLU 49": "OE1" <-> "OE2" Residue "L ASP 124": "OD1" <-> "OD2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J GLU 59": "OE1" <-> "OE2" Residue "J ASP 64": "OD1" <-> "OD2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J GLU 103": "OE1" <-> "OE2" Residue "J PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 6": "OD1" <-> "OD2" Residue "I TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "r GLU 50": "OE1" <-> "OE2" Residue "r GLU 72": "OE1" <-> "OE2" Residue "r GLU 78": "OE1" <-> "OE2" Residue "r GLU 92": "OE1" <-> "OE2" Residue "q GLU 15": "OE1" <-> "OE2" Residue "q GLU 22": "OE1" <-> "OE2" Residue "q TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 34": "OD1" <-> "OD2" Residue "q GLU 45": "OE1" <-> "OE2" Residue "q ASP 59": "OD1" <-> "OD2" Residue "q TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 93": "OD1" <-> "OD2" Residue "q GLU 97": "OE1" <-> "OE2" Residue "q PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 172": "OE1" <-> "OE2" Residue "q ASP 190": "OD1" <-> "OD2" Residue "K PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 320": "OE1" <-> "OE2" Residue "K PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 365": "OE1" <-> "OE2" Residue "K GLU 476": "OE1" <-> "OE2" Residue "K PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 556": "OD1" <-> "OD2" Residue "K GLU 560": "OE1" <-> "OE2" Residue "K PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 656": "OD1" <-> "OD2" Residue "K PHE 685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 715": "OE1" <-> "OE2" Residue "K TYR 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 766": "OE1" <-> "OE2" Residue "K PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 897": "OE1" <-> "OE2" Residue "K TYR 907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 930": "OE1" <-> "OE2" Residue "K GLU 941": "OE1" <-> "OE2" Residue "K TYR 1028": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1075": "OE1" <-> "OE2" Residue "K GLU 1111": "OE1" <-> "OE2" Residue "K ASP 1249": "OD1" <-> "OD2" Residue "M ASP 43": "OD1" <-> "OD2" Residue "M GLU 58": "OE1" <-> "OE2" Residue "M ASP 113": "OD1" <-> "OD2" Residue "f GLU 125": "OE1" <-> "OE2" Residue "f PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 193": "OE1" <-> "OE2" Residue "A GLU 13": "OE1" <-> "OE2" Residue "A PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "C TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 271": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 84177 Number of models: 1 Model: "" Number of chains: 37 Chain: "2" Number of atoms: 33614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1574, 33614 Classifications: {'RNA': 1574} Modifications used: {'rna2p': 1, 'rna2p_pur': 119, 'rna2p_pyr': 95, 'rna3p_pur': 715, 'rna3p_pyr': 644} Link IDs: {'rna2p': 214, 'rna3p': 1359} Chain breaks: 18 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 673 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 78} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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: "B" 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: "c" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 471 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 59} 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: "e" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 179 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "F" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1494 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 183} 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: "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: "Z" 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: "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: "x" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1372 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 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: "w" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2610 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 16, 'TRANS': 314} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "W" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "u" Number of atoms: 5168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5168 Classifications: {'peptide': 642} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 597} Chain breaks: 5 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "T" 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: "S" Number of atoms: 1046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1046 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "Q" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "P" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1006 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain breaks: 1 Chain: "O" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1009 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} 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: "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: "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: "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: "r" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 940 Classifications: {'peptide': 118} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 106} Chain: "q" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1869 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 13, 'TRANS': 221} Chain breaks: 1 Chain: "K" Number of atoms: 7707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7707 Classifications: {'peptide': 993} Link IDs: {'CIS': 1, 'PTRANS': 47, 'TRANS': 944} Chain breaks: 9 Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 2 Chain: "f" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 465 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain breaks: 1 Chain: "z" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 416 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "C" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1674 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "V" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 31.85, per 1000 atoms: 0.38 Number of scatterers: 84177 At special positions: 0 Unit cell: (255.219, 252.042, 202.269, 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 1 29.99 S 238 16.00 P 1574 15.00 O 19874 8.00 N 15360 7.00 C 47130 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: 28.09 Conformation dependent library (CDL) restraints added in 7.5 seconds 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 247 helices and 49 sheets defined 39.4% alpha, 12.2% beta 514 base pairs and 831 stacking pairs defined. Time for finding SS restraints: 31.25 Creating SS restraints... Processing helix chain 'R' and resid 7 through 19 removed outlier: 3.754A pdb=" N VAL R 15 " --> pdb=" O LYS R 11 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 38 Processing helix chain 'R' and resid 44 through 63 removed outlier: 3.540A pdb=" N GLY R 52 " --> pdb=" O ASN R 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN R 62 " --> pdb=" O MET R 58 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 82 removed outlier: 3.554A pdb=" N GLU R 77 " --> pdb=" O LEU R 73 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP R 82 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 17 Processing helix chain 'B' and resid 24 through 27 No H-bonds generated for 'chain 'B' and resid 24 through 27' Processing helix chain 'B' and resid 58 through 61 No H-bonds generated for 'chain 'B' and resid 58 through 61' Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 181 through 189 removed outlier: 3.689A pdb=" N VAL B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.643A pdb=" N LEU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 58 through 67 removed outlier: 3.782A pdb=" N LYS E 62 " --> pdb=" O GLY E 58 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN E 67 " --> pdb=" O LYS E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 120 No H-bonds generated for 'chain 'E' and resid 118 through 120' Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 248 through 261 Processing helix chain 'e' and resid 31 through 41 Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 33 through 35 No H-bonds generated for 'chain 'F' and resid 33 through 35' Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 87 through 103 removed outlier: 3.671A pdb=" N LEU F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 118 Processing helix chain 'F' and resid 145 through 159 removed outlier: 3.512A pdb=" N ALA F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 182 removed outlier: 3.554A pdb=" N ASN F 179 " --> pdb=" O ASP F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 203 Processing helix chain 'H' and resid 18 through 33 removed outlier: 3.588A pdb=" N MET H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 74 removed outlier: 5.203A pdb=" N LYS H 70 " --> pdb=" O PRO H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 86 removed outlier: 3.598A pdb=" N ARG H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS H 85 " --> pdb=" O ARG H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 120 No H-bonds generated for 'chain 'H' and resid 118 through 120' Processing helix chain 'H' and resid 122 through 133 removed