Starting phenix.real_space_refine on Mon Mar 18 11:07:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqc_22433/03_2024/7jqc_22433.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqc_22433/03_2024/7jqc_22433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqc_22433/03_2024/7jqc_22433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqc_22433/03_2024/7jqc_22433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqc_22433/03_2024/7jqc_22433.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqc_22433/03_2024/7jqc_22433.pdb" } resolution = 3.3 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= 0.003 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8402 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1839 5.49 5 S 178 5.16 5 C 41904 2.51 5 N 14267 2.21 5 O 19635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a ARG 80": "NH1" <-> "NH2" Residue "a ARG 85": "NH1" <-> "NH2" Residue "B ASP 44": "OD1" <-> "OD2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ASP 33": "OD1" <-> "OD2" Residue "b GLU 46": "OE1" <-> "OE2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 87": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "C PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ASP 108": "OD1" <-> "OD2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "D ASP 242": "OD1" <-> "OD2" Residue "D GLU 258": "OE1" <-> "OE2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 66": "NH1" <-> "NH2" Residue "d ARG 67": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ASP 169": "OD1" <-> "OD2" Residue "f ARG 81": "NH1" <-> "NH2" Residue "f ARG 101": "NH1" <-> "NH2" Residue "f ARG 104": "NH1" <-> "NH2" Residue "G ASP 27": "OD1" <-> "OD2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 127": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G GLU 160": "OE1" <-> "OE2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 110": "OE1" <-> "OE2" Residue "g ASP 124": "OD1" <-> "OD2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "g TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H ARG 198": "NH1" <-> "NH2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "h ARG 47": "NH1" <-> "NH2" Residue "h ASP 48": "OD1" <-> "OD2" Residue "h GLU 49": "OE1" <-> "OE2" Residue "h TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 60": "NH1" <-> "NH2" Residue "h PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 100": "NH1" <-> "NH2" Residue "h ASP 107": "OD1" <-> "OD2" Residue "h PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 260": "OD1" <-> "OD2" Residue "h GLU 269": "OE1" <-> "OE2" Residue "h TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 304": "OD1" <-> "OD2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I ARG 81": "NH1" <-> "NH2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 131": "OE1" <-> "OE2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "I ASP 149": "OD1" <-> "OD2" Residue "I GLU 191": "OE1" <-> "OE2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 41": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J GLU 70": "OE1" <-> "OE2" Residue "J TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J ARG 141": "NH1" <-> "NH2" Residue "J ASP 150": "OD1" <-> "OD2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 83": "NH1" <-> "NH2" Residue "K ARG 138": "NH1" <-> "NH2" Residue "L GLU 13": "OE1" <-> "OE2" Residue "L ARG 65": "NH1" <-> "NH2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N ASP 43": "OD1" <-> "OD2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "N ASP 80": "OD1" <-> "OD2" Residue "N GLU 87": "OE1" <-> "OE2" Residue "N ASP 95": "OD1" <-> "OD2" Residue "N TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 117": "OE1" <-> "OE2" Residue "N ASP 122": "OD1" <-> "OD2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "R PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "R TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 102": "OE1" <-> "OE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S GLU 77": "OE1" <-> "OE2" Residue "S GLU 79": "OE1" <-> "OE2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "S GLU 94": "OE1" <-> "OE2" Residue "S ASP 99": "OD1" <-> "OD2" Residue "S ASP 101": "OD1" <-> "OD2" Residue "S ASP 110": "OD1" <-> "OD2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 14": "NH1" <-> "NH2" Residue "T ASP 21": "OD1" <-> "OD2" Residue "T ARG 39": "NH1" <-> "NH2" Residue "T ARG 55": "NH1" <-> "NH2" Residue "T TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 121": "NH1" <-> "NH2" Residue "T ARG 142": "NH1" <-> "NH2" Residue "U ARG 16": "NH1" <-> "NH2" Residue "U ARG 62": "NH1" <-> "NH2" Residue "U ARG 84": "NH1" <-> "NH2" Residue "U ARG 102": "NH1" <-> "NH2" Residue "U ASP 118": "OD1" <-> "OD2" Residue "U ARG 121": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 87": "NH1" <-> "NH2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 20": "NH1" <-> "NH2" Residue "Z ASP 26": "OD1" <-> "OD2" Residue "Z ASP 53": "OD1" <-> "OD2" Residue "Z ARG 61": "NH1" <-> "NH2" Residue "Z PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 110": "NH1" <-> "NH2" Residue "F ASP 152": "OD1" <-> "OD2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M GLU 40": "OE1" <-> "OE2" Residue "M ARG 49": "NH1" <-> "NH2" Residue "M ARG 68": "NH1" <-> "NH2" Residue "M PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 176": "OD1" <-> "OD2" Residue "M ARG 191": "NH1" <-> "NH2" Residue "M ARG 198": "NH1" <-> "NH2" Residue "M ASP 206": "OD1" <-> "OD2" Residue "M ARG 221": "NH1" <-> "NH2" Residue "M PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 252": "NH1" <-> "NH2" Residue "O TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 57": "OD1" <-> "OD2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "O ARG 97": "NH1" <-> "NH2" Residue "O PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 32": "OD1" <-> "OD2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P ARG 121": "NH1" <-> "NH2" Residue "X ASP 39": "OD1" <-> "OD2" Residue "X PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 80": "OD1" <-> "OD2" Residue "X GLU 87": "OE1" <-> "OE2" Residue "X ARG 117": "NH1" <-> "NH2" Residue "X GLU 130": "OE1" <-> "OE2" Residue "X ARG 141": "NH1" <-> "NH2" Residue "X ARG 150": "NH1" <-> "NH2" Residue "Y ASP 9": "OD1" <-> "OD2" Residue "Y GLU 18": "OE1" <-> "OE2" Residue "Y PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 85": "OD1" <-> "OD2" Residue "Y PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 5": "NH1" <-> "NH2" Residue "c ARG 8": "NH1" <-> "NH2" Residue "c ARG 17": "NH1" <-> "NH2" Residue "c ARG 67": "NH1" <-> "NH2" Residue "c PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 107": "NH1" <-> "NH2" Residue "e TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 77823 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 36229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36229 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 146, 'rna2p_pyr': 113, 'rna3p_pur': 752, 'rna3p_pyr': 686} Link IDs: {'rna2p': 258, 'rna3p': 1438} Chain breaks: 11 Chain: "a" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "B" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "d" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 488 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "G" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1461 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 3, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "Q" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 889 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 135} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "F" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 280 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 34} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "i" Number of atoms: 3026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 3026 Classifications: {'RNA': 143} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 17, 'rna3p_pur': 57, 'rna3p_pyr': 57} Link IDs: {'rna2p': 29, 'rna3p': 113} Chain: "M" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2083 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 248} Chain: "O" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1296 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 150} Chain: "P" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1208 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 141} Chain: "X" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Y" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "c" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1106 Classifications: {'peptide': 142} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 136} Chain: "e" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 659 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 77} Time building chain proxies: 30.64, per 1000 atoms: 0.39 Number of scatterers: 77823 At special positions: 0 Unit cell: (163.404, 217.872, 274.476, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 178 16.00 P 1839 15.00 O 19635 8.00 N 14267 7.00 C 41904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 30.79 Conformation dependent library (CDL) restraints added in 5.2 seconds 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8966 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 56 sheets defined 30.8% alpha, 14.0% beta 398 base pairs and 893 stacking pairs defined. Time for finding SS restraints: 24.59 Creating SS restraints... Processing helix chain 'a' and resid 69 through 78 removed outlier: 4.213A pdb=" N SER a 74 " --> pdb=" O PRO a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 94 removed outlier: 3.605A pdb=" N GLN a 89 " --> pdb=" O ARG a 85 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLU a 90 " --> pdb=" O ALA a 86 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU a 91 " --> pdb=" O ALA a 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER a 93 " --> pdb=" O GLN a 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 4.289A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' Processing helix chain 'B' and resid 50 through 67 removed outlier: 3.513A pdb=" N ARG