Starting phenix.real_space_refine on Fri Mar 15 05:33:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfd_18382/03_2024/8qfd_18382.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfd_18382/03_2024/8qfd_18382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfd_18382/03_2024/8qfd_18382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfd_18382/03_2024/8qfd_18382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfd_18382/03_2024/8qfd_18382.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qfd_18382/03_2024/8qfd_18382.pdb" } resolution = 2.2 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= 1.000 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 3392 5.49 5 Mg 161 5.21 5 S 229 5.16 5 C 64223 2.51 5 N 23183 2.21 5 O 34179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 80": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "G ASP 228": "OD1" <-> "OD2" Residue "H ASP 11": "OD1" <-> "OD2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H GLU 120": "OE1" <-> "OE2" Residue "I GLU 45": "OE1" <-> "OE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I GLU 180": "OE1" <-> "OE2" Residue "J ASP 101": "OD1" <-> "OD2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L GLU 79": "OE1" <-> "OE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L GLU 172": "OE1" <-> "OE2" Residue "M GLU 126": "OE1" <-> "OE2" Residue "O GLU 162": "OE1" <-> "OE2" Residue "P ASP 7": "OD1" <-> "OD2" Residue "P ASP 79": "OD1" <-> "OD2" Residue "P GLU 128": "OE1" <-> "OE2" Residue "P GLU 132": "OE1" <-> "OE2" Residue "P GLU 144": "OE1" <-> "OE2" Residue "Q GLU 17": "OE1" <-> "OE2" Residue "Q PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 91": "OE1" <-> "OE2" Residue "R GLU 111": "OE1" <-> "OE2" Residue "R ASP 116": "OD1" <-> "OD2" Residue "S PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 41": "OD1" <-> "OD2" Residue "T GLU 137": "OE1" <-> "OE2" Residue "T GLU 157": "OE1" <-> "OE2" Residue "U PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 30": "OD1" <-> "OD2" Residue "V ASP 92": "OD1" <-> "OD2" Residue "X GLU 91": "OE1" <-> "OE2" Residue "X ASP 118": "OD1" <-> "OD2" Residue "X GLU 133": "OE1" <-> "OE2" Residue "X ASP 145": "OD1" <-> "OD2" Residue "X ASP 148": "OD1" <-> "OD2" Residue "Z ASP 30": "OD1" <-> "OD2" Residue "Z ASP 92": "OD1" <-> "OD2" Residue "Z GLU 113": "OE1" <-> "OE2" Residue "b GLU 30": "OE1" <-> "OE2" Residue "c GLU 59": "OE1" <-> "OE2" Residue "d ASP 61": "OD1" <-> "OD2" Residue "f GLU 31": "OE1" <-> "OE2" Residue "g ASP 89": "OD1" <-> "OD2" Residue "g GLU 98": "OE1" <-> "OE2" Residue "h GLU 16": "OE1" <-> "OE2" Residue "h GLU 27": "OE1" <-> "OE2" Residue "i GLU 46": "OE1" <-> "OE2" Residue "i GLU 89": "OE1" <-> "OE2" Residue "l PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 71": "OE1" <-> "OE2" Residue "r ASP 56": "OD1" <-> "OD2" Residue "s GLU 442": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 125372 Number of models: 1 Model: "" Number of chains: 97 Chain: "5" Number of atoms: 67136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3130, 67136 Classifications: {'RNA': 3130} Modifications used: {'rna2p_pur': 330, 'rna2p_pyr': 184, 'rna3p_pur': 1409, 'rna3p_pyr': 1207} Link IDs: {'rna2p': 514, 'rna3p': 2615} Chain breaks: 45 Chain: "7" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2538 Classifications: {'RNA': 119} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 52} Link IDs: {'rna2p': 12, 'rna3p': 106} Chain: "8" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 3071 Classifications: {'RNA': 144} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 59, 'rna3p_pyr': 61} Link IDs: {'rna2p': 23, 'rna3p': 120} Chain breaks: 3 Chain: "A" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1881 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 231} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3176 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 379} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2832 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 336} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2351 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 283} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1632 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1798 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 212} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1722 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1506 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 185} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1627 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1358 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 164} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1500 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 173} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1116 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 131} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "N" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1695 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1644 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 191} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1225 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 144} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Q" Number of atoms: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1509 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1229 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 145} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1444 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1276 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 148} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "U" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 791 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "V" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 973 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "W" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 515 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 109} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1063 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Z" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "a" Number of atoms: 1158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1158 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "b" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 526 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "c" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 713 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "d" Number of atoms: 852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 852 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 99} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1039 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 121} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 863 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "g" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 814 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "h" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 993 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "i" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 776 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 3, 'TRANS': 94} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "j" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 82} Chain: "k" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 527 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 65} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "l" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 438 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "m" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 418 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 48} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 810 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "p" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 666 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 87} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "r" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "s" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 99 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "5" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 151 Unusual residues: {' MG': 151} Classifications: {'undetermined': 151} Link IDs: {None: 150} Chain: "7" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1643, 1643 Classifications: {'water': 1643} Link IDs: {None: 1642} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "8" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "G" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "L" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "O" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "P" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "Q" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "S" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "V" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "X" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "b" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "d" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "e" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "f" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "g" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "h" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "l" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "o" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "p" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "r" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0CHI SG CYS g 46 87.575 116.337 214.949 1.00 60.75 S ATOM A0CHZ SG CYS g 49 85.698 119.433 215.842 1.00 71.42 S ATOM A0CPA SG CYS g 83 88.458 118.410 218.205 1.00 57.51 S ATOM A0CPU SG CYS g 86 85.525 116.136 218.001 1.00 64.24 S ATOM A0EAZ SG CYS j 19 124.135 99.915 171.347 1.00 23.86 S ATOM A0EBR SG CYS j 22 125.635 99.854 167.839 1.00 26.72 S ATOM A0EEA SG CYS j 34 121.926 100.224 168.322 1.00 27.79 S ATOM A0EET SG CYS j 37 123.529 96.882 169.116 1.00 28.34 S ATOM A0FLS SG CYS m 96 76.898 157.967 81.195 1.00 39.10 S ATOM A0FMI SG CYS m 99 79.627 159.674 83.077 1.00 40.21 S ATOM A0FP0 SG CYS m 110 79.516 159.992 79.297 1.00 37.32 S ATOM A0FQ8 SG CYS m 115 80.520 156.720 80.660 1.00 43.67 S ATOM A0FVM SG CYS o 12 71.330 48.178 108.787 1.00 43.22 S ATOM A0FWA SG CYS o 15 70.277 44.750 107.886 1.00 52.84 S ATOM A0G93 SG CYS o 72 68.005 47.123 110.109 1.00 53.46 S ATOM A0GA4 SG CYS o 77 70.580 45.025 111.502 1.00 68.44 S ATOM A0GNP SG CYS p 39 71.671 120.913 208.787 1.00 38.03 S ATOM A0GOC SG CYS p 42 72.564 123.514 211.420 1.00 46.49 S ATOM A0GRQ SG CYS p 57 74.652 123.125 208.215 1.00 37.33 S ATOM A0GS6 SG CYS p 60 74.914 120.459 210.733 1.00 43.34 S Time building chain proxies: 45.26, per 1000 atoms: 0.36 Number of scatterers: 125372 At special positions: 0 Unit cell: (216.08, 227.18, 273.