outlier: 3.961A pdb=" N LEU H 130 " --> pdb=" O HIS H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 181 Processing helix chain 'G' and resid 23 through 26 removed outlier: 4.295A pdb=" N THR G 26 " --> pdb=" O LYS G 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 23 through 26' Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'G' and resid 154 through 156 No H-bonds generated for 'chain 'G' and resid 154 through 156' Processing helix chain 'G' and resid 182 through 228 Processing helix chain 'Z' and resid 52 through 61 removed outlier: 3.520A pdb=" N ASP Z 56 " --> pdb=" O LYS Z 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 77 removed outlier: 3.528A pdb=" N GLU Z 75 " --> pdb=" O ALA Z 71 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG Z 76 " --> pdb=" O VAL Z 72 " (cutoff:3.500A) Processing helix chain 'Z' and resid 81 through 93 removed outlier: 3.995A pdb=" N LEU Z 88 " --> pdb=" O ALA Z 84 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU Z 90 " --> pdb=" O ALA Z 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 48 removed outlier: 3.608A pdb=" N ALA Y 45 " --> pdb=" O ARG Y 41 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS Y 46 " --> pdb=" O GLU Y 42 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET Y 47 " --> pdb=" O LYS Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 79 through 85 Processing helix chain 'Y' and resid 88 through 94 removed outlier: 3.697A pdb=" N HIS Y 94 " --> pdb=" O ARG Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 116 removed outlier: 4.205A pdb=" N LYS Y 116 " --> pdb=" O ASN Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 124 Processing helix chain 'x' and resid 82 through 90 removed outlier: 3.525A pdb=" N TYR x 85 " --> pdb=" O ALA x 82 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR x 86 " --> pdb=" O ASN x 83 " (cutoff:3.500A) Proline residue: x 87 - end of helix Processing helix chain 'x' and resid 96 through 101 Processing helix chain 'x' and resid 127 through 142 removed outlier: 3.634A pdb=" N THR x 131 " --> pdb=" O SER x 128 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL x 137 " --> pdb=" O ALA x 134 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS x 138 " --> pdb=" O ASP x 135 " (cutoff:3.500A) Processing helix chain 'x' and resid 146 through 154 removed outlier: 3.847A pdb=" N LEU x 152 " --> pdb=" O ASP x 148 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE x 153 " --> pdb=" O ALA x 149 " (cutoff:3.500A) Processing helix chain 'x' and resid 165 through 167 No H-bonds generated for 'chain 'x' and resid 165 through 167' Processing helix chain 'x' and resid 174 through 184 removed outlier: 3.519A pdb=" N ILE x 180 " --> pdb=" O LEU x 176 " (cutoff:3.500A) Processing helix chain 'x' and resid 186 through 198 removed outlier: 6.137A pdb=" N THR x 190 " --> pdb=" O GLY x 187 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR x 193 " --> pdb=" O THR x 190 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL x 197 " --> pdb=" O ILE x 194 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR x 198 " --> pdb=" O GLU x 195 " (cutoff:3.500A) Processing helix chain 'x' and resid 215 through 230 Processing helix chain 'x' and resid 234 through 246 removed outlier: 3.654A pdb=" N ARG x 242 " --> pdb=" O TYR x 238 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA x 243 " --> pdb=" O GLY x 239 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER x 246 " --> pdb=" O ARG x 242 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 20 removed outlier: 3.565A pdb=" N ARG X 17 " --> pdb=" O LEU X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 32 removed outlier: 3.691A pdb=" N ALA X 30 " --> pdb=" O GLN X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 34 through 37 No H-bonds generated for 'chain 'X' and resid 34 through 37' Processing helix chain 'X' and resid 89 through 93 removed outlier: 3.533A pdb=" N PHE X 93 " --> pdb=" O CYS X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 134 Processing helix chain 'w' and resid 19 through 27 Processing helix chain 'w' and resid 52 through 70 removed outlier: 3.548A pdb=" N ARG w 57 " --> pdb=" O ARG w 53 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU w 68 " --> pdb=" O GLN w 64 " (cutoff:3.500A) Processing helix chain 'w' and resid 143 through 166 Processing helix chain 'w' and resid 181 through 193 removed outlier: 3.586A pdb=" N VAL w 188 " --> pdb=" O VAL w 184 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG w 189 " --> pdb=" O TYR w 185 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU w 190 " --> pdb=" O ARG w 186 " (cutoff:3.500A) Processing helix chain 'w' and resid 213 through 219 Processing helix chain 'w' and resid 222 through 224 No H-bonds generated for 'chain 'w' and resid 222 through 224' Processing helix chain 'w' and resid 227 through 237 removed outlier: 3.907A pdb=" N TYR w 231 " --> pdb=" O ALA w 227 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE w 236 " --> pdb=" O GLN w 232 " (cutoff:3.500A) Processing helix chain 'w' and resid 243 through 252 Processing helix chain 'w' and resid 254 through 264 removed outlier: 3.780A pdb=" N ASP w 261 " --> pdb=" O ARG w 257 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL w 262 " --> pdb=" O VAL w 258 " (cutoff:3.500A) Processing helix chain 'w' and resid 270 through 279 Processing helix chain 'w' and resid 283 through 287 Processing helix chain 'w' and resid 291 through 295 Processing helix chain 'w' and resid 302 through 314 removed outlier: 3.614A pdb=" N SER w 310 " --> pdb=" O ILE w 306 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE w 311 " --> pdb=" O ILE w 307 " (cutoff:3.500A) Processing helix chain 'w' and resid 319 through 331 Processing helix chain 'w' and resid 338 through 348 removed outlier: 3.597A pdb=" N LEU w 345 " --> pdb=" O PHE w 341 " (cutoff:3.500A) Processing helix chain 'w' and resid 354 through 366 Processing helix chain 'w' and resid 376 through 388 Processing helix chain 'w' and resid 395 through 407 removed outlier: 3.515A pdb=" N LEU w 402 " --> pdb=" O LYS w 398 " (cutoff:3.500A) Processing helix chain 'w' and resid 414 through 422 Processing helix chain 'W' and resid 6 through 19 Processing helix chain 'W' and resid 32 through 43 Processing helix chain 'W' and resid 86 through 93 removed outlier: 3.573A pdb=" N ASN W 92 " --> pdb=" O LYS W 88 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 118 Processing helix chain 'u' and resid 50 through 73 Processing helix chain 'u' and resid 96 through 102 removed outlier: 3.551A pdb=" N LEU u 102 " --> pdb=" O GLU u 98 " (cutoff:3.500A) Processing helix chain 'u' and resid 143 through 150 removed outlier: 3.826A pdb=" N ASP u 148 " --> pdb=" O HIS u 144 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET u 149 " --> pdb=" O VAL u 145 " (cutoff:3.500A) Processing helix chain 'u' and resid 168 through 180 Processing helix chain 'u' and resid 200 through 212 removed outlier: 3.677A pdb=" N LYS u 209 " --> pdb=" O LYS u 205 " (cutoff:3.500A) Processing helix chain 'u' and resid 226 through 237 Processing helix chain 'u' and resid 245 through 248 No H-bonds generated for 'chain 'u' and resid 245 through 248' Processing helix chain 'u' and resid 401 through 404 Processing helix chain 'u' and resid 465 through 483 removed outlier: 3.661A pdb=" N MET u 483 " --> pdb=" O ARG u 479 " (cutoff:3.500A) Processing helix chain 'u' and resid 496 through 499 No H-bonds generated for 'chain 'u' and resid 496 through 499' Processing helix chain 'u' and resid 522 through 525 Processing helix chain 'u' and resid 533 through 545 removed outlier: 3.542A pdb=" N GLU u 545 " --> pdb=" O PHE u 541 " (cutoff:3.500A) Processing helix chain 'u' and resid 567 through 575 removed outlier: 3.794A pdb=" N GLU u 571 " --> pdb=" O SER u 568 " (cutoff:3.500A) Processing helix chain 'u' and resid 722 through 725 No H-bonds generated for 'chain 'u' and resid 722 through 725' Processing helix chain 'T' and resid 6 through 8 No H-bonds generated for 'chain 'T' and resid 6 through 8' Processing helix chain 'T' and resid 11 through 25 Processing helix chain 'T' and resid 32 through 35 removed outlier: 4.412A pdb=" N ASP T 35 " --> pdb=" O GLU T 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 32 through 35' Processing helix chain 'T' and resid 52 through 66 Processing helix chain 'T' and resid 72 through 78 Processing helix chain 'T' and resid 97 through 109 Processing helix chain 'T' and resid 125 through 142 removed outlier: 3.635A pdb=" N GLY T 136 " --> pdb=" O ASP T 132 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN T 137 " --> pdb=" O ARG T 133 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 32 removed outlier: 3.825A pdb=" N ILE S 30 " --> pdb=" O ILE S 26 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N THR S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA S 32 " --> pdb=" O PHE S 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 26 through 32' Processing helix chain 'S' and resid 40 through 47 Processing helix chain 'S' and resid 63 through 71 removed outlier: 3.735A pdb=" N ILE S 68 " --> pdb=" O VAL S 64 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 81 through 83 No H-bonds generated for 'chain 'S' and resid 81 through 