B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 83 through 95 removed outlier: 3.648A pdb=" N VAL B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 137 Processing helix chain 'B' and resid 167 through 186 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 211 through 217 removed outlier: 3.671A pdb=" N GLN B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALA B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 56 removed outlier: 4.591A pdb=" N ASP b 52 " --> pdb=" O ALA b 48 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER b 54 " --> pdb=" O VAL b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'b' and resid 89 through 93 removed outlier: 3.560A pdb=" N ARG b 92 " --> pdb=" O ARG b 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 59 through 63 removed outlier: 3.579A pdb=" N LEU C 62 " --> pdb=" O SER C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.564A pdb=" N CYS C 111 " --> pdb=" O ARG C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 177 removed outlier: 3.510A pdb=" N GLN C 163 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 173 " --> pdb=" O MET C 169 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 187 removed outlier: 3.613A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 201 removed outlier: 4.355A pdb=" N GLU C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.605A pdb=" N MET C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C 230 " --> pdb=" O GLY C 226 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.678A pdb=" N LEU D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.593A pdb=" N TYR D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 93 through 98 removed outlier: 3.724A pdb=" N PHE D 97 " --> pdb=" O ILE D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 159 removed outlier: 3.632A pdb=" N ILE D 156 " --> pdb=" O ARG D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 207 through 218 removed outlier: 4.060A pdb=" N MET D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 239 Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 269 through 277 removed outlier: 3.632A pdb=" N VAL D 274 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 28 removed outlier: 4.026A pdb=" N VAL E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS E 18 " --> pdb=" O ASP E 14 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 19 " --> pdb=" O GLY E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.543A pdb=" N LEU E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.784A pdb=" N LEU E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 Processing helix chain 'E' and resid 97 through 112 Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.538A pdb=" N ALA E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 166 Processing helix chain 'f' and resid 83 through 89 Processing helix chain 'f' and resid 103 through 116 removed outlier: 3.605A pdb=" N ARG f 107 " --> pdb=" O GLY f 103 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG f 114 " --> pdb=" O GLN f 110 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL f 116 " --> pdb=" O ASN f 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.583A pdb=" N GLN G 36 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 72 removed outlier: 3.792A pdb=" N ARG G 71 " --> pdb=" O ILE G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 100 removed outlier: 3.549A pdb=" N THR G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS G 95 " --> pdb=" O ARG G 91 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE G 100 " --> pdb=" O ALA G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 117 removed outlier: 3.830A pdb=" N ALA G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 161 removed outlier: 3.822A pdb=" N VAL G 147 " --> pdb=" O PRO G 143 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA G 150 " --> pdb=" O ARG G 146 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG G 159 " --> pdb=" O CYS G 155 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA G 161 " --> pdb=" O GLY G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 173 Processing helix chain 'G' and resid 173 through 180 Processing helix chain 'G' and resid 187 through 204 removed outlier: 3.812A pdb=" N ASP G 194 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU G 195 " --> pdb=" O LYS G 191 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER G 202 " --> pdb=" O ARG G 198 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 26 through 28 No H-bonds generated for 'chain 'H' and resid 26 through 28' Processing helix chain 'H' and resid 38 through 42 removed outlier: 3.902A pdb=" N GLY H 42 " --> pdb=" O ASP H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 145 removed outlier: 3.749A pdb=" N ILE H 141 " --> pdb=" O ARG H 137 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 156 Processing helix chain 'H' and resid 181 through 230 removed outlier: 3.590A pdb=" N LYS H 201 " --> pdb=" O GLN H 197 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS H 203 " --> pdb=" O THR H 199 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU H 222 " --> pdb=" O LYS H 218 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS H 223 " --> pdb=" O GLU H 219 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE H 228 " --> pdb=" O ARG H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 235 Processing helix chain 'I' and resid 17 through 30 Processing helix chain 'I' and resid 68 through 73 Processing helix chain 'I' and resid 75 through 84 removed outlier: 3.720A pdb=" N VAL I 80 " --> pdb=" O GLN I 76 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 133 removed outlier: 3.543A pdb=" N VAL I 125 " --> pdb=" O THR I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 181 removed outlier: 3.569A pdb=" N SER I 174 " --> pdb=" O VAL I 170 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY I 175 " --> pdb=" O GLU I 171 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS I 178 " --> pdb=" O SER I 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 92 removed outlier: 3.542A pdb=" N LEU J 90 " --> pdb=" O ASN J 87 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL J 91 " --> pdb=" O ASN J 88 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG J 92 " --> pdb=" O GLU J 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 92' Processing helix chain 'J' and resid 106 through 117 removed outlier: 3.807A pdb=" N GLN J 111 " --> pdb=" O THR J 107 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER J 115 " --> pdb=" O GLN J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 137 removed outlier: 3.753A pdb=" N LEU J 137 " --> pdb=" O GLU J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 154 removed outlier: 3.998A pdb=" N ARG J 152 " --> pdb=" O LYS J 148 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS J 154 " --> pdb=" O ASP J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 167 removed outlier: 3.583A pdb=" N GLU J 164 " --> pdb=" O SER J 160 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN J 167 " --> pdb=" O GLU J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 183 Processing helix chain 'J' and resid 191 through 207 Processing helix chain 'K' and resid 21 through 36 removed outlier: 3.756A pdb=" N GLU K 28 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU K 29 " --> pdb=" O LEU K 25 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS K 30 " --> pdb=" O ASP K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 42 removed outlier: 3.535A pdb=" N GLU K 42 " --> pdb=" O ASN K 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 42' Processing helix chain 'K' and resid 43 through 61 removed outlier: 3.651A pdb=" N LYS K 52 " --> pdb=" O PHE K 48 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU K 59 " --> pdb=" O LYS K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 83 removed outlier: 3.664A pdb=" N ASN K 75 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 92 removed outlier: 3.775A pdb=" N MET K 92 " --> pdb=" O GLU K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 100 Processing helix chain 'K' and resid 102 through 107 removed outlier: 3.763A pdb=" N LEU K 106 " --> pdb=" O ILE K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 131 removed outlier: 3.926A pdb=" N ARG K 127 " --> pdb=" O ILE K 123 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL K 128 " --> pdb=" O HIS K 124 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG K 131 " --> pdb=" O ARG K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 184 removed outlier: 3.679A pdb=" N LYS K 179 " --> pdb=" O ARG K 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.628A pdb=" N ILE L 11 " --> pdb=" O ASN L 7 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR L 12 " --> pdb=" O ARG L 8 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU L 14 " --> pdb=" O ALA L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 removed outlier: 4.059A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS L 47 " --> pdb=" O LEU L 43 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN L 50 " --> pdb=" O MET L 46 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER L 51 " --> pdb=" O LYS L 47 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU L 52 " --> pdb=" O ALA L 48 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LYS L 53 " --> pdb=" O MET L 49 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER L 54 " --> pdb=" O GLN L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 77 removed outlier: 3.520A pdb=" N GLN L 77 " --> pdb=" O ASN L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing helix chain 'N' and resid 14 through 18 removed outlier: 3.651A pdb=" N LEU N 18 " --> pdb=" O ASN N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 24 removed outlier: 3.880A pdb=" N LYS N 23 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR N 24 " --> pdb=" O VAL N 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 20 through 24' Processing helix chain 'N' and resid 34 through 40 removed outlier: 3.696A pdb=" N LYS N 40 " --> pdb=" O ARG N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 66 removed outlier: 3.900A pdb=" N VAL N 65 " --> pdb=" O TYR N 61 