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 229 16.00 P 3392 15.00 Mg 161 11.99 O 34179 8.00 N 23183 7.00 C 64223 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: 45.53 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 46 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 86 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 49 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 83 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb=" ZN m 201 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 110 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 115 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 99 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 96 " pdb=" ZN o 201 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 15 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 72 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 12 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 77 " pdb=" ZN p 100 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 60 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 39 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 42 " Number of angles added : 30 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11652 Finding SS restraints... Secondary structure from input PDB file: 247 helices and 72 sheets defined 40.1% alpha, 16.6% beta 1124 base pairs and 1669 stacking pairs defined. Time for finding SS restraints: 40.59 Creating SS restraints... Processing helix chain 'A' and resid 8 through 17 removed outlier: 3.694A pdb=" N GLY A 11 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N SER A 14 " --> pdb=" O GLY A 11 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A 15 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 17 " --> pdb=" O SER A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.685A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 209 removed outlier: 3.624A pdb=" N HIS A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 removed outlier: 3.823A pdb=" N PHE B 16 " --> pdb=" O SER B 13 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 17' Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 139 through 157 Processing helix chain 'B' and resid 167 through 171 Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.609A pdb=" N ARG B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 356 through 361 Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 116 through 131 Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 155 through 161 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.689A pdb=" N ILE C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 removed outlier: 4.061A pdb=" N ASN C 198 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 removed outlier: 3.519A pdb=" N HIS C 245 " --> pdb=" O PRO C 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 245' Processing helix chain 'C' and resid 254 through 265 removed outlier: 3.671A pdb=" N LEU C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 321 through 329 Processing helix chain 'C' and resid 330 through 357 removed outlier: 4.334A pdb=" N THR C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.812A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 44 Processing helix chain 'D' and resid 81 through 87 Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 113 Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.709A pdb=" N GLY D 161 " --> pdb=" O ASN D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 200 removed outlier: 3.673A pdb=" N HIS D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 Processing helix chain 'D' and resid 215 through 229 removed outlier: 6.528A pdb=" N GLN D 225 " --> pdb=" O LYS D 221 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR D 226 " --> pdb=" O GLN D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 250 Processing helix chain 'D' and resid 272 through 295 Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 128 through 132 Processing helix chain 'E' and resid 174 through 179 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 209 through 214 Processing helix chain 'E' and resid 239 through 259 removed outlier: 3.883A pdb=" N GLN E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 262 through 269 Processing helix chain 'E' and resid 278 through 282 Processing helix chain 'F' and resid 32 through 81 removed outlier: 3.730A pdb=" N ILE F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 115 Processing helix chain 'F' and resid 128 through 138 Processing helix chain 'F' and resid 148 through 160 Processing helix chain 'F' and resid 173 through 182 removed outlier: 4.081A pdb=" N ILE F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 188 through 199 Processing helix chain 'F' and resid 202 through 210 Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 241 through 250 removed outlier: 3.844A pdb=" N LEU F 245 " --> pdb=" O GLN F 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 55 removed outlier: 3.508A pdb=" N VAL G 55 " --> pdb=" O THR G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 74 removed outlier: 3.714A pdb=" N ALA G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 82 Processing helix chain 'G' and resid 83 through 85 No H-bonds generated for 'chain 'G' and resid 83 through 85' Processing helix chain 'G' and resid 88 through 101 removed outlier: 3.978A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 117 Processing helix chain 'G' and resid 139 through 149 Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'G' and resid 169 through 178 Processing helix chain 'G' and resid 186 through 195 removed outlier: 3.781A pdb=" N LEU G 190 " --> pdb=" O GLY G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 226 removed outlier: 3.632A pdb=" N ALA G 221 " --> pdb=" O LYS G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 234 Processing helix chain 'G' and resid 243 through 255 Processing helix chain 'H' and resid 63 through 68 removed outlier: 3.711A pdb=" N ALA H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 86 removed outlier: 3.852A pdb=" N THR H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 120 Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.692A pdb=" N THR H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 10 removed outlier: 3.794A pdb=" N ARG I 10 " --> pdb=" O ARG I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 81 Processing helix chain 'I' and resid 144 through 157 removed outlier: 4.056A pdb=" N PHE I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 187 Processing helix chain 'I' and resid 205 through 213 removed outlier: 4.125A pdb=" N TRP I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 14 removed outlier: 3.720A pdb=" N GLU J 14 " --> pdb=" O PRO J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 45 removed outlier: 4.047A pdb=" N THR J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 90 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 111 through 116 Processing helix chain 'J' and resid 138 through 143 removed outlier: 3.634A pdb=" N ALA J 142 " --> pdb=" O PHE J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 156 Processing helix chain 'J' and resid 158 through 171 Processing helix chain 'L' and resid 17 through 20 Processing helix chain 'L' and resid 27 through 47 Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'L' and resid 87 through 92 removed outlier: 4.581A pdb=" N ARG L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 123 removed outlier: 3.776A pdb=" N LEU L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'L' and resid 170 through 176 Processing helix chain 'L' and resid 177 through 189 Processing helix chain 'M' and resid 69 through 81 removed outlier: 3.528A pdb=" N VAL M 73 " --> pdb=" O HIS M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 88 Processing helix chain 'M' and resid 89 through 103 Processing helix chain 'M' and resid 105 through 136 Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 16 through 32 removed outlier: 3.562A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 75 through 79 removed outlier: 3.576A pdb=" N GLY N 78 " --> pdb=" O VAL N 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix removed outlier: 3.537A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 162 Processing helix chain 'N' and resid 165 through 170 removed outlier: 3.627A pdb=" N LYS N 170 " --> pdb=" O SER N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 184 removed outlier: 4.265A pdb=" N HIS N 181 " --> pdb=" O HIS N 178 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N HIS N 182 " --> pdb=" O LYS N 179 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR N 183 " --> pdb=" O PHE N 180 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE N 184 " --> pdb=" O HIS N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 197 Processing helix chain 'O' and resid 15 through 29 Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 46 through 59 Processing helix chain 'O' and resid 65 through 69 Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 92 through 101 Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 145 Processing helix chain 'O' and resid 149 through 185 Processing helix chain 'O' and resid 185 through 199 removed outlier: 5.508A pdb=" N LYS O 191 " --> pdb=" O LYS O 187 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N TYR O 192 " --> pdb=" O LYS O 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 54 through 66 Processing helix chain 'P' and resid 69 through 82 Processing helix chain 'P' and resid 99 through 106 Processing helix chain 'P' and resid 113 through 135 Processing helix chain 'P' and resid 137 through 139 No H-bonds generated for 'chain 'P' and resid 137 through 139' Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 52 removed outlier: 3.658A pdb=" N GLN Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE Q 52 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 53 through 58 removed outlier: 6.449A pdb=" N THR Q 56 " --> pdb=" O MET Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 106 through 116 Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 146 through 151 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 20 No H-bonds generated for 'chain 'R' and resid 18 through 20' Processing helix chain 'R' and resid 28 through 33 Processing helix chain 'R' and resid 37 through 47 Processing helix chain 'R' and resid 60 through 72 removed outlier: 3.870A pdb=" N LYS R 72 " --> pdb=" O LEU R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 81 removed outlier: 3.539A pdb=" N ARG R 81 " --> pdb=" O ILE R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 89 Processing helix chain 'R' and resid 90 through 112 Processing helix chain 'R' and resid 116 through 129 Processing helix chain 'R' and resid 134 through 150 Processing helix chain 'S' and resid 36 through 52 Processing helix chain 'S' and resid 55 through 57 No H-bonds generated for 'chain 'S' and resid 55 through 57' Processing helix chain 'S' and resid 101 through 118 Processing helix chain 'S' and resid 120 through 122 No H-bonds generated for 'chain 'S' and resid 120 through 122' Processing helix chain 'S' and resid 133 through 137 Processing helix chain 'S' and resid 139 through 144 Processing helix chain 'T' and resid 27 through 32 Processing helix chain 'T' and resid 54 through 58 Processing helix chain 'T' and resid 102 through 123 removed outlier: 3.572A pdb=" N GLU T 121 " --> pdb=" O LYS T 117 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS T 122 " --> pdb=" O GLU T 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 32 Processing helix chain 'U' and resid 35 through 47 Processing helix chain 'U' and resid 55 through 60 Processing helix chain 'U' and resid 79 through 94 removed outlier: 3.800A pdb=" N LEU U 83 " --> pdb=" O SER U 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 73 Processing helix chain 'V' and resid 122 through 129 Processing helix chain 'V' and resid 129 through 134 Processing helix chain 'W' and resid 33 through 42 Processing helix chain 'W' and resid 45 through 49 Processing helix chain 'W' and resid 52 through 59 Processing helix chain 'X' and resid 72 through 76 Processing helix chain 'X' and resid 83 through 94 removed outlier: 3.671A pdb=" N ASN X 94 " --> pdb=" O ILE X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 118 