83' Processing helix chain 'S' and resid 102 through 116 removed outlier: 3.652A pdb=" N LEU S 114 " --> pdb=" O ASP S 110 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 127 Processing helix chain 'Q' and resid 39 through 41 No H-bonds generated for 'chain 'Q' and resid 39 through 41' Processing helix chain 'Q' and resid 46 through 58 removed outlier: 4.677A pdb=" N TYR Q 49 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS Q 50 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU Q 53 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Proline residue: Q 54 - end of helix removed outlier: 4.213A pdb=" N LEU Q 57 " --> pdb=" O PRO Q 54 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU Q 58 " --> pdb=" O VAL Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 98 removed outlier: 3.773A pdb=" N ILE Q 81 " --> pdb=" O HIS Q 77 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN Q 86 " --> pdb=" O TYR Q 82 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER Q 89 " --> pdb=" O ARG Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 115 removed outlier: 3.538A pdb=" N ILE Q 113 " --> pdb=" O LYS Q 109 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR Q 115 " --> pdb=" O ILE Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 117 through 119 No H-bonds generated for 'chain 'Q' and resid 117 through 119' Processing helix chain 'P' and resid 22 through 27 Processing helix chain 'P' and resid 39 through 47 Processing helix chain 'P' and resid 51 through 66 Processing helix chain 'P' and resid 87 through 89 No H-bonds generated for 'chain 'P' and resid 87 through 89' Processing helix chain 'P' and resid 117 through 119 No H-bonds generated for 'chain 'P' and resid 117 through 119' Processing helix chain 'O' and resid 71 through 88 removed outlier: 3.512A pdb=" N VAL O 81 " --> pdb=" O ALA O 77 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU O 87 " --> pdb=" O GLN O 83 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 122 removed outlier: 3.518A pdb=" N ALA O 120 " --> pdb=" O LEU O 116 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG O 121 " --> pdb=" O ARG O 117 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER O 122 " --> pdb=" O ALA O 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 removed outlier: 3.828A pdb=" N LYS N 34 " --> pdb=" O SER N 30 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU N 35 " --> pdb=" O ASP N 31 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN N 36 " --> pdb=" O ASP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 56 removed outlier: 3.679A pdb=" N GLY N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 77 removed outlier: 3.580A pdb=" N SER N 77 " --> pdb=" O ARG N 73 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 104 removed outlier: 3.737A pdb=" N LEU N 91 " --> pdb=" O ASP N 87 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU N 103 " --> pdb=" O ARG N 99 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 131 Processing helix chain 'N' and resid 147 through 149 No H-bonds generated for 'chain 'N' and resid 147 through 149' Processing helix chain 'L' and resid 24 through 29 Processing helix chain 'L' and resid 48 through 52 Processing helix chain 'J' and resid 22 through 35 removed outlier: 3.527A pdb=" N ASP J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU J 34 " --> pdb=" O LYS J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 62 removed outlier: 3.739A pdb=" N VAL J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR J 62 " --> pdb=" O ARG J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 83 Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 97 through 99 No H-bonds generated for 'chain 'J' and resid 97 through 99' Processing helix chain 'J' and resid 102 through 108 removed outlier: 3.984A pdb=" N ARG J 108 " --> pdb=" O ASP J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 116 removed outlier: 3.544A pdb=" N PHE J 115 " --> pdb=" O GLN J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 131 Processing helix chain 'J' and resid 172 through 180 removed outlier: 3.679A pdb=" N LYS J 180 " --> pdb=" O LYS J 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' 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 107 through 116 Processing helix chain 'I' and resid 131 through 137 Processing helix chain 'I' and resid 143 through 154 removed outlier: 3.587A pdb=" N LYS I 147 " --> pdb=" O LYS I 143 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG I 152 " --> pdb=" O LYS I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 168 removed outlier: 4.007A pdb=" N GLN I 165 " --> pdb=" O LEU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 182 No H-bonds generated for 'chain 'I' and resid 179 through 182' Processing helix chain 'I' and resid 193 through 205 Processing helix chain 'r' and resid 3 through 7 removed outlier: 3.694A pdb=" N ASN r 7 " --> pdb=" O LEU r 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 3 through 7' Processing helix chain 'r' and resid 39 through 45 removed outlier: 3.826A pdb=" N ARG r 44 " --> pdb=" O ASN r 40 " (cutoff:3.500A) Processing helix chain 'r' and resid 51 through 60 removed outlier: 3.624A pdb=" N GLU r 56 " --> pdb=" O SER r 52 " (cutoff:3.500A) Processing helix chain 'r' and resid 78 through 88 removed outlier: 3.681A pdb=" N THR r 83 " --> pdb=" O GLU r 79 " (cutoff:3.500A) Processing helix chain 'q' and resid 8 through 10 No H-bonds generated for 'chain 'q' and resid 8 through 10' Processing helix chain 'q' and resid 14 through 17 No H-bonds generated for 'chain 'q' and resid 14 through 17' Processing helix chain 'q' and resid 20 through 27 removed outlier: 3.670A pdb=" N LYS q 25 " --> pdb=" O THR q 21 " (cutoff:3.500A) Processing helix chain 'q' and resid 30 through 46 removed outlier: 3.965A pdb=" N THR q 37 " --> pdb=" O ILE q 33 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 74 removed outlier: 3.608A pdb=" N LEU q 71 " --> pdb=" O SER q 67 " (cutoff:3.500A) Processing helix chain 'q' and resid 85 through 93 Processing helix chain 'q' and resid 125 through 128 Processing helix chain 'q' and resid 138 through 152 Processing helix chain 'q' and resid 168 through 181 removed outlier: 3.695A pdb=" N GLN q 177 " --> pdb=" O LEU q 173 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA q 181 " --> pdb=" O GLN q 177 " (cutoff:3.500A) Processing helix chain 'q' and resid 250 through 262 removed outlier: 3.519A pdb=" N GLU q 254 " --> pdb=" O ALA q 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 112 No H-bonds generated for 'chain 'K' and resid 109 through 112' Processing helix chain 'K' and resid 118 through 121 No H-bonds generated for 'chain 'K' and resid 118 through 121' Processing helix chain 'K' and resid 138 through 140 No H-bonds generated for 'chain 'K' and resid 138 through 140' Processing helix chain 'K' and resid 152 through 155 No H-bonds generated for 'chain 'K' and resid 152 through 155' Processing helix chain 'K' and resid 164 through 174 removed outlier: 3.532A pdb=" N LEU K 170 " --> pdb=" O ALA K 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'K' and resid 187 through 195 Processing helix chain 'K' and resid 197 through 204 removed outlier: 3.602A pdb=" N GLN K 201 " --> pdb=" O ILE K 197 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA K 202 " --> pdb=" O MET K 198 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER K 204 " --> pdb=" O ALA K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 223 removed outlier: 4.562A pdb=" N TRP K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL K 213 " --> pdb=" O VAL K 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 244 removed outlier: 3.974A pdb=" N PHE K 244 " --> pdb=" O GLY K 240 " (cutoff:3.500A) Processing helix chain 'K' and resid 250 through 264 removed outlier: 3.635A pdb=" N CYS K 261 " --> pdb=" O GLN K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 294 Processing helix chain 'K' and resid 302 through 312 removed outlier: 4.014A pdb=" N HIS K 306 " --> pdb=" O THR K 302 " (cutoff:3.500A) Processing helix chain 'K' and resid 320 through 335 removed outlier: 3.579A pdb=" N VAL K 333 " --> pdb=" O THR K 329 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET K 334 " --> pdb=" O LEU K 330 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR K 335 " --> pdb=" O LEU K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 354 Processing helix chain 'K' and resid 364 through 376 removed outlier: 3.892A pdb=" N ALA K 368 " --> pdb=" O ALA K 364 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN K 369 " --> pdb=" O GLU K 365 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ASP K 376 " --> pdb=" O THR K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 386 through 404 Processing helix chain 'K' and resid 406 through 425 removed outlier: 3.736A pdb=" N GLY K 411 " --> pdb=" O ASP K 407 " (cutoff:3.500A) Proline residue: K 414 - end of helix removed outlier: 3.593A pdb=" N LEU K 424 " --> pdb=" O ALA K 420 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU K 425 " --> pdb=" O VAL K 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 429 through 445 Processing helix chain 'K' and resid 449 through 454 removed outlier: 4.095A pdb=" N ALA K 452 " --> pdb=" O PRO K 449 