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU N 66 " --> pdb=" O VAL N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 61 through 66' Processing helix chain 'N' and resid 84 through 90 Processing helix chain 'Q' and resid 21 through 26 Processing helix chain 'Q' and resid 29 through 37 removed outlier: 4.101A pdb=" N GLN Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU Q 36 " --> pdb=" O GLN Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 43 removed outlier: 4.202A pdb=" N ARG Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Q' and resid 53 through 58 removed outlier: 3.839A pdb=" N LEU Q 57 " --> pdb=" O GLN Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 63 Processing helix chain 'R' and resid 38 through 42 Processing helix chain 'R' and resid 44 through 48 Processing helix chain 'R' and resid 52 through 59 removed outlier: 3.874A pdb=" N GLY R 59 " --> pdb=" O VAL R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 97 removed outlier: 3.708A pdb=" N LEU R 92 " --> pdb=" O ILE R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 113 Processing helix chain 'R' and resid 116 through 120 removed outlier: 3.799A pdb=" N LEU R 120 " --> pdb=" O ARG R 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 11 Processing helix chain 'S' and resid 16 through 21 Processing helix chain 'S' and resid 31 through 36 removed outlier: 3.614A pdb=" N CYS S 35 " --> pdb=" O ASN S 31 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU S 36 " --> pdb=" O LYS S 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 31 through 36' Processing helix chain 'S' and resid 44 through 59 removed outlier: 3.670A pdb=" N GLY S 52 " --> pdb=" O ASN S 48 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS S 56 " --> pdb=" O GLY S 52 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 83 removed outlier: 3.565A pdb=" N GLU S 79 " --> pdb=" O GLU S 75 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG S 81 " --> pdb=" O GLU S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 108 Processing helix chain 'T' and resid 25 through 33 removed outlier: 4.005A pdb=" N PHE T 28 " --> pdb=" O LYS T 25 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE T 30 " --> pdb=" O ALA T 27 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR T 31 " --> pdb=" O PHE T 28 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA T 32 " --> pdb=" O ALA T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 42 removed outlier: 4.255A pdb=" N ALA T 41 " --> pdb=" O ARG T 38 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N HIS T 42 " --> pdb=" O ARG T 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 38 through 42' Processing helix chain 'T' and resid 43 through 48 Processing helix chain 'T' and resid 60 through 66 removed outlier: 3.655A pdb=" N GLU T 63 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU T 65 " --> pdb=" O ASP T 62 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 72 Processing helix chain 'T' and resid 73 through 78 removed outlier: 3.832A pdb=" N GLN T 76 " --> pdb=" O ASN T 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR T 77 " --> pdb=" O PRO T 74 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS T 78 " --> pdb=" O ARG T 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 73 through 78' Processing helix chain 'T' and resid 99 through 110 removed outlier: 3.972A pdb=" N ASN T 105 " --> pdb=" O ASN T 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 122 through 127 removed outlier: 4.593A pdb=" N TRP T 127 " --> pdb=" O LEU T 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 21 removed outlier: 3.742A pdb=" N PHE U 21 " --> pdb=" O ALA U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 52 through 67 removed outlier: 3.607A pdb=" N THR U 60 " --> pdb=" O ARG U 56 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA U 61 " --> pdb=" O ALA U 57 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU U 66 " --> pdb=" O ARG U 62 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 76 Processing helix chain 'U' and resid 97 through 110 removed outlier: 3.614A pdb=" N LEU U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU U 110 " --> pdb=" O ALA U 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 140 removed outlier: 3.814A pdb=" N ASP U 130 " --> pdb=" O GLN U 126 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU U 131 " --> pdb=" O GLY U 127 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP U 132 " --> pdb=" O GLN U 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 46 removed outlier: 3.661A pdb=" N CYS V 36 " --> pdb=" O LEU V 32 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA V 37 " --> pdb=" O GLU V 33 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU V 39 " --> pdb=" O VAL V 35 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE V 40 " --> pdb=" O CYS V 36 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG V 41 " --> pdb=" O ALA V 37 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 61 removed outlier: 3.519A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 76 removed outlier: 3.518A pdb=" N ASP W 76 " --> pdb=" O LEU W 72 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 39 through 49 removed outlier: 3.956A pdb=" N LYS Z 43 " --> pdb=" O GLU Z 39 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET Z 47 " --> pdb=" O LYS Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 83 removed outlier: 3.774A pdb=" N ALA Z 82 " --> pdb=" O SER Z 78 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 115 Processing helix chain 'Z' and resid 116 through 117 No H-bonds generated for 'chain 'Z' and resid 116 through 117' Processing helix chain 'Z' and resid 118 through 120 No H-bonds generated for 'chain 'Z' and resid 118 through 120' Processing helix chain 'Z' and resid 121 through 126 Processing helix chain 'F' and resid 154 through 161 Processing helix chain 'F' and resid 165 through 178 removed outlier: 3.619A pdb=" N VAL F 169 " --> pdb=" O HIS F 165 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG F 171 " --> pdb=" O SER F 167 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 14 removed outlier: 3.578A pdb=" N ALA M 14 " --> pdb=" O ARG M 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 19 Processing helix chain 'M' and resid 37 through 41 removed outlier: 3.955A pdb=" N CYS M 41 " --> pdb=" O LEU M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 50 Processing helix chain 'M' and resid 57 through 66 removed outlier: 3.836A pdb=" N LYS M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 135 No H-bonds generated for 'chain 'M' and resid 133 through 135' Processing helix chain 'M' and resid 247 through 258 removed outlier: 4.129A pdb=" N ASP M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 52 removed outlier: 3.659A pdb=" N ILE O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 44 Processing helix chain 'P' and resid 46 through 57 removed outlier: 3.893A pdb=" N GLY P 51 " --> pdb=" O PRO P 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL P 52 " --> pdb=" O SER P 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER P 57 " --> pdb=" O ILE P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 67 removed outlier: 3.651A pdb=" N VAL P 66 " --> pdb=" O GLN P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 76 Processing helix chain 'P' and resid 85 through 105 removed outlier: 3.704A pdb=" N LEU P 91 " --> pdb=" O ASP P 87 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE P 92 " --> pdb=" O LEU P 88 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA P 97 " --> pdb=" O LYS P 93 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG P 104 " --> pdb=" O LYS P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 132 removed outlier: 3.640A pdb=" N ILE P 116 " --> pdb=" O LYS P 112 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG P 127 " --> pdb=" O HIS P 123 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR P 128 " --> pdb=" O ARG P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 145 Processing helix chain 'P' and resid 146 through 151 removed outlier: 3.839A pdb=" N VAL P 150 " --> pdb=" O ALA P 146 " (cutoff:3.500A) Processing helix chain 'X' and resid 70 through 88 removed outlier: 3.875A pdb=" N ALA X 74 " --> pdb=" O SER X 70 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET X 75 " --> pdb=" O PRO X 71 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU X 76 " --> pdb=" O TYR X 72 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP X 80 " --> pdb=" O LEU X 76 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS X 86 " --> pdb=" O ALA X 82 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 122 removed outlier: 3.501A pdb=" N LEU X 116 " --> pdb=" O ALA X 112 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG X 117 " --> pdb=" O GLN X 113 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU X 119 " --> pdb=" O ALA X 115 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 20 removed outlier: 3.757A pdb=" N SER Y 13 " --> pdb=" O ASP Y 9 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE Y 14 " --> pdb=" O ALA Y 10 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS Y 19 " --> pdb=" O ASN Y 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 31 through 44 removed outlier: 3.673A pdb=" N VAL Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 93 removed outlier: 3.578A pdb=" N ASN Y 92 " --> pdb=" O LYS Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 113 through 120 removed outlier: 3.973A pdb=" N ARG Y 118 " --> pdb=" O GLU Y 114 " (cutoff:3.500A) Processing helix chain 'c' and resid 11 through 20 removed outlier: 3.540A pdb=" N HIS c 16 " --> pdb=" O LYS c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 33 removed outlier: 3.885A pdb=" N ALA c 30 " --> pdb=" O GLN c 26 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY c 33 " --> pdb=" O LYS c 29 " (cutoff:3.500A) Processing helix chain 'c' and resid 33 through 38 Processing helix chain 'c' and resid 129 through 135 removed outlier: 3.561A pdb=" N LEU c 133 " --> pdb=" O SER c 129 " (cutoff:3.500A) Processing helix chain 'e' and resid 12 through 17 removed outlier: 3.814A