Processing helix chain 'X' and resid 145 through 154 Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 3.912A pdb=" N LYS Y 28 " --> pdb=" O HIS Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 128 Processing helix chain 'Z' and resid 58 through 66 Processing helix chain 'Z' and resid 97 through 102 removed outlier: 3.599A pdb=" N PHE Z 101 " --> pdb=" O LYS Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 125 removed outlier: 3.685A pdb=" N THR Z 124 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 5 Processing helix chain 'a' and resid 6 through 11 removed outlier: 4.267A pdb=" N LYS a 10 " --> pdb=" O ARG a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 49 Processing helix chain 'a' and resid 64 through 69 removed outlier: 3.544A pdb=" N PHE a 69 " --> pdb=" O ASN a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 82 removed outlier: 5.445A pdb=" N TRP a 79 " --> pdb=" O ASP a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 93 Processing helix chain 'a' and resid 103 through 107 Processing helix chain 'a' and resid 130 through 140 Processing helix chain 'b' and resid 11 through 19 removed outlier: 4.416A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 50 Processing helix chain 'b' and resid 53 through 66 Processing helix chain 'c' and resid 15 through 25 Processing helix chain 'c' and resid 30 through 41 Processing helix chain 'c' and resid 53 through 68 Processing helix chain 'c' and resid 77 through 86 Processing helix chain 'd' and resid 29 through 33 Processing helix chain 'd' and resid 37 through 39 No H-bonds generated for 'chain 'd' and resid 37 through 39' Processing helix chain 'd' and resid 40 through 58 Processing helix chain 'd' and resid 65 through 74 Processing helix chain 'e' and resid 43 through 48 Processing helix chain 'e' and resid 57 through 61 Processing helix chain 'e' and resid 81 through 86 Processing helix chain 'e' and resid 87 through 92 removed outlier: 4.620A pdb=" N MET e 90 " --> pdb=" O VAL e 87 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN e 92 " --> pdb=" O LEU e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 119 removed outlier: 3.722A pdb=" N ALA e 110 " --> pdb=" O LYS e 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 43 removed outlier: 4.308A pdb=" N GLU f 40 " --> pdb=" O ASP f 37 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE f 41 " --> pdb=" O GLU f 38 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 97 Processing helix chain 'g' and resid 60 through 67 Processing helix chain 'g' and resid 68 through 73 removed outlier: 3.924A pdb=" N HIS g 73 " --> pdb=" O THR g 70 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 103 Processing helix chain 'h' and resid 5 through 10 Processing helix chain 'h' and resid 13 through 37 removed outlier: 3.565A pdb=" N VAL h 36 " --> pdb=" O ARG h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 40 through 45 Processing helix chain 'h' and resid 46 through 74 Processing helix chain 'h' and resid 80 through 84 Processing helix chain 'h' and resid 88 through 93 removed outlier: 3.505A pdb=" N ARG h 93 " --> pdb=" O ARG h 89 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 101 Processing helix chain 'h' and resid 104 through 114 Processing helix chain 'i' and resid 25 through 30 removed outlier: 3.624A pdb=" N ARG i 30 " --> pdb=" O SER i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 63 removed outlier: 3.696A pdb=" N VAL i 63 " --> pdb=" O GLU i 59 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 99 Processing helix chain 'j' and resid 6 through 11 removed outlier: 3.783A pdb=" N ARG j 11 " --> pdb=" O PHE j 8 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.723A pdb=" N ASN j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 75 removed outlier: 4.064A pdb=" N ARG j 75 " --> pdb=" O TYR j 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 16 Processing helix chain 'k' and resid 49 through 60 removed outlier: 3.538A pdb=" N GLN k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 20 removed outlier: 3.587A pdb=" N ASN l 20 " --> pdb=" O LYS l 16 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 Processing helix chain 'm' and resid 79 through 91 removed outlier: 3.811A pdb=" N TYR m 89 " --> pdb=" O LEU m 85 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 116 removed outlier: 3.855A pdb=" N CYS m 115 " --> pdb=" O LYS m 112 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 46 Processing helix chain 'p' and resid 8 through 15 removed outlier: 3.733A pdb=" N LYS p 13 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.966A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE p 29 " --> pdb=" O MET p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 89 Processing helix chain 'r' and resid 3 through 11 Processing helix chain 'r' and resid 31 through 35 removed outlier: 4.348A pdb=" N ARG r 35 " --> pdb=" O LEU r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 72 through 75 Processing helix chain 'r' and resid 85 through 99 Processing helix chain 'r' and resid 103 through 105 No H-bonds generated for 'chain 'r' and resid 103 through 105' Processing helix chain 'r' and resid 106 through 115 Processing helix chain 'r' and resid 117 through 122 removed outlier: 3.614A pdb=" N LYS r 122 " --> pdb=" O ARG r 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 77 removed outlier: 3.746A pdb=" N ASP A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL A 62 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N VAL A 45 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ARG A 64 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N GLY A 43 " --> pdb=" O ARG A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 removed outlier: 5.697A pdb=" N VAL A 136 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS A 149 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.999A pdb=" N ILE B 160 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 159 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY B 91 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG B 161 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE B 89 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL B 87 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR B 104 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLY B 91 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 43 removed outlier: 4.999A pdb=" N ILE B 160 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 159 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY B 91 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG B 161 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE B 89 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 365 through 368 removed outlier: 6.506A pdb=" N VAL B 57 " --> pdb=" O LYS B 366 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE B 368 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N HIS B 55 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE B 217 " --> pdb=" O ASN B 281 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS B 283 " --> pdb=" O LYS B 334 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N MET B 332 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE B 287 " --> pdb=" O PHE B 330 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE B 330 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 52 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 225 through 229 Processing sheet with id=AA8, first strand: chain 'B' and resid 292 through 294 Processing sheet with id=AA9, first strand: chain 'C' and resid 7 through 11 removed outlier: 4.752A pdb=" N LYS C 20 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AB2, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.604A pdb=" N LEU C 152 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AB4, first strand: chain 'D' and resid 73 through 79 removed outlier: 6.535A pdb=" N ILE D 64 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA D 77 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N CYS D 62 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR D 79 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE D 60 " --> pdb=" O TYR D 79 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N MET D 51 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 183 through 184 Processing sheet with id=AB6, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB7, first strand: chain 'E' and resid 183 through 185 removed outlier: 3.628A pdb=" N LYS E 162 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR E 172 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N PHE E 160 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR E 144 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ILE E 145 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 83 through 85 Processing sheet with id=AB9, first strand: chain 'F' and resid 213 through 214 removed outlier: 4.333A pdb=" N ASN F 121 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 161 through 164 Processing sheet with id=AC2, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AC3, first strand: chain 'G' and resid 137 through 138 removed outlier: 6.474A pdb=" N VAL G 155 " --> pdb=" O CYS G 182 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE G 184 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ILE G 157 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 3 through 12 removed outlier: 6.673A pdb=" N ILE H 4 " --> pdb=" O TRP H 61 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS H 53 " --> pdb=" O ILE H 12 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 17 through 21 Processing sheet with id=AC6, first strand: chain 'H' and resid 133 through 136 removed outlier: 6.898A pdb=" N ARG H 89 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS H 184 " --> pdb=" O ARG H 89 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS H 91 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 102 through 106 Processing sheet with id=AC8, first strand: chain 'I' and resid 35 through 37 removed outlier: 6.737A pdb=" N MET I 52 " --> pdb=" O ILE I 135 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER I 137 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N GLY I 50 " --> pdb=" O SER I 137 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG I 139 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU I 48 " --> pdb=" O ARG I 139 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 58 through 61 removed outlier: 6.693A pdb=" N ILE I 97 " --> pdb=" O GLN I 123 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR I 125 " --> pdb=" O HIS I 95 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N HIS I 95 " --> pdb=" O THR I 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 190 through 193 Processing sheet with id=AD2, first strand: chain 'J' and resid 49 through 52 removed outlier: 3.563A pdb=" N ALA J 69 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ILE J 17 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY J 135 " --> pdb=" O ILE J 17 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 93 through 95 Processing sheet with id=AD4, first strand: chain 'L' and resid 22 through 23 Processing sheet with id=AD5, first strand: chain 'L' and resid 58 through 60 Processing sheet with id=AD6, first strand: chain 'L' and resid 124 through 126 Processing sheet with id=AD7, first strand: chain 'M' and resid 45 through 51 removed outlier: 4.662A pdb=" N ARG M 46 " --> pdb=" O GLY M 40 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLY M 40 " --> pdb=" O ARG M 46 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ARG M 35 " --> pdb=" O VAL M 30 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL M 30 " --> pdb=" O ARG M 35 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU M 37 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VAL M 12 " --> pdb=" O THR M 58 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.625A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR N 127 " --> pdb=" O GLY N 122 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N GLY N 122 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N PHE N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N TRP N 120 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 6 through 10 Processing sheet with id=AE1, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AE2, first strand: chain 'P' and resid 14 through 51 removed outlier: 3.568A pdb=" N ASN P 50 " --> pdb=" O CYS P 173 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N CYS P 173 " --> pdb=" O ASN P 50 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS P 174 " --> pdb=" O VAL P 148 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL P 148 " --> pdb=" O HIS P 174 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU P 176 " --> pdb=" O ILE P 146 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ILE P 146 " --> pdb=" O GLU P 176 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE P 178 " --> pdb=" O GLU P 144 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 87 through 88 Processing sheet with id=AE4, first strand: chain 'P' and resid 154 through 160 removed outlier: 3.627A pdb=" N MET P 154 " --> pdb=" O SER P 170 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 61 through 62 Processing sheet with id=AE6, first strand: chain 'Q' and resid 119 through 121 Processing sheet with id=AE7, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AE8, first strand: chain 'S' and resid 59 through 66 removed outlier: 5.351A pdb=" N ILE S 61 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG S 15 " --> pdb=" O ILE S 61 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 89 through 99 removed outlier: 3.949A pdb=" N GLY S 89 " --> pdb=" O SER S 86 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN S 77 " --> pdb=" O GLU S 131 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU S 131 " --> pdb=" O ASN S 77 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLY S 79 " --> pdb=" O VAL S 129 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N VAL S 129 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP S 81 " --> pdb=" O MET S 127 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 83 through 92 removed outlier: 7.015A pdb=" N ALA T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL T 67 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLY T 73 " --> pdb=" O TYR T 65 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ASN T 77 " --> pdb=" O THR T 61 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR T 61 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'U' and resid 61 through 66 removed outlier: 8.747A pdb=" N TYR U 110 " --> pdb=" O LYS U 20 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR U 22 " --> pdb=" O TYR U 110 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LEU U 112 " --> pdb=" O THR U 22 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASP U 24 " --> pdb=" O LEU U 112 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N TYR U 114 " --> pdb=" O ASP U 24 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER U 109 " --> pdb=" O ASN U 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN U 105 " --> pdb=" O SER U 109 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'V' and resid 20 through 21 Processing sheet with id=AF4, first strand: chain 'V' and resid 25 through 28 removed outlier: 6.629A pdb=" N MET V 62 " --> pdb=" O ILE V 40 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL V 42 " --> pdb=" O MET V 60 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N MET V 60 " --> pdb=" O VAL V 42 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA V 102 " --> pdb=" O ILE V 82 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N GLY V 103 " --> pdb=" O VAL V 25 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN V 27 " --> pdb=" O GLY V 103 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ILE V 105 " --> pdb=" O ASN V 27 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 88 through 89 removed outlier: 6.468A pdb=" N PHE V 95 " --> pdb=" O ARG W 20 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ALA W 22 " --> pdb=" O PHE V 95 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR V 97 " --> pdb=" O ALA W 22 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 120 through 121 Processing sheet with id=AF7, first strand: chain 'W' and resid 4 through 5 Processing sheet with id=AF8, first strand: chain 'X' and resid 77 through 80 removed outlier: 3.537A pdb=" N PHE X 79 " --> pdb=" O ILE X 99 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS X 134 " --> pdb=" O VAL X 100 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS X 135 " --> pdb=" O THR X 126 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR X 126 " --> pdb=" O LYS X 135 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR X 137 " --> pdb=" O VAL X 124 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL X 124 " --> pdb=" O TYR X 137 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ARG X 139 " --> pdb=" O ALA X 122 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AG1, first strand: chain 'Y' and resid 79 through 82 removed outlier: 3.627A pdb=" N GLN Y 72 " --> pdb=" O TYR Y 81 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU Y 54 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Y' and resid 86 through 88 Processing sheet with id=AG3, first strand: chain 'Z' and resid 69 through 76 removed outlier: 6.502A pdb=" N LYS Z 69 " --> pdb=" O ASP Z 47 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N HIS Z 40 " --> pdb=" O ASN Z 28 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN Z 28 " --> pdb=" O HIS Z 40 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS Z 22 " --> pdb=" O ILE Z 46 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL Z 10 " --> pdb=" O THR Z 83 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 72 through 74 removed outlier: 6.332A pdb=" N VAL a 73 " --> pdb=" O LEU a 112 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 100 through 102 removed outlier: 6.275A pdb=" N VAL a 124 " --> pdb=" O VAL a 145 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 26 through 29 removed outlier: 6.291A pdb=" N LYS c 26 " --> pdb=" O ILE c 97 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU c 45 " --> pdb=" O ILE c 96 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL c 46 " --> pdb=" O HIS c 72 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'd' and resid 62 through 64 removed outlier: 6.731A pdb=" N ARG d 63 " --> pdb=" O VAL d 106 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N TYR d 108 " --> pdb=" O ARG d 63 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG d 85 " --> pdb=" O VAL d 109 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'e' and resid 75 through 79 Processing sheet with id=AG9, first strand: chain 'f' and resid 7 through 16 removed outlier: 9.945A pdb=" N SER f 7 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ILE f 30 " --> pdb=" O SER f 7 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ALA f 9 " --> pdb=" O LEU f 28 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LEU f 28 " --> pdb=" O ALA f 9 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N PHE f 11 " --> pdb=" O ALA f 26 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N ALA f 26 " --> pdb=" O PHE f 11 " (cutoff:3.500A) removed outlier: 11.638A pdb=" N GLY f 13 " --> pdb=" O HIS f 24 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N HIS f 24 " --> pdb=" O GLY f 13 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS f 15 " --> pdb=" O ARG f 22 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N HIS f 24 " --> pdb=" O PHE f 88 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE f 88 " --> pdb=" O HIS f 24 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG f 76 " --> pdb=" O ARG f 85 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS f 87 " --> pdb=" O VAL f 74 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL f 74 " --> pdb=" O LYS f 87 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LYS f 66 " --> pdb=" O ALA f 53 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL f 50 " --> pdb=" O ARG f 100 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG f 100 " --> pdb=" O VAL f 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'g' and resid 20 through 24 Processing sheet with id=AH2, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AH3, first strand: chain 'k' and resid 3 through 5 removed outlier: 4.674A pdb=" N VAL k 46 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER k 22 " --> pdb=" O ARG k 37 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL k 23 " --> pdb=" O LYS k 67 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU k 69 " --> pdb=" O VAL k 23 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE k 25 " --> pdb=" O LEU k 69 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'm' and resid 102 through 103 Processing sheet with id=AH5, first strand: chain 'o' and resid 3 through 4 Processing sheet with id=AH6, first strand: chain 'o' and resid 7 through 12 removed outlier: 6.779A pdb=" N LYS o 64 " --> pdb=" O ARG o 87 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG o 87 " --> pdb=" O LYS o 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE o 66 " --> pdb=" O ILE o 85 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'p' and resid 47 through 51 removed outlier: 6.883A pdb=" N ILE p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'r' and resid 17 through 20 Processing sheet with id=AH9, first strand: chain 'r' and resid 49 through 53 2047 hydrogen bonds defined for protein. 5544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2900 hydrogen bonds 4844 hydrogen bond angles 0 basepair planarities 1124 basepair parallelities 1669 stacking parallelities Total time for adding SS restraints: 291.93 Time building geometry restraints manager: 49.