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP K 453 " --> pdb=" O HIS K 450 " (cutoff:3.500A) Processing helix chain 'K' and resid 464 through 479 removed outlier: 3.616A pdb=" N VAL K 468 " --> pdb=" O PRO K 464 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU K 477 " --> pdb=" O ARG K 473 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY K 478 " --> pdb=" O ALA K 474 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU K 479 " --> pdb=" O VAL K 475 " (cutoff:3.500A) Processing helix chain 'K' and resid 487 through 501 removed outlier: 3.546A pdb=" N GLN K 492 " --> pdb=" O SER K 488 " (cutoff:3.500A) Processing helix chain 'K' and resid 510 through 519 removed outlier: 3.614A pdb=" N GLN K 514 " --> pdb=" O ARG K 510 " (cutoff:3.500A) Processing helix chain 'K' and resid 528 through 542 removed outlier: 3.657A pdb=" N GLN K 533 " --> pdb=" O ALA K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 544 through 550 Processing helix chain 'K' and resid 567 through 574 removed outlier: 3.562A pdb=" N LEU K 570 " --> pdb=" O SER K 567 " (cutoff:3.500A) Proline residue: K 571 - end of helix removed outlier: 3.612A pdb=" N ARG K 574 " --> pdb=" O PRO K 571 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 567 through 574' Processing helix chain 'K' and resid 582 through 604 removed outlier: 3.655A pdb=" N THR K 586 " --> pdb=" O GLY K 583 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR K 588 " --> pdb=" O PHE K 585 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N PHE K 589 " --> pdb=" O THR K 586 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N LEU K 590 " --> pdb=" O THR K 587 " (cutoff:3.500A) Proline residue: K 591 - end of helix removed outlier: 3.808A pdb=" N ASN K 594 " --> pdb=" O PRO K 591 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR K 595 " --> pdb=" O LEU K 592 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU K 596 " --> pdb=" O ALA K 593 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET K 601 " --> pdb=" O SER K 598 " (cutoff:3.500A) Processing helix chain 'K' and resid 611 through 623 Processing helix chain 'K' and resid 625 through 629 Processing helix chain 'K' and resid 636 through 642 removed outlier: 3.616A pdb=" N PHE K 640 " --> pdb=" O VAL K 636 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS K 641 " --> pdb=" O ALA K 637 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLY K 642 " --> pdb=" O ILE K 638 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 636 through 642' Processing helix chain 'K' and resid 644 through 652 removed outlier: 3.541A pdb=" N SER K 652 " --> pdb=" O GLY K 648 " (cutoff:3.500A) Processing helix chain 'K' and resid 658 through 671 removed outlier: 3.889A pdb=" N ARG K 666 " --> pdb=" O CYS K 662 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR K 667 " --> pdb=" O GLN K 663 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU K 668 " --> pdb=" O ALA K 664 " (cutoff:3.500A) Processing helix chain 'K' and resid 676 through 684 removed outlier: 3.742A pdb=" N ALA K 680 " --> pdb=" O GLU K 676 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU K 681 " --> pdb=" O ALA K 677 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL K 682 " --> pdb=" O ASP K 678 " (cutoff:3.500A) Processing helix chain 'K' and resid 686 through 698 removed outlier: 3.596A pdb=" N LEU K 690 " --> pdb=" O ALA K 686 " (cutoff:3.500A) Proline residue: K 691 - end of helix Processing helix chain 'K' and resid 710 through 722 removed outlier: 3.575A pdb=" N THR K 716 " --> pdb=" O ALA K 712 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR K 722 " --> pdb=" O ARG K 718 " (cutoff:3.500A) Processing helix chain 'K' and resid 726 through 741 Processing helix chain 'K' and resid 747 through 760 removed outlier: 3.556A pdb=" N LEU K 756 " --> pdb=" O SER K 752 " (cutoff:3.500A) Processing helix chain 'K' and resid 766 through 781 Proline residue: K 778 - end of helix removed outlier: 5.137A pdb=" N GLU K 781 " --> pdb=" O ARG K 777 " (cutoff:3.500A) Processing helix chain 'K' and resid 785 through 799 removed outlier: 3.859A pdb=" N CYS K 799 " --> pdb=" O LEU K 795 " (cutoff:3.500A) Processing helix chain 'K' and resid 805 through 812 removed outlier: 3.629A pdb=" N VAL K 810 " --> pdb=" O GLY K 806 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLN K 811 " --> pdb=" O ALA K 807 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER K 812 " --> pdb=" O LEU K 808 " (cutoff:3.500A) Processing helix chain 'K' and resid 814 through 825 removed outlier: 3.505A pdb=" N LYS K 818 " --> pdb=" O LEU K 814 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU K 825 " --> pdb=" O LEU K 821 " (cutoff:3.500A) Processing helix chain 'K' and resid 831 through 844 removed outlier: 3.808A pdb=" N ARG K 834 " --> pdb=" O PRO K 831 " (cutoff:3.500A) Proline residue: K 835 - end of helix removed outlier: 3.675A pdb=" N ILE K 843 " --> pdb=" O LEU K 840 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL K 844 " --> pdb=" O LEU K 841 " (cutoff:3.500A) Processing helix chain 'K' and resid 852 through 856 Processing helix chain 'K' and resid 859 through 867 removed outlier: 4.497A pdb=" N LYS K 867 " --> pdb=" O ILE K 863 " (cutoff:3.500A) Processing helix chain 'K' and resid 872 through 889 Processing helix chain 'K' and resid 895 through 905 removed outlier: 3.619A pdb=" N LEU K 905 " --> pdb=" O CYS K 901 " (cutoff:3.500A) Processing helix chain 'K' and resid 907 through 910 Processing helix chain 'K' and resid 914 through 928 removed outlier: 3.542A pdb=" N SER K 918 " --> pdb=" O VAL K 914 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE K 921 " --> pdb=" O VAL K 917 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU K 922 " --> pdb=" O SER K 918 " (cutoff:3.500A) Processing helix chain 'K' and resid 937 through 952 removed outlier: 4.197A pdb=" N GLU K 941 " --> pdb=" O SER K 938 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN K 942 " --> pdb=" O THR K 939 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL K 947 " --> pdb=" O LEU K 944 " (cutoff:3.500A) Processing helix chain 'K' and resid 956 through 972 removed outlier: 3.523A pdb=" N GLY K 964 " --> pdb=" O LYS K 960 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL K 970 " --> pdb=" O ILE K 966 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR K 971 " --> pdb=" O LYS K 967 " (cutoff:3.500A) Processing helix chain 'K' and resid 975 through 990 removed outlier: 3.511A pdb=" N LYS K 980 " --> pdb=" O ALA K 976 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N HIS K 981 " --> pdb=" O HIS K 977 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN K 983 " --> pdb=" O ALA K 979 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LEU K 984 " --> pdb=" O LYS K 980 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET K 986 " --> pdb=" O VAL K 982 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA K 988 " --> pdb=" O LEU K 984 " (cutoff:3.500A) Processing helix chain 'K' and resid 994 through 999 Processing helix chain 'K' and resid 1001 through 1014 removed outlier: 3.541A pdb=" N PHE K1011 " --> pdb=" O LEU K1007 " (cutoff:3.500A) Processing helix chain 'K' and resid 1019 through 1023 removed outlier: 3.761A pdb=" N LEU K1023 " --> pdb=" O LEU K1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1019 through 1023' Processing helix chain 'K' and resid 1027 through 1042 removed outlier: 4.059A pdb=" N VAL K1031 " --> pdb=" O GLU K1027 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN K1034 " --> pdb=" O ARG K1030 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE K1035 " --> pdb=" O VAL K1031 " (cutoff:3.500A) Processing helix chain 'K' and resid 1073 through 1076 No H-bonds generated for 'chain 'K' and resid 1073 through 1076' Processing helix chain 'K' and resid 1125 through 1127 No H-bonds generated for 'chain 'K' and resid 1125 through 1127' Processing helix chain 'K' and resid 1231 through 1233 No H-bonds generated for 'chain 'K' and resid 1231 through 1233' Processing helix chain 'M' and resid 15 through 28 removed outlier: 4.110A pdb=" N GLU M 20 " --> pdb=" O THR M 16 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 35 through 44 removed outlier: 3.833A pdb=" N ASP M 43 " --> pdb=" O ALA M 39 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS M 44 " --> pdb=" O LYS M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 62 No H-bonds generated for 'chain 'M' and resid 59 through 62' Processing helix chain 'M' and resid 64 through 71 Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 120 through 128 removed outlier: 3.828A pdb=" N PHE M 128 " --> pdb=" O ILE M 124 " (cutoff:3.500A) Processing helix chain 'z' and resid 183 through 198 removed outlier: 3.710A pdb=" N GLN z 187 " --> pdb=" O ALA z 183 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN z 188 " --> pdb=" O ALA z 184 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU z 189 " --> pdb=" O GLN z 185 " (cutoff:3.500A) Processing helix chain 'z' and resid 205 through 207 No H-bonds generated for 'chain 'z' and resid 205 through 207' Processing helix chain 'z' and resid 210 through 224 Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.505A pdb=" N LEU A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 66 removed outlier: 