pdb=" N LYS e 16 " --> pdb=" O PRO e 12 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG e 17 " --> pdb=" O GLU e 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 12 through 17' Processing sheet with id=AA1, first strand: chain 'a' and resid 98 through 102 removed outlier: 7.245A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 41 removed outlier: 7.062A pdb=" N ILE B 48 " --> pdb=" O TYR B 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.757A pdb=" N VAL B 74 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ILE B 99 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 76 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 147 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AA5, first strand: chain 'b' and resid 36 through 43 Processing sheet with id=AA6, first strand: chain 'C' and resid 43 through 50 removed outlier: 8.670A pdb=" N CYS C 96 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP C 32 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N THR C 98 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS C 34 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N PHE C 100 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 13.810A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.065A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG C 136 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 127 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 125 " --> pdb=" O LEU C 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 69 removed outlier: 5.622A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 13.810A pdb=" N ASN C 99 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 13.065A pdb=" N LYS C 219 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N HIS C 101 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET C 217 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS C 214 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG C 136 " --> pdb=" O LYS C 216 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU C 134 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 104 through 115 removed outlier: 6.846A pdb=" N PHE D 127 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE D 109 " --> pdb=" O LYS D 125 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS D 125 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG D 123 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLN D 113 " --> pdb=" O ARG D 121 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ARG D 121 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 130 " --> pdb=" O GLY D 138 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 184 through 188 removed outlier: 3.519A pdb=" N SER D 225 " --> pdb=" O ARG D 194 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'd' and resid 41 through 47 removed outlier: 6.371A pdb=" N ARG d 31 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL d 17 " --> pdb=" O ARG d 31 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLU d 33 " --> pdb=" O THR d 15 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR d 15 " --> pdb=" O GLU d 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS d 10 " --> pdb=" O LEU d 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 34 through 42 removed outlier: 4.258A pdb=" N GLY E 36 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 51 " --> pdb=" O GLY E 36 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE E 50 " --> pdb=" O TYR E 87 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 155 removed outlier: 3.513A pdb=" N ASP E 154 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY E 133 " --> pdb=" O MET E 189 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LYS E 141 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL E 181 " --> pdb=" O LYS E 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 209 through 210 removed outlier: 4.281A pdb=" N SER E 209 " --> pdb=" O ILE S 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 223 through 224 Processing sheet with id=AB6, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.846A pdb=" N PHE G 20 " --> pdb=" O TRP G 23 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TRP G 23 " --> pdb=" O PHE G 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'g' and resid 106 through 107 removed outlier: 4.475A pdb=" N SER g 115 " --> pdb=" O LYS g 107 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'g' and resid 139 through 140 removed outlier: 3.778A pdb=" N HIS g 139 " --> pdb=" O TYR g 148 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR g 148 " --> pdb=" O HIS g 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'H' and resid 12 through 17 removed outlier: 6.617A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 72 through 77 Processing sheet with id=AC2, first strand: chain 'H' and resid 160 through 162 Processing sheet with id=AC3, first strand: chain 'h' and resid 5 through 11 removed outlier: 3.543A pdb=" N ARG h 8 " --> pdb=" O VAL h 309 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL h 309 " --> pdb=" O ARG h 8 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N THR h 10 " --> pdb=" O VAL h 307 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL h 307 " --> pdb=" O THR h 10 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'h' and resid 30 through 34 removed outlier: 3.598A pdb=" N ILE h 31 " --> pdb=" O TRP h 43 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP h 43 " --> pdb=" O ILE h 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'h' and resid 87 through 89 removed outlier: 4.422A pdb=" N LEU h 87 " --> pdb=" O PHE h 101 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE h 101 " --> pdb=" O LEU h 87 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'h' and resid 121 through 122 Processing sheet with id=AC7, first strand: chain 'h' and resid 164 through 166 Processing sheet with id=AC8, first strand: chain 'h' and resid 197 through 200 removed outlier: 3.839A pdb=" N THR h 197 " --> pdb=" O GLY h 210 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY h 210 " --> pdb=" O THR h 197 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 215 through 217 Processing sheet with id=AD1, first strand: chain 'h' and resid 248 through 250 Processing sheet with id=AD2, first strand: chain 'I' and resid 47 through 53 removed outlier: 4.253A pdb=" N ARG I 57 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS I 91 " --> pdb=" O LYS I 58 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 185 through 188 removed outlier: 3.574A pdb=" N ASN I 186 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL I 156 " --> pdb=" O ASN I 186 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU I 188 " --> pdb=" O VAL I 156 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU I 158 " --> pdb=" O GLU I 188 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU I 153 " --> pdb=" O ILE I 144 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE I 144 " --> pdb=" O LEU I 153 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS I 155 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYS I 142 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N HIS I 157 " --> pdb=" O VAL I 140 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS I 142 " --> pdb=" O ASP Y 54 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 3 through 4 removed outlier: 4.043A pdb=" N ILE J 3 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 37 through 38 removed outlier: 6.553A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 62 through 66 removed outlier: 7.439A pdb=" N ILE J 78 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP J 105 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP J 80 " --> pdb=" O LEU J 103 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 140 through 141 Processing sheet with id=AD8, first strand: chain 'L' and resid 23 through 24 Processing sheet with id=AD9, first strand: chain 'Q' and resid 97 through 98 removed outlier: 4.140A pdb=" N THR Q 101 " --> pdb=" O ASN Q 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 14 through 15 removed outlier: 3.500A pdb=" N GLY R 14 " --> pdb=" O ALA R 21 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 96 through 98 Processing sheet with id=AE3, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE4, first strand: chain 'V' and resid 54 through 55 Processing sheet with id=AE5, first strand: chain 'V' and resid 54 through 55 removed outlier: 3.918A pdb=" N GLU V 113 " --> pdb=" O THR V 23 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU V 111 " --> pdb=" O THR V 25 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'V' and resid 63 through 66 Processing sheet with id=AE7, first strand: chain 'W' and resid 32 through 39 removed outlier: 5.556A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 6 through 15 removed outlier: 4.661A pdb=" N PHE Z 12 " --> pdb=" O GLN Z 22 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLN Z 22 " --> pdb=" O PHE Z 12 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N THR Z 14 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ARG Z 20 " --> pdb=" O THR Z 14 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N LYS Z 68 " --> pdb=" O THR Z 62 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N THR Z 62 " --> pdb=" O LYS Z 68 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 42 through 43 Processing sheet with id=AF1, first strand: chain 'M' and resid 75 through 76 removed outlier: 3.507A pdb=" N GLU M 97 " --> pdb=" O ILE M 92 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN M 98 " --> pdb=" O ILE M 114 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 102 through 103 removed outlier: 4.437A pdb=" N ILE M 102 " --> pdb=" O ALA M 110 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 146 through 148 removed outlier: 6.378A pdb=" N HIS M 138 " --> pdb=" O ILE M 129 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE M 129 " --> pdb=" O HIS M 138 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL M 140 " --> pdb=" O ARG M 127 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP M 171 " --> pdb=" O GLN M 161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 