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 22484 1.33 - 1.46: 53987 1.46 - 1.59: 49037 1.59 - 1.71: 6725 1.71 - 1.84: 364 Bond restraints: 132597 Sorted by residual: bond pdb=" CA PRO Q 59 " pdb=" C PRO Q 59 " ideal model delta sigma weight residual 1.514 1.502 0.012 5.50e-03 3.31e+04 4.89e+00 bond pdb=" N MET W 1 " pdb=" CA MET W 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N MET H 1 " pdb=" CA MET H 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.75e+00 bond pdb=" N MET Y 1 " pdb=" CA MET Y 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.66e+00 bond pdb=" N MET S 1 " pdb=" CA MET S 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.43e+00 ... (remaining 132592 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.56: 21050 106.56 - 113.54: 77508 113.54 - 120.53: 50550 120.53 - 127.51: 39345 127.51 - 134.50: 6982 Bond angle restraints: 195435 Sorted by residual: angle pdb=" O2' C 51071 " pdb=" C2' C 51071 " pdb=" C1' C 51071 " ideal model delta sigma weight residual 108.40 117.61 -9.21 1.50e+00 4.44e-01 3.77e+01 angle pdb=" C3' C 51071 " pdb=" C2' C 51071 " pdb=" O2' C 51071 " ideal model delta sigma weight residual 110.70 119.13 -8.43 1.50e+00 4.44e-01 3.16e+01 angle pdb=" C4' C 51071 " pdb=" C3' C 51071 " pdb=" O3' C 51071 " ideal model delta sigma weight residual 113.00 121.13 -8.13 1.50e+00 4.44e-01 2.93e+01 angle pdb=" O3' C 51071 " pdb=" C3' C 51071 " pdb=" C2' C 51071 " ideal model delta sigma weight residual 113.70 121.72 -8.02 1.50e+00 4.44e-01 2.86e+01 angle pdb=" O4' G 5 412 " pdb=" C1' G 5 412 " pdb=" N9 G 5 412 " ideal model delta sigma weight residual 108.20 114.78 -6.58 1.50e+00 4.44e-01 1.92e+01 ... (remaining 195430 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 75735 35.95 - 71.90: 8512 71.90 - 107.84: 1003 107.84 - 143.79: 21 143.79 - 179.74: 37 Dihedral angle restraints: 85308 sinusoidal: 67222 harmonic: 18086 Sorted by residual: dihedral pdb=" O4' C 54413 " pdb=" C1' C 54413 " pdb=" N1 C 54413 " pdb=" C2 C 54413 " ideal model delta sinusoidal sigma weight residual -160.00 19.74 -179.74 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 5 469 " pdb=" C1' C 5 469 " pdb=" N1 C 5 469 " pdb=" C2 C 5 469 " ideal model delta sinusoidal sigma weight residual -160.00 16.56 -176.56 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 51178 " pdb=" C1' U 51178 " pdb=" N1 U 51178 " pdb=" C2 U 51178 " ideal model delta sinusoidal sigma weight residual -160.00 11.09 -171.09 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 85305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 24311 0.165 - 0.330: 35 0.330 - 0.495: 0 0.495 - 0.660: 0 0.660 - 0.825: 2 Chirality restraints: 24348 Sorted by residual: chirality pdb=" C3' C 51071 " pdb=" C4' C 51071 " pdb=" O3' C 51071 " pdb=" C2' C 51071 " both_signs ideal model delta sigma weight residual False -2.48 -1.65 -0.82 2.00e-01 2.50e+01 1.70e+01 chirality pdb=" C2' C 51071 " pdb=" C3' C 51071 " pdb=" O2' C 51071 " pdb=" C1' C 51071 " both_signs ideal model delta sigma weight residual False -2.75 -2.07 -0.68 2.00e-01 2.50e+01 1.17e+01 chirality pdb=" C3' G 54871 " pdb=" C4' G 54871 " pdb=" O3' G 54871 " pdb=" C2' G 54871 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 24345 not shown) Planarity restraints: 12106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 5 412 " 0.054 2.00e-02 2.50e+03 2.38e-02 1.69e+01 pdb=" N9 G 5 412 " -0.058 2.00e-02 2.50e+03 pdb=" C8 G 5 412 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G 5 412 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G 5 412 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G 5 412 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G 5 412 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G 5 412 " 0.007 2.00e-02 2.50e+03 pdb=" C2 G 5 412 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G 5 412 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G 5 412 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G 5 412 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 51544 " 0.050 2.00e-02 2.50e+03 2.13e-02 1.36e+01 pdb=" N9 G 51544 " -0.051 2.00e-02 2.50e+03 pdb=" C8 G 51544 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G 51544 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G 51544 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G 51544 " 0.008 2.00e-02 2.50e+03 pdb=" O6 G 51544 " 0.010 2.00e-02 2.50e+03 pdb=" N1 G 51544 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G 51544 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G 51544 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G 51544 " -0.009 2.00e-02 2.50e+03 pdb=" C4 G 51544 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 51515 " -0.049 2.00e-02 2.50e+03 2.15e-02 1.27e+01 pdb=" N9 A 51515 " 0.048 2.00e-02 2.50e+03 pdb=" C8 A 51515 " 0.006 2.00e-02 2.50e+03 pdb=" N7 A 51515 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 51515 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 51515 " -0.008 2.00e-02 2.50e+03 pdb=" N6 A 51515 " -0.013 2.00e-02 2.50e+03 pdb=" N1 A 51515 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 51515 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A 51515 " 0.008 2.00e-02 2.50e+03 pdb=" C4 A 51515 " 0.008 2.00e-02 2.50e+03 ... (remaining 12103 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 475 2.42 - 3.04: 68551 3.04 - 3.66: 220420 3.66 - 4.28: 370534 4.28 - 4.90: 493759 Nonbonded interactions: 1153739 Sorted by model distance: nonbonded pdb=" OP2 G 52272 " pdb="MG MG 55250 " model vdw 1.804 2.170 nonbonded pdb=" OP1 U 53644 " pdb="MG MG 55112 " model vdw 1.820 2.170 nonbonded pdb="MG MG 55210 " pdb=" O HOH 55301 " model vdw 1.824 2.170 nonbonded pdb=" O2' C 5 451 " pdb=" OP1 G 5 452 " model vdw 1.829 2.440 nonbonded pdb=" OP1 C 52786 " pdb="MG MG 55188 " model vdw 1.842 2.170 ... (remaining 1153734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 41.850 Check model and map are aligned: 1.330 Set scattering table: 0.800 Process input model: 530.770 Find NCS groups from input model: 2.760 Set up NCS constraints: 0.280 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:8.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 593.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 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 : 0.004 0.043 132597 Z= 0.229 Angle : 0.596 9.207 195435 Z= 0.323 Chirality : 0.039 0.825 24348 Planarity : 0.005 0.071 12106 Dihedral : 22.975 179.739 73656 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.56 % Favored : 98.43 % Rotamer: Outliers : 0.95 % Allowed : 14.01 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % 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: 0.87 (0.10), residues: 6159 helix: 1.62 (0.12), residues: 2073 sheet: 0.33 (0.17), residues: 898 loop : 0.03 (0.10), residues: 3188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 120 HIS 0.008 0.001 HIS a 40 PHE 0.013 0.001 PHE C 92 TYR 0.021 0.002 TYR Q 32 ARG 0.007 0.000 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 765 time to evaluate : 6.073 Fit side-chains REVERT: G 252 LYS cc_start: 0.7672 (ttpp) cc_final: 0.6188 (mppt) REVERT: L 165 LYS cc_start: 0.7451 (mmmt) cc_final: 0.6800 (mtpm) REVERT: Y 86 GLN cc_start: 0.9150 (pt0) cc_final: 0.8926 (pt0) REVERT: m 98 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7485 (tttt) REVERT: r 58 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8506 (mptt) outliers start: 50 outliers final: 42 residues processed: 810 average time/residue: 2.3407 time to fit residues: 2540.0572 Evaluate side-chains 778 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 736 time to evaluate : 6.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain H residue 121 LYS Chi-restraints excluded: chain I residue 195 CYS Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain L residue 129 ARG Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 102 ARG Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Z residue 124 THR Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 105 SER Chi-restraints excluded: chain f residue 47 CYS Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain r residue 5 LEU Chi-restraints excluded: chain r residue 26 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 797 optimal weight: 7.9990 chunk 716 optimal weight: 8.9990 chunk 397 optimal weight: 3.9990 chunk 244 optimal weight: 20.0000 chunk 483 optimal weight: 10.0000 chunk 382 optimal weight: 2.9990 chunk 740 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 450 optimal weight: 0.8980 chunk 551 optimal weight: 0.0670 chunk 858 optimal weight: 2.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN B 138 GLN C 41 HIS E 39 HIS G 100 HIS G 206 GLN H 106 GLN M 75 GLN M 78 GLN N 15 GLN N 29 GLN P 10 ASN ** P 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 108 ASN X 93 ASN Y 43 ASN Y 72 GLN Z 28 ASN b 27 GLN i 92 ASN p 72 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.0421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 132597 Z= 0.177 Angle : 0.555 7.949 195435 Z= 0.297 Chirality : 0.037 0.269 24348 Planarity : 0.004 0.062 12106 Dihedral : 23.169 179.529 60687 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.30 % Favored : 98.68 % Rotamer: Outliers : 1.63 % Allowed : 13.73 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.11), residues: 6159 helix: 1.84 (0.12), residues: 2080 sheet: 0.46 (0.17), residues: 906 loop : 0.17 (0.11), residues: 3173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 120 HIS 0.008 0.001 HIS a 40 PHE 0.015 0.001 PHE Z 101 TYR 0.021 0.001 TYR Q 32 ARG 0.006 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 747 time to evaluate : 6.327 Fit side-chains revert: symmetry clash REVERT: D 117 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8311 (mptt) REVERT: D 186 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: E 237 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: F 43 MET cc_start: 0.8411 (mmm) cc_final: 0.8107 (mmp) REVERT: G 88 ASP cc_start: 0.8197 (p0) cc_final: 0.7815 (p0) REVERT: G 252 LYS cc_start: 0.7707 (ttpp) cc_final: 0.6191 (mppt) REVERT: H 14 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: H 56 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7896 (ttm-80) REVERT: L 165 LYS cc_start: 0.7296 (mmmt) cc_final: 0.6715 (mtpm) REVERT: N 161 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8806 (mtt) REVERT: N 182 HIS cc_start: 0.8735 (OUTLIER) cc_final: 0.7897 (m90) REVERT: P 132 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: R 3 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8189 (tmm) REVERT: R 39 GLN cc_start: 0.8208 (tp-100) cc_final: 0.7943 (mm110) REVERT: T 159 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7299 (mpp) REVERT: a 87 ARG cc_start: 0.8538 (ttp80) cc_final: 0.8220 (ttp80) REVERT: g 88 ARG cc_start: 0.8267 (ttp-170) cc_final: 0.7413 (ttm-80) REVERT: h 4 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7809 (mm) REVERT: i 4 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6900 (mtt180) REVERT: j 46 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8339 (ptmt) REVERT: m 98 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7478 (tttt) REVERT: o 74 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6792 (tm-30) outliers start: 86 outliers final: 35 residues processed: 801 average time/residue: 2.3558 time to fit residues: 2525.6958 Evaluate side-chains 783 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 735 time to evaluate : 6.