3.624A pdb=" N GLU A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.657A pdb=" N LYS A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 137 removed outlier: 3.699A pdb=" N THR A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 136 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 186 removed outlier: 3.541A pdb=" N GLY A 172 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 173 " --> pdb=" O HIS A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.502A pdb=" N GLU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 92 through 101 removed outlier: 3.661A pdb=" N PHE C 97 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 98 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 100 " --> pdb=" O PHE C 96 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N SER C 101 " --> pdb=" O PHE C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 161 Processing helix chain 'C' and resid 208 through 216 removed outlier: 3.521A pdb=" N LEU C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.688A pdb=" N THR C 240 " --> pdb=" O PHE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 265 through 274 removed outlier: 3.691A pdb=" N PHE C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR C 270 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASP C 271 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N HIS C 272 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 273 " --> pdb=" O PHE C 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 62 removed outlier: 3.501A pdb=" N MET V 62 " --> pdb=" O ALA V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 75 removed outlier: 3.639A pdb=" N LEU V 70 " --> pdb=" O ASP V 66 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'b' and resid 43 through 47 removed outlier: 3.523A pdb=" N THR b 44 " --> pdb=" O VAL b 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 65 through 70 removed outlier: 3.587A pdb=" N ARG B 65 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 120 through 128 removed outlier: 3.651A pdb=" N LEU B 134 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS B 219 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG B 136 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N MET B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 29 through 34 removed outlier: 3.777A pdb=" N GLY B 45 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'c' and resid 55 through 58 removed outlier: 7.040A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'c' and resid 19 through 21 removed outlier: 3.509A pdb=" N GLY c 19 " --> pdb=" O GLN c 29 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 70 through 72 Processing sheet with id= H, first strand: chain 'E' and resid 121 through 125 removed outlier: 3.682A pdb=" N ASP E 171 " --> pdb=" O GLN E 161 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 128 through 131 removed outlier: 3.532A pdb=" N LYS E 128 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 225 through 227 removed outlier: 6.562A pdb=" N HIS E 209 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG E 198 " --> pdb=" O VAL E 207 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL E 207 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 123 through 129 Processing sheet with id= L, first strand: chain 'H' and resid 47 through 53 removed outlier: 6.298A pdb=" N HIS H 91 " --> pdb=" O ILE H 60 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE H 62 " --> pdb=" O HIS H 91 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL H 93 " --> pdb=" O ILE H 62 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL H 64 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE H 95 " --> pdb=" O VAL H 64 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 185 through 189 removed outlier: 8.461A pdb=" N ASN H 186 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE H 154 " --> pdb=" O ASN H 186 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N GLU H 188 " --> pdb=" O ILE H 154 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL H 156 " --> pdb=" O GLU H 188 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 12 through 17 removed outlier: 6.829A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 72 through 77 Processing sheet with id= P, first strand: chain 'G' and resid 159 through 162 Processing sheet with id= Q, first strand: chain 'G' and resid 54 through 57 Processing sheet with id= R, first strand: chain 'Z' and resid 98 through 101 removed outlier: 6.704A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Y' and resid 6 through 9 Processing sheet with id= T, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id= U, first strand: chain 'x' and resid 75 through 79 removed outlier: 3.514A pdb=" N GLN x 106 " --> pdb=" O ARG x 119 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'x' and resid 159 through 164 Processing sheet with id= W, first strand: chain 'X' and resid 80 through 84 removed outlier: 3.535A pdb=" N GLU X 53 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA X 103 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL X 122 " --> pdb=" O ALA X 103 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= Y, first strand: chain 'W' and resid 72 through 74 removed outlier: 6.764A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'u' and resid 220 through 222 removed outlier: 9.418A pdb=" N LEU u 221 " --> pdb=" O TYR u 185 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU u 187 " --> pdb=" O LEU u 221 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER u 137 " --> pdb=" O GLN u 120 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN u 120 " --> pdb=" O SER u 137 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'u' and resid 252 through 254 Processing sheet with id= AB, first strand: chain 'u' and resid 257 through 264 removed outlier: 7.532A pdb=" N VAL u 269 " --> pdb=" O SER u 263 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'u' and resid 629 through 631 removed outlier: 6.042A pdb=" N VAL u 597 " --> pdb=" O LEU u 684 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU u 684 " --> pdb=" O VAL u 597 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ARG u 599 " --> pdb=" O GLY u 682 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLY u 682 " --> pdb=" O ARG u 599 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU u 667 " --> pdb=" O ILE u 679 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR u 681 " --> pdb=" O VAL u 665 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL u 665 " --> pdb=" O THR u 681 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLN u 670 " --> pdb=" O GLU u 613 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N GLU u 613 " --> pdb=" O GLN u 670 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'u' and resid 764 through 773 removed outlier: 4.432A pdb=" N VAL u 693 " --> pdb=" O VAL u 773 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL u 712 " --> pdb=" O PHE u 704 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE u 706 " --> pdb=" O MET u 710 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET u 710 " --> pdb=" O ILE u 706 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET u 751 " --> pdb=" O VAL u 713 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER u 754 " --> pdb=" O ILE u 741 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE u 741 " --> pdb=" O SER u 754 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'T' and resid 81 through 83 Processing sheet with id= AF, first strand: chain 'T' and resid 113 through 115 Processing sheet with id= AG, first strand: chain 'S' and resid 12 through 15 Processing sheet with id= AH, first strand: chain 'Q' and resid 9 through 15 Processing sheet with id= AI, first strand: chain 'P' and resid 76 through 78 removed outlier: 3.534A pdb=" N TYR P 97 " --> pdb=" O THR P 78 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 52 through 56 removed outlier: 6.908A pdb=" N VAL O 44 " --> pdb=" O ILE O 53 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG O 55 " --> pdb=" O VAL O 42 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL O 42 " --> pdb=" O ARG O 55 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA O 92 " --> pdb=" O GLY O 29 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N CYS O 31 " --> pdb=" O ALA O 92 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N HIS O 94 " --> pdb=" O CYS O 31 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE O 33 " --> pdb=" O HIS O 94 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS O 96 " --> pdb=" O ILE O 33 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ALA O 35 " --> pdb=" O LYS O 96 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARG O 98 " --> pdb=" O ALA O 35 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU O 130 " --> pdb=" O ILE O 95 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'L' and resid 125 through 129 removed outlier: 18.285A pdb=" N ILE L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 14.971A pdb=" N LEU L 93 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N SER L 74 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP L 91 " --> pdb=" O SER L 74 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL L 87 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG L 101 " --> pdb=" O