192 through 194 removed outlier: 6.453A pdb=" N LEU M 180 " --> pdb=" O ILE M 228 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS M 230 " --> pdb=" O LYS M 233 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 208 through 211 Processing sheet with id=AF6, first strand: chain 'O' and resid 72 through 79 removed outlier: 18.259A pdb=" N ILE O 72 " --> pdb=" O LEU O 93 " (cutoff:3.500A) removed outlier: 15.192A pdb=" N LEU O 93 " --> pdb=" O ILE O 72 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N SER O 74 " --> pdb=" O ASP O 91 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP O 91 " --> pdb=" O SER O 74 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL O 87 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N PHE O 140 " --> pdb=" O ASN O 108 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER O 110 " --> pdb=" O PHE O 140 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL O 142 " --> pdb=" O SER O 110 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N HIS O 112 " --> pdb=" O VAL O 142 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N LYS O 144 " --> pdb=" O HIS O 112 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR O 127 " --> pdb=" O LEU O 143 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL O 145 " --> pdb=" O ILE O 125 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE O 125 " --> pdb=" O VAL O 145 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'X' and resid 44 through 45 removed outlier: 3.961A pdb=" N VAL X 44 " --> pdb=" O ILE X 53 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'X' and resid 92 through 97 removed outlier: 6.334A pdb=" N LEU X 93 " --> pdb=" O ILE X 126 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ARG X 128 " --> pdb=" O LEU X 93 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Y' and resid 109 through 112 removed outlier: 5.708A pdb=" N THR Y 105 " --> pdb=" O ILE Y 125 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ILE Y 125 " --> pdb=" O THR Y 105 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'c' and resid 80 through 83 removed outlier: 7.328A pdb=" N ARG c 71 " --> pdb=" O LEU c 52 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA c 103 " --> pdb=" O VAL c 122 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N VAL c 122 " --> pdb=" O ALA c 103 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 32 through 34 1047 hydrogen bonds defined for protein. 2889 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 960 hydrogen bonds 1514 hydrogen bond angles 0 basepair planarities 398 basepair parallelities 893 stacking parallelities Total time for adding SS restraints: 54.65 Time building geometry restraints manager: 33.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10919 1.32 - 1.45: 31337 1.45 - 1.57: 36912 1.57 - 1.69: 3667 1.69 - 1.82: 274 Bond restraints: 83109 Sorted by residual: bond pdb=" C ASP E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.337 1.383 -0.046 9.80e-03 1.04e+04 2.23e+01 bond pdb=" C THR J 130 " pdb=" N PRO J 131 " ideal model delta sigma weight residual 1.337 1.379 -0.042 1.11e-02 8.12e+03 1.44e+01 bond pdb=" C VAL B 197 " pdb=" N MET B 198 " ideal model delta sigma weight residual 1.329 1.284 0.045 1.86e-02 2.89e+03 5.75e+00 bond pdb=" O3' C A1518 " pdb=" P U A1519 " ideal model delta sigma weight residual 1.607 1.641 -0.034 1.50e-02 4.44e+03 5.25e+00 bond pdb=" C3' G A 752 " pdb=" O3' G A 752 " ideal model delta sigma weight residual 1.427 1.459 -0.032 1.50e-02 4.44e+03 4.41e+00 ... (remaining 83104 not shown) Histogram of bond angle deviations from ideal: 98.72 - 106.68: 11842 106.68 - 114.64: 52101 114.64 - 122.61: 42964 122.61 - 130.57: 13319 130.57 - 138.53: 790 Bond angle restraints: 121016 Sorted by residual: angle pdb=" C GLU a 61 " pdb=" N VAL a 62 " pdb=" CA VAL a 62 " ideal model delta sigma weight residual 120.24 124.73 -4.49 6.30e-01 2.52e+00 5.09e+01 angle pdb=" C VAL G 139 " pdb=" N ASP G 140 " pdb=" CA ASP G 140 " ideal model delta sigma weight residual 121.70 133.69 -11.99 1.80e+00 3.09e-01 4.44e+01 angle pdb=" C3' A i6143 " pdb=" O3' A i6143 " pdb=" P G i6144 " ideal model delta sigma weight residual 120.20 128.82 -8.62 1.50e+00 4.44e-01 3.30e+01 angle pdb=" N VAL S 15 " pdb=" CA VAL S 15 " pdb=" C VAL S 15 " ideal model delta sigma weight residual 113.53 107.90 5.63 9.80e-01 1.04e+00 3.30e+01 angle pdb=" C3' G A 752 " pdb=" O3' G A 752 " pdb=" P C A 753 " ideal model delta sigma weight residual 120.20 128.20 -8.00 1.50e+00 4.44e-01 2.85e+01 ... (remaining 121011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 47456 35.99 - 71.98: 4847 71.98 - 107.97: 617 107.97 - 143.96: 17 143.96 - 179.95: 30 Dihedral angle restraints: 52967 sinusoidal: 39068 harmonic: 13899 Sorted by residual: dihedral pdb=" CA SER G 142 " pdb=" C SER G 142 " pdb=" N PRO G 143 " pdb=" CA PRO G 143 " ideal model delta harmonic sigma weight residual -180.00 -126.24 -53.76 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" O4' U A1551 " pdb=" C1' U A1551 " pdb=" N1 U A1551 " pdb=" C2 U A1551 " ideal model delta sinusoidal sigma weight residual -160.00 19.95 -179.95 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A 427 " pdb=" C1' U A 427 " pdb=" N1 U A 427 " pdb=" C2 U A 427 " ideal model delta sinusoidal sigma weight residual -160.00 9.82 -169.82 1 1.50e+01 4.44e-03 8.47e+01 ... (remaining 52964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 13693 0.080 - 0.159: 1222 0.159 - 0.239: 96 0.239 - 0.318: 21 0.318 - 0.398: 6 Chirality restraints: 15038 Sorted by residual: chirality pdb=" CB VAL M 89 " pdb=" CA VAL M 89 " pdb=" CG1 VAL M 89 " pdb=" CG2 VAL M 89 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CB ILE a 68 " pdb=" CA ILE a 68 " pdb=" CG1 ILE a 68 " pdb=" CG2 ILE a 68 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" C3' C A 24 " pdb=" C4' C A 24 " pdb=" O3' C A 24 " pdb=" C2' C A 24 " both_signs ideal model delta sigma weight residual False -2.48 -2.12 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 15035 not shown) Planarity restraints: 8535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG G 122 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C ARG G 122 " -0.060 2.00e-02 2.50e+03 pdb=" O ARG G 122 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU G 123 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL P 22 " -0.057 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO P 23 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO P 23 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO P 23 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 132 " 0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO B 133 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " 0.045 5.00e-02 4.00e+02 ... (remaining 8532 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 11934 2.75 - 3.29: 68677 3.29 - 3.82: 155934 3.82 - 4.36: 184003 4.36 - 4.90: 261960 Nonbonded interactions: 682508 Sorted by model distance: nonbonded pdb=" OG1 THR M 115 " pdb=" O GLU M 117 " model vdw 2.211 2.440 nonbonded pdb=" O2' C A 930 " pdb=" OP1 G A1104 " model vdw 2.231 2.440 nonbonded pdb=" O2' C A1529 " pdb=" O VAL U 87 " model vdw 2.237 2.440 nonbonded pdb=" O LEU U 39 " pdb=" OG SER U 96 " model vdw 2.240 2.440 nonbonded pdb=" O2' G A1550 " pdb=" O2 C A1558 " model vdw 2.241 2.440 ... (remaining 682503 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.430 Construct map_model_manager: 0.100 Extract box with map and model: 9.750 Check model and map are aligned: 0.860 Set scattering table: 0.550 Process input model: 198.840 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 : 0.006 0.085 83109 Z= 0.363 Angle : 0.928 14.556 121016 Z= 0.492 Chirality : 0.048 0.398 15038 Planarity : 0.006 0.086 8535 Dihedral : 23.160 179.955 44001 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.55 % Favored : 92.28 % Rotamer: Outliers : 0.50 % Allowed : 9.88 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.07 % Twisted Proline : 1.03 % Twisted General : 0.35 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.09), residues: 4767 helix: -4.37 (0.07), residues: 1255 sheet: -2.01 (0.19), residues: 650 loop : -2.67 (0.10), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP K 7 HIS 0.009 0.002 HIS h 188 PHE 0.033 0.003 PHE c 105 TYR 0.047 0.002 TYR O 99 ARG 0.015 0.001 ARG d 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 902 time to evaluate : 4.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.8856 (pttt) cc_final: 0.8544 (pttt) REVERT: B 89 LYS cc_start: 0.7856 (mmtm) cc_final: 0.7295 (mmtp) REVERT: B 164 ASN cc_start: 0.7894 (t0) cc_final: 0.7411 (t0) REVERT: B 176 TRP cc_start: 0.8373 (t60) cc_final: 0.7693 (t60) REVERT: B 177 MET cc_start: 0.8801 (ttm) cc_final: 0.8593 (mtp) REVERT: C 44 ILE cc_start: 0.8736 (mm) cc_final: 0.8448 (mm) REVERT: C 111 CYS cc_start: 0.8726 (m) cc_final: 0.8402 (m) REVERT: C 133 TYR cc_start: 0.8390 (m-80) cc_final: 0.8131 (m-80) REVERT: C 229 MET cc_start: 0.8519 (mmm) cc_final: 0.8245 (mmm) REVERT: D 221 ASP cc_start: 0.7391 (m-30) cc_final: 0.7070 (m-30) REVERT: E 18 LYS cc_start: 0.2454 (pptt) cc_final: 0.2162 (tmmt) REVERT: E 32 ASP cc_start: 0.8425 (p0) cc_final: 0.8217 (p0) REVERT: E 77 PHE cc_start: 0.8425 (m-80) cc_final: 0.8094 (m-10) REVERT: E 119 CYS cc_start: 0.8419 (m) cc_final: 0.8171 (m) REVERT: E 126 ILE cc_start: 0.8847 (mm) cc_final: 0.8601 (mm) REVERT: E 127 MET cc_start: 0.8888 (mmm) cc_final: 0.8590 (mmm) REVERT: E 152 PHE cc_start: 0.8085 (m-80) cc_final: 0.7727 (m-10) REVERT: E 179 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7433 (mm-40) REVERT: E 207 HIS cc_start: 0.8162 (t70) cc_final: 0.7861 (t-170) REVERT: E 216 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7477 (mp0) REVERT: f 95 GLN cc_start: 0.8769 (pp30) cc_final: 0.8408 (pp30) REVERT: G 76 MET cc_start: 0.6073 (mmp) cc_final: 0.5779 (mmp) REVERT: G 81 ARG cc_start: 0.5837 (mmp80) cc_final: 0.5181 (mmp80) REVERT: h 140 TYR cc_start: 0.7915 (t80) cc_final: 0.7493 (t80) REVERT: h 147 HIS cc_start: 0.3713 (p-80) cc_final: 0.3461 (p90) REVERT: h 217 MET cc_start: 0.6375 (mmt) cc_final: 0.4616 (mmt) REVERT: h 256 