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 182 HIS Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain U residue 73 THR Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 124 THR Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 113 GLU Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain j residue 46 LYS Chi-restraints excluded: chain k residue 18 LYS Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain p residue 26 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 476 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 714 optimal weight: 8.9990 chunk 584 optimal weight: 6.9990 chunk 236 optimal weight: 10.0000 chunk 859 optimal weight: 8.9990 chunk 928 optimal weight: 7.9990 chunk 765 optimal weight: 2.9990 chunk 852 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 689 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN G 100 HIS G 206 GLN M 75 GLN M 78 GLN N 29 GLN O 184 ASN U 44 GLN V 108 ASN Y 43 ASN Y 72 GLN Z 28 ASN b 27 GLN i 92 ASN p 72 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.0496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 132597 Z= 0.469 Angle : 0.782 9.363 195435 Z= 0.404 Chirality : 0.048 0.347 24348 Planarity : 0.007 0.092 12106 Dihedral : 23.263 178.940 60637 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.43 % Favored : 98.55 % Rotamer: Outliers : 2.10 % Allowed : 13.67 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % 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: 0.78 (0.10), residues: 6159 helix: 1.45 (0.11), residues: 2073 sheet: 0.30 (0.16), residues: 939 loop : 0.05 (0.10), residues: 3147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP N 120 HIS 0.011 0.002 HIS a 40 PHE 0.019 0.003 PHE S 145 TYR 0.028 0.003 TYR Q 32 ARG 0.006 0.001 ARG h 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 728 time to evaluate : 6.175 Fit side-chains revert: symmetry clash REVERT: B 69 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8198 (mmtp) REVERT: B 70 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8362 (mmtp) REVERT: B 362 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8506 (mttm) REVERT: C 150 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8616 (mp) REVERT: D 117 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8272 (mptt) REVERT: D 186 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7066 (mt-10) REVERT: D 236 MET cc_start: 0.8394 (mtp) cc_final: 0.8165 (mtp) REVERT: E 106 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6861 (ttm170) REVERT: E 237 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: F 43 MET cc_start: 0.8449 (mmm) cc_final: 0.8160 (mmp) REVERT: G 88 ASP cc_start: 0.8157 (p0) cc_final: 0.7948 (p0) REVERT: G 175 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7073 (tmm-80) REVERT: H 14 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7291 (tp30) REVERT: H 56 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7919 (ttm-80) REVERT: L 165 LYS cc_start: 0.7332 (mmmt) cc_final: 0.6762 (mtpm) REVERT: N 182 HIS cc_start: 0.8824 (OUTLIER) cc_final: 0.7978 (m90) REVERT: P 132 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7670 (mm-30) REVERT: T 116 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6924 (mtmt) REVERT: T 159 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7320 (mpp) REVERT: U 52 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7984 (mmtp) REVERT: U 75 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7147 (mt-10) REVERT: Y 86 GLN cc_start: 0.9153 (pt0) cc_final: 0.8929 (pt0) REVERT: a 84 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: b 54 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8376 (tt) REVERT: f 46 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7398 (ttt180) REVERT: i 4 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6939 (mtt180) REVERT: l 27 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8416 (mp) REVERT: m 98 LYS cc_start: 0.8377 (ttmt) cc_final: 0.7495 (tttt) REVERT: o 97 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7405 (mttt) outliers start: 111 outliers final: 46 residues processed: 798 average time/residue: 2.3876 time to fit residues: 2545.7078 Evaluate side-chains 790 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 721 time to evaluate : 6.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 175 ARG Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain L residue 172 GLU Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 182 HIS Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain U residue 52 LYS Chi-restraints excluded: chain U residue 75 GLU Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Z residue 31 ASP Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 124 THR Chi-restraints excluded: chain a residue 84 GLU Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 LEU Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain f residue 46 ARG Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 95 LYS Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain j residue 36 LYS Chi-restraints excluded: chain l residue 27 ILE Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain o residue 97 LYS Chi-restraints excluded: chain p residue 26 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 849 optimal weight: 0.8980 chunk 646 optimal weight: 5.9990 chunk 446 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 410 optimal weight: 0.9990 chunk 577 optimal weight: 7.9990 chunk 862 optimal weight: 7.9990 chunk 913 optimal weight: 0.9980 chunk 450 optimal weight: 4.9990 chunk 817 optimal weight: 6.9990 chunk 246 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN B 245 HIS F 121 ASN G 100 HIS G 206 GLN H 106 GLN M 75 GLN M 78 GLN N 29 GLN ** P 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 GLN V 108 ASN Y 43 ASN Y 72 GLN Z 28 ASN b 27 GLN e 80 HIS i 92 ASN p 72 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 132597 Z= 0.153 Angle : 0.538 8.102 195435 Z= 0.288 Chirality : 0.036 0.265 24348 Planarity : 0.004 0.063 12106 Dihedral : 23.088 179.598 60637 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.23 % Favored : 98.75 % Rotamer: Outliers : 1.59 % Allowed : 14.10 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.11), residues: 6159 helix: 1.83 (0.12), residues: 2075 sheet: 0.49 (0.17), residues: 917 loop : 0.19 (0.11), residues: 3167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 120 HIS 0.007 0.001 HIS a 40 PHE 0.013 0.001 PHE J 130 TYR 0.019 0.001 TYR Q 32 ARG 0.006 0.000 ARG S 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 748 time to evaluate : 6.278 Fit side-chains revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8049 (mmtp) REVERT: D 117 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8298 (mptt) REVERT: D 186 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7055 (mt-10) REVERT: E 237 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: G 175 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7003 (tmm-80) REVERT: G 252 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.6207 (mppt) REVERT: H 14 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7276 (tp30) REVERT: H 56 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7876 (ttm-80) REVERT: J 38 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7822 (tptm) REVERT: L 165 LYS cc_start: 0.7233 (mmmt) cc_final: 0.6713 (mtpm) REVERT: N 182 HIS cc_start: 0.8715 (OUTLIER) cc_final: 0.7866 (m90) REVERT: O 37 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8688 (ttp-170) REVERT: P 132 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7559 (mm-30) REVERT: R 3 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8193 (tmm) REVERT: R 122 SER cc_start: 0.8666 (t) cc_final: 0.8325 (p) REVERT: T 159 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7304 (mpp) REVERT: a 87 ARG cc_start: 0.8549 (ttp80) cc_final: 0.8195 (ttp80) REVERT: e 9 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8741 (tttt) REVERT: l 27 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8405 (mp) REVERT: m 98 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7431 (tttt) outliers start: 84 outliers final: 35 residues processed: 800 average time/residue: 2.4038 time to fit residues: 2571.0876 Evaluate side-chains 789 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 738 time to evaluate : 5.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 175 ARG Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain G residue 252 LYS Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain J residue 38 LYS Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 129 ARG Chi-restraints excluded: chain N residue 182 HIS Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 9 LYS Chi-restraints excluded: chain e residue 113 GLU Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain k residue 18 LYS Chi-restraints excluded: chain l residue 27 ILE Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 77 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 760 optimal weight: 7.9990 chunk 518 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 680 optimal weight: 9.9990 chunk 376 optimal weight: 8.9990 chunk 779 optimal weight: 10.0000 chunk 631 optimal weight: 0.6980 chunk 1 optimal weight: 10.0000 chunk 466 optimal weight: 10.0000 chunk 819 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 overall best weight: 7.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN G 100 HIS G 206 GLN M 78 GLN N 29 GLN U 44 GLN V 108 ASN Y 43 ASN Y 72 GLN Y 127 GLN Z 28 ASN b 27 GLN i 92 ASN p 72 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.0559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 132597 Z= 0.502 Angle : 0.803 9.340 195435 Z= 0.413 Chirality : 0.049 0.354 24348 Planarity : 0.007 0.099 12106 Dihedral : 23.237 178.738 60632 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.49 % Favored : 98.49 % Rotamer: Outliers : 2.26 % Allowed : 13.78 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % 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: 0.74 (0.10), residues: 6159 helix: 1.39 (0.11), residues: 2079 sheet: 0.28 (0.16), residues: 926 loop : 0.04 (0.10), residues: 3154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP N 120 HIS 0.011 0.002 HIS a 40 PHE 0.019 0.003 PHE S 145 TYR 0.029 0.003 TYR Q 32 ARG 0.007 0.001 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 730 time to evaluate : 6.276 Fit side-chains revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8384 (mmtp) REVERT: D 117 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8282 (mptt) REVERT: D 186 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: D 236 MET cc_start: 0.8363 (mtp) cc_final: 0.8136 (mtp) REVERT: E 106 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6872 (ttm170) REVERT: E 237 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: G 175 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7059 (tmm-80) REVERT: H 14 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7292 (tp30) REVERT: H 56 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.7915 (ttm-80) REVERT: H 106 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7726 (mt0) REVERT: L 165 LYS cc_start: 0.7285 (mmmt) cc_final: 0.6769 (mtpm) REVERT: N 182 HIS cc_start: 0.8828 (OUTLIER) cc_final: 0.7980 (m90) REVERT: O 37 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8814 (ttp-170) REVERT: P 132 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7664 (mm-30) REVERT: T 116 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6995 (ttmt) REVERT: T 159 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7303 (mpp) REVERT: U 52 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7994 (mmtp) REVERT: U 75 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: Y 86 GLN cc_start: 0.9161 (pt0) cc_final: 0.8940 (pt0) REVERT: b 54 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8348 (tt) REVERT: f 89 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7366 (mmt90) REVERT: h 71 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7941 (tmmt) REVERT: i 4 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6941 (mtt180) REVERT: l 27 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8434 (mp) REVERT: m 98 LYS cc_start: 0.8394 (ttmt) cc_final: 0.7513 (tttt) REVERT: o 97 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7408 (mttt) outliers start: 119 outliers final: 59 residues processed: 807 average time/residue: 2.3995 time to fit residues: 2589.4531 Evaluate side-chains 803 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 722 time to evaluate : 6.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 175 ARG Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 106 GLN Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain J residue 38 LYS Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 129 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 182 HIS Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain U residue 52 LYS Chi-restraints excluded: chain U residue 75 GLU Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain Y residue 41 LYS Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain Z residue 124 THR Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 LEU Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 113 GLU Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 89 ARG Chi-restraints excluded: chain f residue 95 LYS Chi-restraints excluded: chain h residue 71 LYS Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain j residue 36 LYS Chi-restraints excluded: chain l residue 27 ILE Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain o residue 97 LYS Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 36 LYS Chi-restraints excluded: chain r residue 5 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 307 optimal weight: 8.9990 chunk 822 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 536 optimal weight: 6.9990 chunk 225 optimal weight: 40.0000 chunk 914 optimal weight: 0.8980 chunk 759 optimal weight: 8.9990 chunk 423 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 302 optimal weight: 10.0000 chunk 480 optimal weight: 9.