ILE L 96 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG L 139 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N HIS L 112 " --> pdb=" O ARG L 139 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN L 141 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 62 through 67 Processing sheet with id= AM, first strand: chain 'I' and resid 187 through 189 removed outlier: 5.996A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 42 through 47 removed outlier: 6.370A pdb=" N HIS I 44 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA I 57 " --> pdb=" O HIS I 44 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL I 46 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR I 55 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'r' and resid 30 through 32 Processing sheet with id= AP, first strand: chain 'r' and resid 24 through 29 removed outlier: 3.635A pdb=" N THR r 97 " --> pdb=" O GLN r 26 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU r 95 " --> pdb=" O THR r 28 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'q' and resid 184 through 190 removed outlier: 4.494A pdb=" N PHE q 200 " --> pdb=" O LEU q 163 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU q 163 " --> pdb=" O PHE q 200 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY q 118 " --> pdb=" O TYR q 56 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ILE q 122 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR q 77 " --> pdb=" O LEU q 57 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASP q 59 " --> pdb=" O TYR q 77 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL q 79 " --> pdb=" O ASP q 59 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP q 99 " --> pdb=" O GLY q 80 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASP q 82 " --> pdb=" O ASP q 99 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU q 101 " --> pdb=" O ASP q 82 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'M' and resid 75 through 79 removed outlier: 3.640A pdb=" N LEU M 49 " --> pdb=" O VAL M 111 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'f' and resid 132 through 134 Processing sheet with id= AT, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.475A pdb=" N LEU A 121 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE A 77 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL A 123 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL A 124 " --> pdb=" O PRO A 143 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE A 145 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE A 159 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS A 148 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE A 161 " --> pdb=" O CYS A 148 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'C' and resid 137 through 144 removed outlier: 3.890A pdb=" N GLY C 119 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS C 114 " --> pdb=" O ARG C 121 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG C 123 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 112 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'C' and resid 184 through 188 Processing sheet with id= AW, first strand: chain 'V' and resid 32 through 37 removed outlier: 3.543A pdb=" N ILE V 55 " --> pdb=" O ILE V 32 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL V 36 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS V 51 " --> pdb=" O VAL V 36 " (cutoff:3.500A) 1737 hydrogen bonds defined for protein. 4896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1268 hydrogen bonds 1952 hydrogen bond angles 0 basepair planarities 514 basepair parallelities 831 stacking parallelities Total time for adding SS restraints: 58.03 Time building geometry restraints manager: 30.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 10337 1.31 - 1.44: 32461 1.44 - 1.56: 42744 1.56 - 1.69: 3132 1.69 - 1.82: 370 Bond restraints: 89044 Sorted by residual: bond pdb=" C ASP u 348 " pdb=" N PRO u 349 " ideal model delta sigma weight residual 1.331 1.384 -0.052 1.27e-02 6.20e+03 1.70e+01 bond pdb=" C2 SAH q 301 " pdb=" N3 SAH q 301 " ideal model delta sigma weight residual 1.322 1.374 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" C8 SAH q 301 " pdb=" N7 SAH q 301 " ideal model delta sigma weight residual 1.299 1.348 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C2 SAH q 301 " pdb=" N1 SAH q 301 " ideal model delta sigma weight residual 1.330 1.376 -0.046 2.00e-02 2.50e+03 5.21e+00 bond pdb=" CB ASN J 143 " pdb=" CG ASN J 143 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.08e+00 ... (remaining 89039 not shown) Histogram of bond angle deviations from ideal: 89.26 - 98.48: 6 98.48 - 107.70: 13643 107.70 - 116.93: 59426 116.93 - 126.15: 49277 126.15 - 135.37: 5383 Bond angle restraints: 127735 Sorted by residual: angle pdb=" N VAL A 140 " pdb=" CA VAL A 140 " pdb=" C VAL A 140 " ideal model delta sigma weight residual 111.88 105.47 6.41 1.06e+00 8.90e-01 3.66e+01 angle pdb=" N ILE L 4 " pdb=" CA ILE L 4 " pdb=" C ILE L 4 " ideal model delta sigma weight residual 113.71 108.47 5.24 9.50e-01 1.11e+00 3.04e+01 angle pdb=" C LEU T 45 " pdb=" N ALA T 46 " pdb=" CA ALA T 46 " ideal model delta sigma weight residual 121.48 131.92 -10.44 2.04e+00 2.40e-01 2.62e+01 angle pdb=" N SER O 137 " pdb=" CA SER O 137 " pdb=" C SER O 137 " ideal model delta sigma weight residual 110.97 105.48 5.49 1.09e+00 8.42e-01 2.53e+01 angle pdb=" O3' U 21304 " pdb=" C3' U 21304 " pdb=" C2' U 21304 " ideal model delta sigma weight residual 113.70 120.52 -6.82 1.50e+00 4.44e-01 2.07e+01 ... (remaining 127730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 50879 35.92 - 71.83: 3513 71.83 - 107.75: 479 107.75 - 143.67: 19 143.67 - 179.58: 25 Dihedral angle restraints: 54915 sinusoidal: 36557 harmonic: 18358 Sorted by residual: 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 22.70 177.30 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 427 " pdb=" C1' U 2 427 " pdb=" N1 U 2 427 " pdb=" C2 U 2 427 " ideal model delta sinusoidal sigma weight residual -160.00 12.87 -172.87 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U 2 823 " pdb=" C1' U 2 823 " pdb=" N1 U 2 823 " pdb=" C2 U 2 823 " ideal model delta sinusoidal sigma weight residual 200.00 30.54 169.46 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 54912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 14250 0.078 - 0.156: 1251 0.156 - 0.233: 81 0.233 - 0.311: 28 0.311 - 0.389: 7 Chirality restraints: 15617 Sorted by residual: chirality pdb=" CG LEU x 230 " pdb=" CB LEU x 230 " pdb=" CD1 LEU x 230 " pdb=" CD2 LEU x 230 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.78e+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 -2.39 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" C1' U 2 918 " pdb=" O4' U 2 918 " pdb=" C2' U 2 918 " pdb=" N1 U 2 918 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 15614 not shown) Planarity restraints: 10365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' G7M 21639 " -0.665 2.00e-02 2.50e+03 5.00e-01 5.63e+03 pdb=" C4' G7M 21639 " 0.247 2.00e-02 2.50e+03 pdb=" O4' G7M 21639 " 0.433 2.00e-02 2.50e+03 pdb=" C3' G7M 21639 " -0.231 2.00e-02 2.50e+03 pdb=" O3' G7M 21639 " 0.864 2.00e-02 2.50e+03 pdb=" C2' G7M 21639 " -0.608 2.00e-02 2.50e+03 pdb=" O2' G7M 21639 " -0.486 2.00e-02 2.50e+03 pdb=" C1' G7M 21639 " 0.393 2.00e-02 2.50e+03 pdb=" N9 G7M 21639 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 21374 " 0.000 2.00e-02 2.50e+03 3.77e-02 3.20e+01 pdb=" N1 C 21374 " -0.001 2.00e-02 2.50e+03 pdb=" C2 C 21374 " -0.090 2.00e-02 2.50e+03 pdb=" O2 C 21374 " 0.061 2.00e-02 2.50e+03 pdb=" N3 C 21374 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C 21374 " -0.018 2.00e-02 2.50e+03 pdb=" N4 C 21374 " 0.013 2.00e-02 2.50e+03 pdb=" C5 C 21374 " 0.016 2.00e-02 2.50e+03 pdb=" C6 C 21374 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 97 " 0.068 5.00e-02 4.00e+02 1.05e-01 1.76e+01 pdb=" N PRO A 98 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 98 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 98 " 0.056 5.00e-02 4.00e+02 ... (remaining 10362 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 3081 2.67 - 3.23: 71151 3.23 - 3.78: 148815 3.78 - 4.34: 198852 4.34 - 4.90: 286835 Nonbonded interactions: 708734 Sorted by model distance: nonbonded pdb=" O4 U 2 749 " pdb=" O6 G 2 793 " model vdw 2.111 3.040 nonbonded pdb=" O4 U 21730 " pdb=" O6 G 21805 " model vdw 2.140 3.040 nonbonded pdb=" O6 G 21302 " pdb=" O4 U 21307 " model vdw 2.143 2.432 nonbonded pdb=" O2' U 21314 " pdb=" O PHE w 281 " model vdw 2.145 2.440 nonbonded pdb=" O6 G 21286 " pdb="ZN ZN 21901 " model vdw 2.184 2.230 ... (remaining 708729 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 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: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 13.110 Check model and map are aligned: 0.920 Set scattering table: 0.560 Process input model: 211.050 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.250 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 233.