ILE cc_start: 0.7154 (mm) cc_final: 0.6922 (mm) REVERT: h 268 ASP cc_start: 0.5457 (OUTLIER) cc_final: 0.4881 (m-30) REVERT: I 187 PHE cc_start: 0.8191 (m-80) cc_final: 0.7380 (m-80) REVERT: I 189 PHE cc_start: 0.8769 (m-80) cc_final: 0.8489 (m-80) REVERT: J 150 ASP cc_start: 0.9046 (t0) cc_final: 0.8652 (t0) REVERT: K 144 ILE cc_start: 0.9105 (mm) cc_final: 0.8819 (mm) REVERT: L 29 MET cc_start: 0.8395 (ttm) cc_final: 0.7690 (ttt) REVERT: L 49 MET cc_start: 0.6752 (mmt) cc_final: 0.6360 (mmt) REVERT: Q 50 ARG cc_start: 0.7060 (mmt-90) cc_final: 0.6272 (tpp80) REVERT: Q 54 HIS cc_start: 0.7679 (m-70) cc_final: 0.7159 (m90) REVERT: Q 111 MET cc_start: 0.1687 (mtt) cc_final: 0.1264 (mtt) REVERT: R 67 ASP cc_start: 0.8012 (t0) cc_final: 0.7791 (t0) REVERT: R 92 LEU cc_start: 0.8425 (tp) cc_final: 0.8180 (tp) REVERT: R 107 GLU cc_start: 0.9026 (pp20) cc_final: 0.8715 (pp20) REVERT: S 48 ASN cc_start: 0.7841 (t0) cc_final: 0.7640 (t0) REVERT: T 65 GLU cc_start: 0.8515 (mp0) cc_final: 0.8300 (mp0) REVERT: T 126 PHE cc_start: 0.3388 (t80) cc_final: 0.2450 (t80) REVERT: V 21 ARG cc_start: 0.6173 (ttm170) cc_final: 0.5499 (ttm110) REVERT: V 99 LYS cc_start: 0.6200 (tptp) cc_final: 0.5560 (mttm) REVERT: W 81 LYS cc_start: 0.9086 (mmmt) cc_final: 0.8708 (mmtm) REVERT: M 66 MET cc_start: 0.8462 (mmt) cc_final: 0.8235 (mmm) REVERT: M 80 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9146 (mm) REVERT: M 87 MET cc_start: 0.9289 (mmt) cc_final: 0.8666 (mmm) REVERT: M 157 ASN cc_start: 0.8447 (t0) cc_final: 0.7914 (t0) REVERT: M 206 ASP cc_start: 0.7722 (m-30) cc_final: 0.7477 (m-30) REVERT: O 1 MET cc_start: 0.5068 (mmt) cc_final: 0.4643 (mmt) REVERT: O 10 TYR cc_start: 0.8488 (t80) cc_final: 0.8040 (t80) REVERT: O 11 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8660 (mm110) REVERT: O 37 TYR cc_start: 0.9280 (p90) cc_final: 0.9072 (p90) REVERT: O 55 TYR cc_start: 0.7363 (p90) cc_final: 0.7083 (p90) REVERT: O 98 LYS cc_start: 0.8546 (tttt) cc_final: 0.8210 (tttt) REVERT: O 121 GLN cc_start: 0.8196 (mp10) cc_final: 0.7964 (mp10) REVERT: P 62 GLN cc_start: 0.7857 (tp40) cc_final: 0.7533 (mm-40) REVERT: X 56 VAL cc_start: 0.8925 (p) cc_final: 0.8494 (p) REVERT: Y 4 MET cc_start: 0.8631 (mmt) cc_final: 0.8396 (mmt) REVERT: Y 15 ASN cc_start: 0.8875 (t0) cc_final: 0.8105 (t0) REVERT: Y 72 CYS cc_start: 0.8404 (p) cc_final: 0.8091 (p) REVERT: Y 90 GLN cc_start: 0.9125 (pt0) cc_final: 0.8674 (pt0) REVERT: Y 111 MET cc_start: 0.8482 (ptt) cc_final: 0.8224 (ptp) REVERT: Y 112 ASP cc_start: 0.8942 (p0) cc_final: 0.8459 (p0) REVERT: c 1 MET cc_start: 0.0812 (mmt) cc_final: 0.0505 (mtt) REVERT: c 53 GLU cc_start: 0.8400 (pt0) cc_final: 0.8155 (pt0) REVERT: c 94 ILE cc_start: 0.9065 (mt) cc_final: 0.8627 (mt) REVERT: e 36 LYS cc_start: 0.7966 (mmmt) cc_final: 0.7328 (mttm) REVERT: e 51 GLN cc_start: 0.8176 (mt0) cc_final: 0.7919 (mt0) outliers start: 21 outliers final: 9 residues processed: 918 average time/residue: 0.7908 time to fit residues: 1205.0470 Evaluate side-chains 612 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 601 time to evaluate : 4.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain h residue 268 ASP Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain c residue 128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 550 optimal weight: 8.9990 chunk 494 optimal weight: 20.0000 chunk 274 optimal weight: 10.0000 chunk 168 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 chunk 264 optimal weight: 8.9990 chunk 511 optimal weight: 0.0000 chunk 197 optimal weight: 9.9990 chunk 310 optimal weight: 2.9990 chunk 380 optimal weight: 9.9990 chunk 592 optimal weight: 20.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 45 ASN ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 ASN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN C 157 GLN C 158 HIS D 113 GLN D 136 HIS D 277 HIS ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN f 110 GLN f 117 ASN G 74 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 ASN g 139 HIS H 146 ASN H 177 GLN h 76 GLN ** h 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN J 168 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 HIS L 77 GLN Q 32 GLN Q 54 HIS ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 26 ASN T 10 GLN T 101 ASN T 105 ASN U 85 ASN ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 2 GLN Z 106 GLN F 178 ASN M 17 HIS M 50 ASN ** M 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 GLN P 5 HIS ** P 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 105 ASN ** X 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 49 HIS ** e 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 83109 Z= 0.312 Angle : 0.734 10.060 121016 Z= 0.376 Chirality : 0.042 0.265 15038 Planarity : 0.006 0.087 8535 Dihedral : 24.237 179.887 34058 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.37 % Favored : 91.61 % Rotamer: Outliers : 3.12 % Allowed : 17.26 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.09 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.11), residues: 4767 helix: -2.71 (0.11), residues: 1334 sheet: -1.78 (0.19), residues: 668 loop : -2.25 (0.11), residues: 2765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP h 150 HIS 0.015 0.001 HIS G 51 PHE 0.021 0.002 PHE I 135 TYR 0.023 0.002 TYR a 55 ARG 0.012 0.001 ARG M 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 642 time to evaluate : 4.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 57 LYS cc_start: 0.8985 (tptp) cc_final: 0.8583 (tptt) REVERT: B 52 LYS cc_start: 0.8838 (pttt) cc_final: 0.8405 (pttt) REVERT: B 164 ASN cc_start: 0.7837 (t0) cc_final: 0.7363 (t0) REVERT: B 176 TRP cc_start: 0.8390 (t60) cc_final: 0.7953 (t60) REVERT: B 177 MET cc_start: 0.8995 (ttm) cc_final: 0.8612 (ttm) REVERT: C 68 GLU cc_start: 0.7636 (tp30) cc_final: 0.7388 (tp30) REVERT: C 83 LYS cc_start: 0.8003 (ptpt) cc_final: 0.7440 (ptpp) REVERT: C 99 ASN cc_start: 0.8132 (t0) cc_final: 0.7878 (t0) REVERT: C 111 CYS cc_start: 0.8783 (m) cc_final: 0.8407 (m) REVERT: C 133 TYR cc_start: 0.8490 (m-80) cc_final: 0.8281 (m-80) REVERT: C 155 TYR cc_start: 0.7812 (m-80) cc_final: 0.7105 (m-80) REVERT: C 172 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8401 (mtp) REVERT: E 32 ASP cc_start: 0.8572 (p0) cc_final: 0.8145 (p0) REVERT: E 119 CYS cc_start: 0.8378 (m) cc_final: 0.8078 (m) REVERT: E 125 PHE cc_start: 0.8183 (t80) cc_final: 0.7911 (t80) REVERT: E 127 MET cc_start: 0.8905 (mmm) cc_final: 0.8674 (mmm) REVERT: E 152 PHE cc_start: 0.8329 (m-80) cc_final: 0.7911 (m-80) REVERT: E 179 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7523 (mm-40) REVERT: E 207 HIS cc_start: 0.8165 (t70) cc_final: 0.7842 (t-170) REVERT: f 95 GLN cc_start: 0.8764 (pp30) cc_final: 0.8302 (pp30) REVERT: G 81 ARG cc_start: 0.6150 (mmp80) cc_final: 0.5509 (mmp80) REVERT: h 140 TYR cc_start: 0.8046 (t80) cc_final: 0.7777 (t80) REVERT: h 268 ASP cc_start: 0.5680 (OUTLIER) cc_final: 0.5385 (m-30) REVERT: I 72 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.7152 (t80) REVERT: I 189 PHE cc_start: 0.8722 (m-80) cc_final: 0.8475 (m-80) REVERT: J 150 ASP cc_start: 0.8676 (t0) cc_final: 0.8315 (t0) REVERT: L 1 MET cc_start: 0.3524 (ttt) cc_final: 0.2889 (ttt) REVERT: L 7 ASN cc_start: 0.7312 (m110) cc_final: 0.6789 (m110) REVERT: L 29 MET cc_start: 0.8031 (ttm) cc_final: 0.7828 (ttm) REVERT: L 49 MET cc_start: 0.6925 (mmt) cc_final: 0.6478 (mmt) REVERT: Q 54 HIS cc_start: 0.7539 (m170) cc_final: 0.7053 (m90) REVERT: Q 111 MET cc_start: 0.1869 (mtt) cc_final: 0.1296 (mtt) REVERT: R 62 ARG cc_start: 0.7173 (mtm180) cc_final: 0.6969 (mtm180) REVERT: R 67 ASP cc_start: 0.8091 (t0) cc_final: 0.7887 (t0) REVERT: S 48 ASN cc_start: 0.7910 (t0) cc_final: 0.7632 (t0) REVERT: T 21 ASP cc_start: 0.8220 (t70) cc_final: 0.7949 (t70) REVERT: T 126 PHE cc_start: 0.3347 (t80) cc_final: 0.2722 (t80) REVERT: U 88 MET cc_start: 0.8286 (mmm) cc_final: 0.8047 (mmm) REVERT: V 21 ARG cc_start: 0.6336 (ttm170) cc_final: 0.5899 (ttm110) REVERT: V 28 ASN cc_start: 0.8550 (t0) cc_final: 0.8222 (t0) REVERT: V 99 LYS cc_start: 0.6327 (tptp) cc_final: 0.5719 (mttt) REVERT: W 81 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8707 (mmtm) REVERT: F 166 SER cc_start: 0.9384 (OUTLIER) cc_final: 0.8864 (m) REVERT: F 176 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8610 (tm-30) REVERT: M 66 MET cc_start: 0.8504 (mmt) cc_final: 0.8253 (mmm) REVERT: M 87 MET cc_start: 0.9318 (mmt) cc_final: 0.8824 (mmm) REVERT: M 126 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8524 (p) REVERT: M 157 ASN cc_start: 0.8688 (t0) cc_final: 0.8048 (t0) REVERT: O 37 TYR cc_start: 0.9309 (p90) cc_final: 0.9079 (p90) REVERT: O 98 LYS cc_start: 0.8488 (tttt) cc_final: 0.8093 (tttt) REVERT: O 121 GLN cc_start: 0.8268 (mp10) cc_final: 0.7534 (mp-120) REVERT: P 62 GLN cc_start: 0.7794 (tp40) cc_final: 0.7392 (mm-40) REVERT: X 75 MET cc_start: 0.7717 (mmm) cc_final: 0.7489 (ttt) REVERT: X 103 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7353 (p0) REVERT: X 124 MET cc_start: 0.8296 (mmm) cc_final: 0.8000 (mmm) REVERT: X 138 ASP cc_start: 0.7039 (t0) cc_final: 0.6782 (t0) REVERT: Y 4 MET cc_start: 0.8596 (mmt) cc_final: 0.8325 (mmt) REVERT: Y 15 ASN cc_start: 0.8659 (t0) cc_final: 0.8420 (t0) REVERT: Y 42 MET cc_start: 0.8915 (tmm) cc_final: 0.8510 (tmm) REVERT: Y 62 VAL cc_start: 0.9525 (t) cc_final: 0.9265 (m) REVERT: Y 72 CYS cc_start: 0.8384 (p) cc_final: 0.8013 (p) REVERT: Y 111 MET cc_start: 0.8807 (ptt) cc_final: 0.8295 (ptp) REVERT: Y 112 ASP cc_start: 0.8856 (p0) cc_final: 0.8261 (p0) REVERT: c 1 MET cc_start: 0.1080 (mmt) cc_final: 0.0385 (mtt) REVERT: e 14 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7729 (pt0) REVERT: e 17 ARG cc_start: 0.7984 (ptp-170) cc_final: 0.7743 (mtp85) outliers start: 130 outliers final: 73 residues processed: 723 average time/residue: 0.7333 time to fit residues: 908.3920 Evaluate side-chains 647 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 568 time to evaluate : 4.