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN G 100 HIS G 206 GLN M 78 GLN N 29 GLN U 44 GLN V 108 ASN Y 43 ASN Y 72 GLN Z 28 ASN b 27 GLN i 92 ASN p 72 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.0501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 132597 Z= 0.325 Angle : 0.675 9.408 195435 Z= 0.356 Chirality : 0.042 0.312 24348 Planarity : 0.006 0.071 12106 Dihedral : 23.213 179.484 60632 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.38 % Favored : 98.60 % Rotamer: Outliers : 1.93 % Allowed : 14.27 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % 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: 0.79 (0.10), residues: 6159 helix: 1.47 (0.11), residues: 2078 sheet: 0.28 (0.16), residues: 927 loop : 0.06 (0.10), residues: 3154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 120 HIS 0.009 0.001 HIS a 40 PHE 0.017 0.002 PHE G 204 TYR 0.026 0.002 TYR Q 32 ARG 0.005 0.000 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 841 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 739 time to evaluate : 5.571 Fit side-chains revert: symmetry clash REVERT: B 69 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8201 (mmtp) REVERT: B 70 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8219 (mmtp) REVERT: B 362 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8507 (mttm) REVERT: C 150 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8596 (mp) REVERT: D 117 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8279 (mptt) REVERT: D 236 MET cc_start: 0.8351 (mtp) cc_final: 0.8091 (mtp) REVERT: E 106 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.6865 (ttm170) REVERT: E 237 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: G 175 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7014 (tmm-80) REVERT: H 14 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7284 (tp30) REVERT: H 56 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.7902 (ttm-80) REVERT: L 165 LYS cc_start: 0.7271 (mmmt) cc_final: 0.6765 (mtpm) REVERT: N 182 HIS cc_start: 0.8784 (OUTLIER) cc_final: 0.7946 (m90) REVERT: O 37 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8723 (ttp-170) REVERT: P 132 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7650 (mm-30) REVERT: R 3 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8192 (tmm) REVERT: R 43 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7896 (tttm) REVERT: T 159 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7293 (mpp) REVERT: U 52 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7978 (mmtp) REVERT: U 75 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6368 (mp0) REVERT: Y 86 GLN cc_start: 0.9156 (pt0) cc_final: 0.8928 (pt0) REVERT: b 54 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8338 (tt) REVERT: f 89 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7305 (mmt90) REVERT: h 71 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7878 (tmmt) REVERT: i 4 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6930 (mtt180) REVERT: j 36 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8876 (tptt) REVERT: l 27 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8422 (mp) REVERT: m 98 LYS cc_start: 0.8372 (ttmt) cc_final: 0.7488 (tttt) REVERT: o 97 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7405 (mttt) outliers start: 102 outliers final: 54 residues processed: 803 average time/residue: 2.3431 time to fit residues: 2518.5334 Evaluate side-chains 810 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 731 time to evaluate : 6.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 175 ARG Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 14 GLU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 129 ARG Chi-restraints excluded: chain N residue 182 HIS Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 107 LYS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain U residue 52 LYS Chi-restraints excluded: chain U residue 75 GLU Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain Y residue 41 LYS Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Z residue 31 ASP Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 40 LEU Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 113 GLU Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain f residue 89 ARG Chi-restraints excluded: chain f residue 95 LYS Chi-restraints excluded: chain h residue 71 LYS Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 21 VAL Chi-restraints excluded: chain j residue 36 LYS Chi-restraints excluded: chain l residue 27 ILE Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain o residue 97 LYS Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain r residue 5 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 881 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 520 optimal weight: 0.9990 chunk 667 optimal weight: 0.9990 chunk 517 optimal weight: 0.9990 chunk 769 optimal weight: 5.9990 chunk 510 optimal weight: 1.9990 chunk 910 optimal weight: 0.9990 chunk 570 optimal weight: 0.5980 chunk 555 optimal weight: 9.9990 chunk 420 optimal weight: 0.9980 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN G 64 GLN G 100 HIS G 206 GLN M 78 GLN N 29 GLN ** P 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 GLN V 108 ASN Y 43 ASN Y 72 GLN Y 127 GLN Z 28 ASN b 27 GLN i 92 ASN p 72 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 132597 Z= 0.121 Angle : 0.511 8.619 195435 Z= 0.272 Chirality : 0.035 0.275 24348 Planarity : 0.004 0.063 12106 Dihedral : 23.026 179.601 60632 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.36 % Favored : 98.62 % Rotamer: Outliers : 1.25 % Allowed : 15.01 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.11), residues: 6159 helix: 1.91 (0.12), residues: 2071 sheet: 0.57 (0.17), residues: 920 loop : 0.25 (0.11), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 120 HIS 0.007 0.001 HIS a 40 PHE 0.011 0.001 PHE k 11 TYR 0.016 0.001 TYR I 75 ARG 0.008 0.000 ARG S 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 755 time to evaluate : 6.299 Fit side-chains revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8038 (mmtp) REVERT: C 348 LYS cc_start: 0.8457 (ttpt) cc_final: 0.7973 (tmtt) REVERT: E 106 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6855 (ttm170) REVERT: E 237 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: G 175 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6992 (tmm-80) REVERT: H 56 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7849 (ttm-80) REVERT: L 165 LYS cc_start: 0.7169 (mmmt) cc_final: 0.6738 (mtpm) REVERT: O 37 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8658 (ttp-170) REVERT: P 132 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7614 (tp30) REVERT: R 3 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8209 (tmm) REVERT: R 39 GLN cc_start: 0.8167 (tp-100) cc_final: 0.7919 (mm110) REVERT: R 122 SER cc_start: 0.8616 (t) cc_final: 0.8279 (p) REVERT: X 145 ASP cc_start: 0.8626 (t70) cc_final: 0.8368 (t70) REVERT: Y 86 GLN cc_start: 0.9147 (pt0) cc_final: 0.8886 (pt0) REVERT: a 87 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8182 (ttp80) REVERT: i 4 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6912 (mtt180) REVERT: j 36 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8782 (tptt) REVERT: l 27 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8408 (mp) REVERT: m 98 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7407 (tttt) REVERT: o 97 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7389 (mttt) outliers start: 66 outliers final: 30 residues processed: 795 average time/residue: 2.3604 time to fit residues: 2516.9154 Evaluate side-chains 787 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 745 time to evaluate : 6.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 175 ARG Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 147 GLU Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain j residue 36 LYS Chi-restraints excluded: chain l residue 27 ILE Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain o residue 97 LYS Chi-restraints excluded: chain p residue 45 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 563 optimal weight: 3.9990 chunk 363 optimal weight: 20.0000 chunk 543 optimal weight: 5.9990 chunk 274 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 579 optimal weight: 20.0000 chunk 620 optimal weight: 3.9990 chunk 450 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 715 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN G 64 GLN G 100 HIS G 206 GLN J 98 ASN M 78 GLN ** P 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 GLN V 108 ASN Y 43 ASN Y 72 GLN Z 28 ASN b 27 GLN i 92 ASN p 72 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.0542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 132597 Z= 0.366 Angle : 0.692 9.688 195435 Z= 0.362 Chirality : 0.044 0.303 24348 Planarity : 0.006 0.079 12106 Dihedral : 23.124 179.016 60628 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.33 % Favored : 98.65 % Rotamer: Outliers : 1.80 % Allowed : 14.73 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % 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: 0.95 (0.10), residues: 6159 helix: 1.61 (0.12), residues: 2079 sheet: 0.38 (0.17), residues: 917 loop : 0.13 (0.10), residues: 3163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 120 HIS 0.010 0.001 HIS a 40 PHE 0.017 0.002 PHE G 204 TYR 0.026 0.002 TYR Q 32 ARG 0.007 0.001 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 740 time to evaluate : 6.382 Fit side-chains revert: symmetry clash REVERT: B 70 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8252 (mmtp) REVERT: C 348 LYS cc_start: 0.8492 (ttpt) cc_final: 0.7994 (tmtt) REVERT: D 117 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8300 (mptt) REVERT: D 133 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: D 186 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7075 (mt-10) REVERT: E 106 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6861 (ttm170) REVERT: E 237 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: G 175 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7014 (tmm-80) REVERT: H 56 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7903 (ttm-80) REVERT: J 38 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7861 (tptm) REVERT: L 158 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.6893 (mtt90) REVERT: L 165 LYS cc_start: 0.7227 (mmmt) cc_final: 0.6756 (mtpm) REVERT: N 182 HIS cc_start: 0.8780 (OUTLIER) cc_final: 0.7930 (m90) REVERT: O 37 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8802 (ttp-170) REVERT: P 132 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7634 (mm-30) REVERT: T 116 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6826 (mtmt) REVERT: T 159 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7313 (mpp) REVERT: X 145 ASP cc_start: 0.8655 (t70) cc_final: 0.8383 (t70) REVERT: Y 86 GLN cc_start: 0.9158 (pt0) cc_final: 0.8923 (pt0) REVERT: a 87 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8285 (ttp80) REVERT: b 54 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8319 (tt) REVERT: h 4 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7818 (mm) REVERT: i 4 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6944 (mtt180) REVERT: l 27 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8410 (mp) REVERT: m 98 LYS cc_start: 0.8367 (ttmt) cc_final: 0.7481 (tttt) REVERT: o 97 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7406 (mttt) outliers start: 95 outliers final: 50 residues processed: 801 average time/residue: 2.3676 time to fit residues: 2540.7736 Evaluate side-chains 802 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 732 time to evaluate : 6.