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 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 : 0.005 0.072 89044 Z= 0.337 Angle : 0.838 15.892 127735 Z= 0.418 Chirality : 0.046 0.389 15617 Planarity : 0.008 0.500 10365 Dihedral : 20.595 179.585 43019 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.06 % Favored : 95.93 % Rotamer: Outliers : 0.02 % Allowed : 0.39 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.05 % Twisted Proline : 0.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.09), residues: 6238 helix: -2.62 (0.07), residues: 2523 sheet: -0.25 (0.17), residues: 872 loop : -1.13 (0.11), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 623 HIS 0.010 0.002 HIS K 306 PHE 0.053 0.002 PHE K 417 TYR 0.034 0.002 TYR O 72 ARG 0.017 0.001 ARG c 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 930 time to evaluate : 6.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 931 average time/residue: 0.8059 time to fit residues: 1279.8845 Evaluate side-chains 669 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 668 time to evaluate : 5.242 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5906 time to fit residues: 7.7047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 657 optimal weight: 20.0000 chunk 590 optimal weight: 5.9990 chunk 327 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 398 optimal weight: 0.8980 chunk 315 optimal weight: 0.0000 chunk 610 optimal weight: 50.0000 chunk 236 optimal weight: 6.9990 chunk 371 optimal weight: 1.9990 chunk 454 optimal weight: 9.9990 chunk 707 optimal weight: 10.0000 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN e 39 ASN G 163 ASN Y 15 ASN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 61 GLN ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 125 HIS Q 48 GLN N 90 HIS L 19 ASN L 39 ASN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 262 GLN ** K 506 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 727 GLN K 851 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6687 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 89044 Z= 0.161 Angle : 0.599 12.349 127735 Z= 0.304 Chirality : 0.037 0.330 15617 Planarity : 0.005 0.113 10365 Dihedral : 21.542 179.659 30112 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.92 % Favored : 97.07 % Rotamer: Outliers : 1.21 % Allowed : 8.23 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.05 % Twisted Proline : 0.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.10), residues: 6238 helix: -0.77 (0.09), residues: 2538 sheet: 0.01 (0.18), residues: 823 loop : -0.94 (0.11), residues: 2877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 30 HIS 0.011 0.001 HIS P 54 PHE 0.023 0.001 PHE q 146 TYR 0.017 0.001 TYR q 143 ARG 0.010 0.000 ARG V 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 735 time to evaluate : 5.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 37 residues processed: 767 average time/residue: 0.8060 time to fit residues: 1074.1680 Evaluate side-chains 697 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 660 time to evaluate : 5.191 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.6593 time to fit residues: 52.5586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 393 optimal weight: 0.2980 chunk 219 optimal weight: 2.9990 chunk 588 optimal weight: 7.9990 chunk 481 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 708 optimal weight: 20.0000 chunk 765 optimal weight: 4.9990 chunk 631 optimal weight: 6.9990 chunk 702 optimal weight: 40.0000 chunk 241 optimal weight: 7.9990 chunk 568 optimal weight: 20.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 51 GLN b 65 GLN B 118 GLN B 208 HIS B 232 HIS ** c 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN F 82 ASN G 163 ASN Y 15 ASN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 65 GLN ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 170 GLN ** q 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 HIS K 886 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 89044 Z= 0.291 Angle : 0.640 12.966 127735 Z= 0.321 Chirality : 0.040 0.344 15617 Planarity : 0.005 0.111 10365 Dihedral : 21.500 179.337 30112 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 1.05 % Allowed : 11.85 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.05 % Twisted Proline : 0.72 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.10), residues: 6238 helix: -0.07 (0.10), residues: 2527 sheet: -0.12 (0.18), residues: 832 loop : -0.86 (0.11), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP u 133 HIS 0.007 0.001 HIS X 46 PHE 0.025 0.002 PHE J 159 TYR 0.017 0.001 TYR q 56 ARG 0.008 0.001 ARG X 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 686 time to evaluate : 5.729 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: 57 outliers final: 34 residues processed: 720 average time/residue: 0.8020 time to fit residues: 1001.0259 Evaluate side-chains 656 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 622 time to evaluate : 5.181 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.6189 time to fit residues: 46.9226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 700 optimal weight: 8.9990 chunk 532 optimal weight: 2.9990 chunk 367 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 338 optimal weight: 0.0980 chunk 475 optimal weight: 0.2980 chunk 711 optimal weight: 9.9990 chunk 752 optimal weight: 5.9990 chunk 371 optimal weight: 1.9990 chunk 674 optimal weight: 20.0000 chunk 202 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 26 GLN ** c 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN G 163 ASN Y 15 ASN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 595 ASN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 ASN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 89044 Z= 0.152 Angle : 0.558 12.240 127735 Z= 0.282 Chirality : 0.036 0.334 15617 Planarity : 0.004 0.111 10365 Dihedral : 21.430 179.502 30112 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.08 % Favored : 96.91 % Rotamer: Outliers : 0.99 % Allowed : 13.12 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.05 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.11), residues: 6238 helix: 0.36 (0.11), residues: 2522 sheet: -0.03 (0.18), residues: 823 loop : -0.76 (0.11), residues: 2893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP q 127 HIS 0.010 0.001 HIS r 86 PHE 0.018 0.001 PHE J 147 TYR 0.013 0.001 TYR Z 109 ARG 0.006 0.000 ARG c 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 682 time to evaluate : 5.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 26 residues processed: 715 average time/residue: 0.8138 time to fit residues: 1014.5713 Evaluate side-chains 656 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 630 time to evaluate : 5.206 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.6304 time to fit residues: 38.3186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 627 optimal weight: 10.0000 chunk 427 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 560 optimal weight: 0.9980 chunk 310 optimal weight: 5.9990 chunk 642 optimal weight: 50.0000 chunk 520 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 384 optimal weight: 5.9990 chunk 675 optimal weight: 50.0000 chunk 190 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN Y 15 ASN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 70 ASN ** u 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 GLN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 130 ASN ** q 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1029 HIS K1127 GLN C 134 ASN V 2 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 89044 Z= 0.328 Angle : 0.650 12.738 127735 Z= 0.326 Chirality : 0.041 0.353 15617 Planarity : 0.005 0.112 10365 Dihedral : 21.459 179.618 30112 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.83 % Rotamer: Outliers : 1.29 % Allowed : 14.78 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.05 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.11), residues: 6238 helix: 0.43 (0.11), residues: 2538 sheet: -0.17 (0.18), residues: 833 loop : -0.80 (0.11), residues: 2867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP u 133 HIS 0.009 0.001 HIS r 86 PHE 0.029 0.002 PHE r 41 TYR 0.015 0.001 TYR u 294 ARG 0.008 0.000 ARG X 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 659 time to evaluate : 5.