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 172 MET Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain h residue 62 HIS Chi-restraints excluded: chain h residue 98 THR Chi-restraints excluded: chain h residue 268 ASP Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 206 LYS Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 116 ASN Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain U residue 60 THR Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain X residue 103 ASN Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain c residue 4 CYS Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain e residue 53 VAL Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 67 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 329 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 492 optimal weight: 0.0970 chunk 403 optimal weight: 2.9990 chunk 163 optimal weight: 30.0000 chunk 593 optimal weight: 5.9990 chunk 640 optimal weight: 10.0000 chunk 528 optimal weight: 10.0000 chunk 588 optimal weight: 2.9990 chunk 202 optimal weight: 0.5980 chunk 475 optimal weight: 20.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 64 ASN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 HIS h 104 HIS h 181 ASN h 188 HIS h 191 HIS J 64 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 HIS S 62 GLN T 10 GLN ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 GLN T 101 ASN ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 35 ASN ** M 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 HIS X 32 HIS ** Y 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 83109 Z= 0.159 Angle : 0.605 9.636 121016 Z= 0.310 Chirality : 0.037 0.269 15038 Planarity : 0.004 0.074 8535 Dihedral : 24.020 179.621 34053 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.12 % Allowed : 19.18 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.09 % Twisted Proline : 1.03 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.11), residues: 4767 helix: -1.88 (0.13), residues: 1338 sheet: -1.59 (0.19), residues: 662 loop : -1.92 (0.11), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 55 HIS 0.009 0.001 HIS K 124 PHE 0.026 0.001 PHE D 269 TYR 0.023 0.001 TYR L 70 ARG 0.007 0.000 ARG L 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 705 time to evaluate : 4.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.8800 (pttt) cc_final: 0.8493 (pttt) REVERT: B 164 ASN cc_start: 0.7771 (t0) cc_final: 0.7292 (t0) REVERT: B 176 TRP cc_start: 0.8303 (t60) cc_final: 0.8028 (t60) REVERT: b 46 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7076 (pt0) REVERT: b 64 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8348 (mm) REVERT: C 44 ILE cc_start: 0.8376 (mm) cc_final: 0.7975 (mm) REVERT: C 71 LEU cc_start: 0.8562 (mt) cc_final: 0.8231 (mt) REVERT: C 99 ASN cc_start: 0.8007 (t0) cc_final: 0.7693 (t0) REVERT: C 172 MET cc_start: 0.8552 (mtp) cc_final: 0.8317 (mtt) REVERT: D 72 ASP cc_start: 0.8240 (t0) cc_final: 0.8000 (t0) REVERT: D 221 ASP cc_start: 0.7326 (m-30) cc_final: 0.6987 (m-30) REVERT: D 224 THR cc_start: 0.8810 (m) cc_final: 0.8171 (p) REVERT: D 269 PHE cc_start: 0.8771 (m-10) cc_final: 0.8566 (m-10) REVERT: E 32 ASP cc_start: 0.8440 (p0) cc_final: 0.8058 (p0) REVERT: E 119 CYS cc_start: 0.8326 (m) cc_final: 0.7930 (m) REVERT: E 127 MET cc_start: 0.8878 (mmm) cc_final: 0.8622 (mmm) REVERT: E 152 PHE cc_start: 0.8407 (m-80) cc_final: 0.7873 (m-80) REVERT: E 179 GLN cc_start: 0.7818 (mm-40) cc_final: 0.7381 (mm-40) REVERT: E 207 HIS cc_start: 0.8178 (t70) cc_final: 0.7911 (t-170) REVERT: f 95 GLN cc_start: 0.8642 (pp30) cc_final: 0.8388 (pp30) REVERT: G 88 MET cc_start: 0.6448 (ttp) cc_final: 0.6210 (ttm) REVERT: G 89 THR cc_start: 0.8228 (m) cc_final: 0.7927 (p) REVERT: H 217 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6054 (tmm) REVERT: h 140 TYR cc_start: 0.7977 (t80) cc_final: 0.7666 (t80) REVERT: h 147 HIS cc_start: 0.3615 (p-80) cc_final: 0.3414 (p90) REVERT: h 217 MET cc_start: 0.6562 (mmt) cc_final: 0.5077 (mmt) REVERT: I 72 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.7032 (t80) REVERT: I 76 GLN cc_start: 0.7157 (tt0) cc_final: 0.6894 (mt0) REVERT: J 153 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8491 (mttt) REVERT: J 154 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8210 (mmtm) REVERT: L 49 MET cc_start: 0.7058 (mmt) cc_final: 0.6459 (mmt) REVERT: Q 34 MET cc_start: 0.7443 (mmt) cc_final: 0.7236 (mmp) REVERT: Q 50 ARG cc_start: 0.6971 (mmt-90) cc_final: 0.6188 (tpp80) REVERT: Q 52 LYS cc_start: 0.6947 (mmmt) cc_final: 0.6503 (mmtt) REVERT: Q 54 HIS cc_start: 0.7684 (m170) cc_final: 0.7209 (m90) REVERT: Q 97 TYR cc_start: 0.1807 (t80) cc_final: 0.1451 (t80) REVERT: Q 111 MET cc_start: 0.1093 (mtt) cc_final: 0.0512 (mtt) REVERT: R 107 GLU cc_start: 0.8544 (pp20) cc_final: 0.8258 (pp20) REVERT: S 47 ARG cc_start: 0.8160 (ppt170) cc_final: 0.7938 (ptp90) REVERT: T 23 ARG cc_start: 0.2689 (tpt170) cc_final: 0.2413 (tpt90) REVERT: T 126 PHE cc_start: 0.3293 (t80) cc_final: 0.2758 (t80) REVERT: T 132 ARG cc_start: 0.2703 (OUTLIER) cc_final: 0.0501 (tpp80) REVERT: V 21 ARG cc_start: 0.6383 (ttm170) cc_final: 0.6145 (ttm110) REVERT: V 28 ASN cc_start: 0.8043 (t0) cc_final: 0.7644 (t0) REVERT: V 99 LYS cc_start: 0.6395 (tptp) cc_final: 0.5911 (mttt) REVERT: W 27 LYS cc_start: 0.6904 (mptt) cc_final: 0.6638 (mptt) REVERT: W 64 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6599 (mm-30) REVERT: W 81 LYS cc_start: 0.9032 (mmmt) cc_final: 0.8735 (mmtt) REVERT: F 155 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7893 (tp30) REVERT: F 166 SER cc_start: 0.9312 (t) cc_final: 0.8857 (m) REVERT: M 87 MET cc_start: 0.9295 (mmt) cc_final: 0.8615 (mmt) REVERT: M 157 ASN cc_start: 0.8574 (t0) cc_final: 0.7801 (t0) REVERT: M 199 GLU cc_start: 0.7956 (mp0) cc_final: 0.7143 (mp0) REVERT: O 98 LYS cc_start: 0.8289 (tttt) cc_final: 0.7894 (tttt) REVERT: O 121 GLN cc_start: 0.8193 (mp10) cc_final: 0.7613 (mp10) REVERT: O 124 ASP cc_start: 0.8166 (m-30) cc_final: 0.7962 (m-30) REVERT: X 93 LEU cc_start: 0.8342 (tp) cc_final: 0.8008 (tp) REVERT: X 103 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7556 (p0) REVERT: Y 4 MET cc_start: 0.8612 (mmt) cc_final: 0.8291 (mmt) REVERT: Y 15 ASN cc_start: 0.8721 (t0) cc_final: 0.8181 (t0) REVERT: Y 62 VAL cc_start: 0.9485 (t) cc_final: 0.9261 (m) REVERT: Y 70 ASN cc_start: 0.8487 (m-40) cc_final: 0.8049 (m110) REVERT: Y 90 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8702 (pt0) REVERT: Y 111 MET cc_start: 0.8528 (ptt) cc_final: 0.8108 (ptp) REVERT: Y 112 ASP cc_start: 0.8700 (p0) cc_final: 0.7914 (p0) REVERT: e 14 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7605 (pt0) REVERT: e 36 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7141 (mptt) REVERT: e 51 GLN cc_start: 0.8388 (mt0) cc_final: 0.8159 (mt0) outliers start: 130 outliers final: 71 residues processed: 782 average time/residue: 0.8349 time to fit residues: 1141.3676 Evaluate side-chains 683 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 605 time to evaluate : 4.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 45 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 116 ASN Chi-restraints excluded: chain T residue 10 GLN Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 82 TRP Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 129 LEU Chi-restraints excluded: chain T residue 132 ARG Chi-restraints excluded: chain U residue 51 ASN Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 65 SER Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 156 MET Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 69 ASN Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 103 ASN Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain Y residue 105 THR Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 586 optimal weight: 7.9990 chunk 445 optimal weight: 50.0000 chunk 307 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 283 optimal weight: 4.9990 chunk 398 optimal weight: 0.9990 chunk 595 optimal weight: 8.9990 chunk 630 optimal weight: 20.0000 chunk 311 optimal weight: 30.0000 chunk 564 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 72 HIS C 148 ASN f 88 GLN f 95 GLN G 148 ASN G 203 ASN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 GLN ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN T 134 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 HIS M 188 ASN ** Y 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 83109 Z= 0.250 Angle : 0.640 11.561 121016 Z= 0.327 Chirality : 0.039 0.272 15038 Planarity : 0.005 0.091 8535 Dihedral : 23.941 179.506 34051 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 3.97 % Allowed : 20.96 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.09 % Twisted Proline : 0.52 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.12), residues: 4767 helix: -1.44 (0.14), residues: 1329 sheet: -1.55 (0.19), residues: 693 loop : -1.83 (0.11), residues: 2745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP h 259 HIS 0.009 0.001 HIS G 51 PHE 0.021 0.002 PHE R 63 TYR 0.027 0.002 TYR b 68 ARG 0.007 0.000 ARG G 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 624 time to evaluate : 4.