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 70 LYS Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 62 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 185 THR Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 175 ARG Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain J residue 38 LYS Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain L residue 129 ARG Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 125 SER Chi-restraints excluded: chain N residue 182 HIS Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain T residue 76 VAL Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 159 MET Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain Y residue 41 LYS Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 113 GLU Chi-restraints excluded: chain f residue 54 LYS Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain h residue 4 ILE Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain l residue 27 ILE Chi-restraints excluded: chain l residue 31 THR Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain o residue 97 LYS Chi-restraints excluded: chain p residue 26 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 828 optimal weight: 0.9980 chunk 872 optimal weight: 3.9990 chunk 796 optimal weight: 6.9990 chunk 848 optimal weight: 4.9990 chunk 510 optimal weight: 0.9990 chunk 369 optimal weight: 7.9990 chunk 666 optimal weight: 1.9990 chunk 260 optimal weight: 10.0000 chunk 766 optimal weight: 2.9990 chunk 802 optimal weight: 1.9990 chunk 845 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN C 116 ASN G 64 GLN G 100 HIS G 206 GLN J 98 ASN M 78 GLN N 29 GLN ** P 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 GLN V 108 ASN Y 43 ASN Y 72 GLN Y 127 GLN Z 28 ASN b 27 GLN i 92 ASN p 72 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 132597 Z= 0.125 Angle : 0.516 9.848 195435 Z= 0.277 Chirality : 0.035 0.266 24348 Planarity : 0.004 0.062 12106 Dihedral : 23.006 179.485 60628 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.32 % Favored : 98.67 % Rotamer: Outliers : 1.12 % Allowed : 15.51 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.11), residues: 6159 helix: 1.92 (0.12), residues: 2071 sheet: 0.58 (0.17), residues: 922 loop : 0.26 (0.11), residues: 3166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 120 HIS 0.007 0.001 HIS a 40 PHE 0.011 0.001 PHE k 11 TYR 0.024 0.001 TYR W 55 ARG 0.007 0.000 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 747 time to evaluate : 6.259 Fit side-chains revert: symmetry clash REVERT: C 348 LYS cc_start: 0.8470 (ttpt) cc_final: 0.7982 (tmtt) REVERT: E 106 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6832 (ttm170) REVERT: E 237 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: G 175 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7016 (tmm-80) REVERT: H 56 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7850 (ttm-80) REVERT: J 38 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7738 (tptm) REVERT: L 165 LYS cc_start: 0.7161 (mmmt) cc_final: 0.6745 (mtpm) REVERT: M 124 LYS cc_start: 0.8252 (ttmm) cc_final: 0.7689 (ttpp) REVERT: O 37 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8754 (ttp-170) REVERT: P 104 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7964 (tt0) REVERT: P 132 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: R 122 SER cc_start: 0.8646 (t) cc_final: 0.8317 (p) REVERT: T 116 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6886 (mtmt) REVERT: X 145 ASP cc_start: 0.8627 (t70) cc_final: 0.8375 (t70) REVERT: Y 86 GLN cc_start: 0.9150 (pt0) cc_final: 0.8880 (pt0) REVERT: a 87 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8153 (ttp80) REVERT: b 54 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8323 (tt) REVERT: i 4 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6943 (mtt180) REVERT: l 27 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8404 (mp) REVERT: m 98 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7412 (tttt) REVERT: o 97 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7367 (mttt) REVERT: r 122 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8113 (mtpt) outliers start: 59 outliers final: 30 residues processed: 784 average time/residue: 2.3944 time to fit residues: 2514.0435 Evaluate side-chains 790 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 746 time to evaluate : 6.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 175 ARG Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain J residue 38 LYS Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain P residue 104 GLN Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 147 GLU Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 113 GLU Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain l residue 27 ILE Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 97 LYS Chi-restraints excluded: chain r residue 122 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 557 optimal weight: 9.9990 chunk 897 optimal weight: 8.9990 chunk 547 optimal weight: 0.2980 chunk 425 optimal weight: 5.9990 chunk 623 optimal weight: 8.9990 chunk 941 optimal weight: 8.9990 chunk 866 optimal weight: 5.9990 chunk 749 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 579 optimal weight: 9.9990 chunk 459 optimal weight: 4.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN C 116 ASN G 64 GLN G 100 HIS G 206 GLN L 111 GLN M 78 GLN N 29 GLN ** P 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 GLN V 108 ASN Y 43 ASN Y 72 GLN Z 28 ASN b 27 GLN i 92 ASN p 72 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.0573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 132597 Z= 0.271 Angle : 0.614 10.036 195435 Z= 0.324 Chirality : 0.040 0.271 24348 Planarity : 0.005 0.065 12106 Dihedral : 23.047 179.246 60626 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.32 % Favored : 98.67 % Rotamer: Outliers : 1.02 % Allowed : 15.68 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.10), residues: 6159 helix: 1.76 (0.12), residues: 2075 sheet: 0.47 (0.17), residues: 898 loop : 0.19 (0.10), residues: 3186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 120 HIS 0.008 0.001 HIS a 40 PHE 0.016 0.002 PHE G 204 TYR 0.024 0.002 TYR d 25 ARG 0.007 0.000 ARG C 291 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 739 time to evaluate : 6.264 Fit side-chains revert: symmetry clash REVERT: B 300 LYS cc_start: 0.8249 (pptt) cc_final: 0.7879 (pptt) REVERT: C 348 LYS cc_start: 0.8488 (ttpt) cc_final: 0.7989 (tmtt) REVERT: D 133 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: E 106 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6868 (ttm170) REVERT: E 237 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: G 175 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.6997 (tmm-80) REVERT: H 56 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7899 (ttm-80) REVERT: I 182 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: J 38 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7817 (tptm) REVERT: L 165 LYS cc_start: 0.7170 (mmmt) cc_final: 0.6744 (mtpm) REVERT: O 37 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.8791 (ttp-170) REVERT: P 132 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7642 (mm-30) REVERT: T 116 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6840 (mtmt) REVERT: X 145 ASP cc_start: 0.8641 (t70) cc_final: 0.8373 (t70) REVERT: Y 86 GLN cc_start: 0.9147 (pt0) cc_final: 0.8881 (pt0) REVERT: a 87 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8186 (ttp80) REVERT: b 54 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8308 (tt) REVERT: i 4 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6954 (mtt180) REVERT: l 27 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8412 (mp) REVERT: m 98 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7464 (tttt) REVERT: o 97 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7409 (mttt) outliers start: 54 outliers final: 35 residues processed: 773 average time/residue: 2.3988 time to fit residues: 2484.9010 Evaluate side-chains 786 residues out of total 5390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 737 time to evaluate : 6.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain G residue 175 ARG Chi-restraints excluded: chain G residue 235 ARG Chi-restraints excluded: chain H residue 56 ARG Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain J residue 38 LYS Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 51 SER Chi-restraints excluded: chain L residue 122 SER Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 132 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 169 SER Chi-restraints excluded: chain R residue 2 SER Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain Y residue 94 THR Chi-restraints excluded: chain Y residue 125 SER Chi-restraints excluded: chain Z residue 34 SER Chi-restraints excluded: chain a residue 85 GLN Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 113 GLU Chi-restraints excluded: chain f residue 57 THR Chi-restraints excluded: chain f residue 59 THR Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain l residue 27 ILE Chi-restraints excluded: chain l residue 47 THR Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 97 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 945 random chunks: chunk 595 optimal weight: 7.9990 chunk 798 optimal weight: 0.1980 chunk 229 optimal weight: 20.0000 chunk 691 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 750 optimal weight: 4.9990 chunk 314 optimal weight: 10.0000 chunk 771 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN G 100 HIS G 206 GLN M 78 GLN N 29 GLN U 44 GLN V 108 ASN Y 43 ASN Y 72 GLN Y 127 GLN Z 28 ASN b 27 GLN i 92 ASN p 72 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.115598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.085737 restraints weight = 119494.385| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 0.77 r_work: 0.2845 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.0557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 132597 Z= 0.282 Angle : 0.630 9.940 195435 Z= 0.334 Chirality : 0.041 0.279 24348 Planarity : 0.005 0.064 12106 Dihedral : 23.088 178.912 60626 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.32 % Favored : 98.67 % Rotamer: Outliers : 1.04 % Allowed : 15.64 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % Cis-general : 0.00 % 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: 0.99 (0.10), residues: 6159 helix: 1.67 (0.12), residues: 2075 sheet: 0.38 (0.17), residues: 915 loop : 0.16 (0.10), residues: 3169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 120 HIS 0.008 0.001 HIS a 40 PHE 0.016 0.002 PHE G 204 TYR 0.025 0.002 TYR Q 32 ARG 0.007 0.000 ARG C 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39160.66 seconds wall clock time: 679 minutes 48.30 seconds (40788.30 seconds total)