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 41 residues processed: 700 average time/residue: 0.8490 time to fit residues: 1032.8993 Evaluate side-chains 663 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 622 time to evaluate : 5.220 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.6854 time to fit residues: 59.8342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 253 optimal weight: 5.9990 chunk 678 optimal weight: 0.0270 chunk 148 optimal weight: 30.0000 chunk 442 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 753 optimal weight: 6.9990 chunk 625 optimal weight: 6.9990 chunk 348 optimal weight: 40.0000 chunk 62 optimal weight: 5.9990 chunk 249 optimal weight: 8.9990 chunk 395 optimal weight: 8.9990 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 595 ASN ** T 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 247 HIS C 134 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 89044 Z= 0.322 Angle : 0.651 13.652 127735 Z= 0.326 Chirality : 0.041 0.361 15617 Planarity : 0.005 0.112 10365 Dihedral : 21.474 179.448 30112 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.06 % Rotamer: Outliers : 0.92 % Allowed : 16.01 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.05 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.11), residues: 6238 helix: 0.49 (0.11), residues: 2534 sheet: -0.30 (0.18), residues: 828 loop : -0.80 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP u 133 HIS 0.009 0.001 HIS X 46 PHE 0.036 0.002 PHE q 146 TYR 0.015 0.001 TYR q 18 ARG 0.012 0.000 ARG K 845 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 653 time to evaluate : 5.203 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: 50 outliers final: 19 residues processed: 681 average time/residue: 0.8063 time to fit residues: 951.6986 Evaluate side-chains 640 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 621 time to evaluate : 5.211 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.6340 time to fit residues: 29.5470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 726 optimal weight: 40.0000 chunk 84 optimal weight: 7.9990 chunk 429 optimal weight: 7.9990 chunk 550 optimal weight: 0.9980 chunk 426 optimal weight: 5.9990 chunk 634 optimal weight: 40.0000 chunk 420 optimal weight: 0.9990 chunk 750 optimal weight: 5.9990 chunk 469 optimal weight: 6.9990 chunk 457 optimal weight: 0.0370 chunk 346 optimal weight: 50.0000 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN c 45 ASN E 197 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN Y 15 ASN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 595 ASN ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 89044 Z= 0.242 Angle : 0.611 16.330 127735 Z= 0.308 Chirality : 0.038 0.338 15617 Planarity : 0.004 0.112 10365 Dihedral : 21.448 178.681 30112 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.83 % Allowed : 16.89 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.05 % Twisted Proline : 0.36 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 6238 helix: 0.60 (0.11), residues: 2525 sheet: -0.28 (0.18), residues: 831 loop : -0.76 (0.11), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 175 HIS 0.007 0.001 HIS r 86 PHE 0.029 0.001 PHE q 145 TYR 0.017 0.001 TYR q 18 ARG 0.015 0.000 ARG c 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 653 time to evaluate : 5.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 22 residues processed: 680 average time/residue: 0.8641 time to fit residues: 1021.7523 Evaluate side-chains 651 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 629 time to evaluate : 5.503 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.6543 time to fit residues: 34.2584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 464 optimal weight: 30.0000 chunk 299 optimal weight: 3.9990 chunk 448 optimal weight: 9.9990 chunk 226 optimal weight: 2.9990 chunk 147 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 477 optimal weight: 8.9990 chunk 511 optimal weight: 0.0980 chunk 371 optimal weight: 0.7980 chunk 69 optimal weight: 30.0000 chunk 590 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN E 197 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN Y 15 ASN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 GLN N 90 HIS ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 89044 Z= 0.269 Angle : 0.628 12.654 127735 Z= 0.316 Chirality : 0.039 0.343 15617 Planarity : 0.004 0.112 10365 Dihedral : 21.441 179.148 30112 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.62 % Allowed : 17.72 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.11), residues: 6238 helix: 0.68 (0.11), residues: 2517 sheet: -0.34 (0.18), residues: 830 loop : -0.77 (0.11), residues: 2891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 175 HIS 0.008 0.001 HIS r 86 PHE 0.026 0.001 PHE J 147 TYR 0.020 0.001 TYR q 18 ARG 0.013 0.000 ARG K1001 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 631 time to evaluate : 5.289 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: 34 outliers final: 15 residues processed: 651 average time/residue: 0.8323 time to fit residues: 941.7354 Evaluate side-chains 635 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 620 time to evaluate : 5.314 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6254 time to fit residues: 24.7751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 683 optimal weight: 9.9990 chunk 719 optimal weight: 30.0000 chunk 656 optimal weight: 0.5980 chunk 699 optimal weight: 50.0000 chunk 421 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 549 optimal weight: 0.9990 chunk 214 optimal weight: 0.4980 chunk 632 optimal weight: 30.0000 chunk 661 optimal weight: 10.0000 chunk 697 optimal weight: 30.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN E 197 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN Y 15 ASN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 103 ASN N 58 HIS ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 398 HIS K 851 HIS C 134 ASN C 272 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 89044 Z= 0.171 Angle : 0.585 17.664 127735 Z= 0.294 Chirality : 0.037 0.332 15617 Planarity : 0.004 0.112 10365 Dihedral : 21.383 179.074 30112 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.40 % Allowed : 18.10 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.11), residues: 6238 helix: 0.75 (0.11), residues: 2521 sheet: -0.22 (0.18), residues: 831 loop : -0.70 (0.11), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 175 HIS 0.008 0.001 HIS r 86 PHE 0.053 0.001 PHE F 163 TYR 0.013 0.001 TYR q 18 ARG 0.011 0.000 ARG K1001 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 648 time to evaluate : 5.247 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 outliers start: 22 outliers final: 12 residues processed: 658 average time/residue: 0.8321 time to fit residues: 947.0763 Evaluate side-chains 636 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 624 time to evaluate : 5.253 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.6677 time to fit residues: 21.5832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 459 optimal weight: 30.0000 chunk 739 optimal weight: 9.9990 chunk 451 optimal weight: 20.0000 chunk 350 optimal weight: 50.0000 chunk 514 optimal weight: 3.9990 chunk 776 optimal weight: 5.9990 chunk 714 optimal weight: 0.9990 chunk 618 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 477 optimal weight: 0.9980 chunk 378 optimal weight: 0.0010 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 GLN E 197 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN Y 15 ASN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 105 ASN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 89044 Z= 0.219 Angle : 0.608 13.485 127735 Z= 0.305 Chirality : 0.038 0.329 15617 Planarity : 0.004 0.112 10365 Dihedral : 21.363 178.340 30112 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.20 % Allowed : 18.60 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.11), residues: 6238 helix: 0.75 (0.11), residues: 2523 sheet: -0.19 (0.18), residues: 818 loop : -0.70 (0.11), residues: 2897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 175 HIS 0.008 0.001 HIS r 86 PHE 0.039 0.001 PHE q 146 TYR 0.014 0.001 TYR Z 65 ARG 0.011 0.000 ARG K1001 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12476 Ramachandran restraints generated. 6238 Oldfield, 0 Emsley, 6238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 633 time to evaluate : 5.355 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: 11 outliers final: 5 residues processed: 640 average time/residue: 0.8407 time to fit residues: 934.9854 Evaluate side-chains 621 residues out of total 5477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 616 time to evaluate : 5.178 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6727 time to fit residues: 13.1066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 779 random chunks: chunk 490 optimal weight: 0.0670 chunk 658 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 chunk 569 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 618 optimal weight: 40.0000 chunk 259 optimal weight: 3.9990 chunk 635 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 114 optimal weight: 80.0000 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 159 GLN F 118 ASN ** H 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN Y 15 ASN ** x 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.162121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.144378 restraints weight = 166711.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.140471 restraints weight = 168068.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136084 restraints weight = 169247.981| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 89044 Z= 0.343 Angle : 0.682 13.470 127735 Z= 0.340 Chirality : 0.041 0.418 15617 Planarity : 0.005 0.113 10365 Dihedral : 21.439 179.947 30112 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.28 % Allowed : 18.71 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 6238 helix: 0.65 (0.11), residues: 2524 sheet: -0.31 (0.18), residues: 811 loop : -0.81 (0.11), residues: 2903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP w 225 HIS 0.009 0.001 HIS X 46 PHE 0.032 0.002 PHE W 99 TYR 0.020 0.001 TYR Z 65 ARG 0.010 0.001 ARG K1001 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16349.96 seconds wall clock time: 291 minutes 7.46 seconds (17467.46 seconds total)