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 LYS cc_start: 0.8807 (pttt) cc_final: 0.8398 (pttt) REVERT: B 131 HIS cc_start: 0.8108 (p90) cc_final: 0.7781 (p90) REVERT: B 164 ASN cc_start: 0.7861 (t0) cc_final: 0.7265 (t0) REVERT: B 176 TRP cc_start: 0.8408 (t60) cc_final: 0.8107 (t60) REVERT: b 46 GLU cc_start: 0.7680 (pt0) cc_final: 0.7287 (pt0) REVERT: C 103 MET cc_start: 0.7341 (tmm) cc_final: 0.6723 (tmm) REVERT: C 191 ASP cc_start: 0.7037 (p0) cc_final: 0.6386 (p0) REVERT: D 221 ASP cc_start: 0.7371 (m-30) cc_final: 0.7138 (m-30) REVERT: D 224 THR cc_start: 0.8799 (m) cc_final: 0.8145 (p) REVERT: D 269 PHE cc_start: 0.8861 (m-10) cc_final: 0.8606 (m-10) REVERT: d 59 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7475 (pt) REVERT: E 32 ASP cc_start: 0.8503 (p0) cc_final: 0.8044 (p0) REVERT: E 87 TYR cc_start: 0.6996 (m-80) cc_final: 0.6756 (m-80) REVERT: E 119 CYS cc_start: 0.8472 (m) cc_final: 0.8031 (m) REVERT: E 127 MET cc_start: 0.8683 (mmm) cc_final: 0.8395 (mmm) REVERT: E 152 PHE cc_start: 0.8135 (m-80) cc_final: 0.7860 (m-80) REVERT: E 179 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7457 (mm-40) REVERT: E 207 HIS cc_start: 0.8186 (t70) cc_final: 0.7927 (t-170) REVERT: f 95 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8368 (pp30) REVERT: G 88 MET cc_start: 0.6595 (ttp) cc_final: 0.6280 (ttt) REVERT: H 217 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6059 (tmm) REVERT: h 140 TYR cc_start: 0.7978 (t80) cc_final: 0.7387 (t80) REVERT: h 217 MET cc_start: 0.6924 (mmt) cc_final: 0.5335 (mmt) REVERT: I 72 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7194 (t80) REVERT: J 154 LYS cc_start: 0.8789 (mmtm) cc_final: 0.8534 (mmtm) REVERT: K 26 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7562 (t0) REVERT: L 1 MET cc_start: 0.2775 (ttt) cc_final: 0.2574 (ttt) REVERT: L 49 MET cc_start: 0.7109 (mmt) cc_final: 0.6409 (mmt) REVERT: Q 34 MET cc_start: 0.7623 (mmm) cc_final: 0.7417 (mmm) REVERT: Q 52 LYS cc_start: 0.6956 (mmmt) cc_final: 0.6532 (mmtt) REVERT: Q 54 HIS cc_start: 0.7723 (m170) cc_final: 0.7276 (m90) REVERT: Q 111 MET cc_start: 0.1221 (mtt) cc_final: 0.0637 (mtt) REVERT: R 107 GLU cc_start: 0.8555 (pp20) cc_final: 0.8333 (pp20) REVERT: R 109 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8939 (mmtm) REVERT: T 21 ASP cc_start: 0.8259 (t70) cc_final: 0.7970 (t70) REVERT: T 23 ARG cc_start: 0.3017 (tpt170) cc_final: 0.2571 (tpt90) REVERT: T 126 PHE cc_start: 0.3286 (t80) cc_final: 0.2798 (t80) REVERT: T 132 ARG cc_start: 0.2778 (OUTLIER) cc_final: 0.0333 (tpp80) REVERT: V 21 ARG cc_start: 0.6512 (ttm170) cc_final: 0.6300 (ttm110) REVERT: V 28 ASN cc_start: 0.7971 (t0) cc_final: 0.7629 (t0) REVERT: V 99 LYS cc_start: 0.6449 (tptp) cc_final: 0.5950 (mttt) REVERT: W 1 MET cc_start: 0.6320 (tpp) cc_final: 0.6119 (tpp) REVERT: W 81 LYS cc_start: 0.9031 (mmmt) cc_final: 0.8723 (mmtt) REVERT: F 155 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8130 (tp30) REVERT: F 166 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8742 (m) REVERT: M 87 MET cc_start: 0.9306 (mmt) cc_final: 0.8605 (mmt) REVERT: M 157 ASN cc_start: 0.8698 (t0) cc_final: 0.7993 (t0) REVERT: M 166 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7687 (p) REVERT: M 199 GLU cc_start: 0.8022 (mp0) cc_final: 0.7270 (mp0) REVERT: O 11 GLN cc_start: 0.8909 (mm110) cc_final: 0.8571 (mm110) REVERT: O 121 GLN cc_start: 0.8223 (mp10) cc_final: 0.7334 (mp10) REVERT: X 93 LEU cc_start: 0.8475 (tp) cc_final: 0.8133 (tp) REVERT: Y 4 MET cc_start: 0.8657 (mmt) cc_final: 0.8318 (mmt) REVERT: Y 15 ASN cc_start: 0.8667 (t0) cc_final: 0.8446 (t0) REVERT: Y 62 VAL cc_start: 0.9503 (t) cc_final: 0.9225 (m) REVERT: Y 70 ASN cc_start: 0.8377 (m-40) cc_final: 0.7988 (m110) REVERT: Y 111 MET cc_start: 0.8700 (ptt) cc_final: 0.8166 (ptp) REVERT: Y 112 ASP cc_start: 0.8751 (p0) cc_final: 0.7913 (p0) REVERT: e 17 ARG cc_start: 0.7996 (ptp-170) cc_final: 0.7749 (mtp85) REVERT: e 36 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7350 (mttm) REVERT: e 51 GLN cc_start: 0.8417 (mt0) cc_final: 0.8177 (mt0) outliers start: 165 outliers final: 123 residues processed: 731 average time/residue: 0.7206 time to fit residues: 910.4033 Evaluate side-chains 707 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 575 time to evaluate : 4.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain f residue 95 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 45 TYR Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain h residue 19 THR Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 98 THR Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain h residue 313 THR Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 70 MET Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 116 ASN Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 82 TRP Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 129 LEU Chi-restraints excluded: chain T residue 132 ARG Chi-restraints excluded: chain U residue 21 PHE Chi-restraints excluded: chain U residue 45 LEU Chi-restraints excluded: chain U residue 51 ASN Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 79 TYR Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 75 LYS Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 156 MET Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain P residue 31 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 103 ASN Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 27 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain c residue 4 CYS Chi-restraints excluded: chain c residue 15 SER Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 53 VAL Chi-restraints excluded: chain e residue 67 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 524 optimal weight: 9.9990 chunk 357 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 469 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 chunk 537 optimal weight: 50.0000 chunk 435 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 321 optimal weight: 10.0000 chunk 565 optimal weight: 6.9990 chunk 159 optimal weight: 40.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 GLN ** f 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 ASN ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 10 GLN ** T 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 83109 Z= 0.354 Angle : 0.722 10.401 121016 Z= 0.368 Chirality : 0.042 0.265 15038 Planarity : 0.005 0.093 8535 Dihedral : 24.032 179.420 34048 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 5.58 % Allowed : 21.61 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.09 % Twisted Proline : 0.52 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.12), residues: 4767 helix: -1.38 (0.14), residues: 1330 sheet: -1.65 (0.19), residues: 696 loop : -1.85 (0.12), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP h 259 HIS 0.010 0.002 HIS G 51 PHE 0.020 0.002 PHE R 63 TYR 0.033 0.002 TYR C 133 ARG 0.008 0.001 ARG T 142 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 576 time to evaluate : 4.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 ASN cc_start: 0.7836 (t0) cc_final: 0.7168 (t0) REVERT: B 176 TRP cc_start: 0.8464 (t60) cc_final: 0.8144 (t60) REVERT: b 46 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7506 (pt0) REVERT: C 99 ASN cc_start: 0.8311 (t0) cc_final: 0.8075 (t0) REVERT: C 103 MET cc_start: 0.7447 (tmm) cc_final: 0.6770 (tmm) REVERT: C 191 ASP cc_start: 0.6936 (p0) cc_final: 0.6169 (p0) REVERT: D 72 ASP cc_start: 0.8261 (t0) cc_final: 0.8044 (t0) REVERT: D 221 ASP cc_start: 0.7278 (m-30) cc_final: 0.7069 (m-30) REVERT: D 269 PHE cc_start: 0.8925 (m-10) cc_final: 0.8691 (m-10) REVERT: d 47 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7598 (ttmt) REVERT: d 59 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7442 (pt) REVERT: E 87 TYR cc_start: 0.7146 (m-80) cc_final: 0.6850 (m-80) REVERT: E 119 CYS cc_start: 0.8527 (m) cc_final: 0.8025 (m) REVERT: E 127 MET cc_start: 0.8659 (mmm) cc_final: 0.8392 (mmm) REVERT: E 152 PHE cc_start: 0.8061 (m-80) cc_final: 0.7734 (m-80) REVERT: E 179 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7475 (mm-40) REVERT: E 207 HIS cc_start: 0.8146 (t70) cc_final: 0.7863 (t-170) REVERT: f 95 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8499 (pp30) REVERT: G 89 THR cc_start: 0.8279 (m) cc_final: 0.8007 (p) REVERT: H 217 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.6064 (tmm) REVERT: h 140 TYR cc_start: 0.7884 (t80) cc_final: 0.7278 (t80) REVERT: h 145 GLU cc_start: 0.0445 (OUTLIER) cc_final: 0.0244 (mm-30) REVERT: h 149 GLU cc_start: -0.1043 (OUTLIER) cc_final: -0.1700 (tm-30) REVERT: h 268 ASP cc_start: 0.5254 (OUTLIER) cc_final: 0.5037 (m-30) REVERT: I 72 PHE cc_start: 0.7373 (OUTLIER) cc_final: 0.7124 (t80) REVERT: J 181 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8371 (mm-40) REVERT: K 20 PHE cc_start: 0.7974 (m-80) cc_final: 0.7643 (m-10) REVERT: K 26 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7591 (t0) REVERT: L 38 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6305 (ptpp) REVERT: L 49 MET cc_start: 0.6994 (mmt) cc_final: 0.6627 (mmt) REVERT: L 91 PRO cc_start: 0.8461 (Cg_endo) cc_final: 0.8247 (Cg_exo) REVERT: Q 52 LYS cc_start: 0.6959 (mmmt) cc_final: 0.6612 (mmtt) REVERT: Q 54 HIS cc_start: 0.7761 (m170) cc_final: 0.7311 (m90) REVERT: Q 111 MET cc_start: 0.1313 (mtt) cc_final: 0.0548 (mtt) REVERT: T 40 TYR cc_start: 0.5237 (OUTLIER) cc_final: 0.1919 (t80) REVERT: T 126 PHE cc_start: 0.3307 (t80) cc_final: 0.2795 (t80) REVERT: T 132 ARG cc_start: 0.2647 (OUTLIER) cc_final: 0.0238 (tpp80) REVERT: V 28 ASN cc_start: 0.8011 (t0) cc_final: 0.7675 (t0) REVERT: W 81 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8706 (mmtm) REVERT: F 155 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8064 (tp30) REVERT: F 166 SER cc_start: 0.9305 (OUTLIER) cc_final: 0.8671 (m) REVERT: M 87 MET cc_start: 0.9317 (mmt) cc_final: 0.8890 (mmm) REVERT: M 117 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8328 (pt0) REVERT: M 157 ASN cc_start: 0.8758 (t0) cc_final: 0.8052 (t0) REVERT: M 166 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7828 (p) REVERT: M 199 GLU cc_start: 0.8105 (mp0) cc_final: 0.7243 (mp0) REVERT: O 98 LYS cc_start: 0.8589 (tttt) cc_final: 0.8338 (pttt) REVERT: O 121 GLN cc_start: 0.8304 (mp10) cc_final: 0.7657 (mp10) REVERT: O 124 ASP cc_start: 0.8249 (m-30) cc_final: 0.7832 (m-30) REVERT: X 39 ASP cc_start: 0.7680 (t70) cc_final: 0.7147 (m-30) REVERT: X 50 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7994 (mmmt) REVERT: X 93 LEU cc_start: 0.8513 (tp) cc_final: 0.8189 (tp) REVERT: Y 4 MET cc_start: 0.8744 (mmt) cc_final: 0.8465 (mmt) REVERT: Y 15 ASN cc_start: 0.8707 (t0) cc_final: 0.8493 (t0) REVERT: Y 111 MET cc_start: 0.8827 (ptt) cc_final: 0.8248 (ptp) REVERT: Y 112 ASP cc_start: 0.8876 (p0) cc_final: 0.8098 (p0) REVERT: c 87 ASN cc_start: 0.7742 (m-40) cc_final: 0.7486 (m-40) REVERT: e 17 ARG cc_start: 0.8137 (ptp-170) cc_final: 0.7872 (mtp85) REVERT: e 36 LYS cc_start: 0.7799 (mmmt) cc_final: 0.7224 (mttm) REVERT: e 51 GLN cc_start: 0.8469 (mt0) cc_final: 0.8264 (mt0) outliers start: 232 outliers final: 161 residues processed: 733 average time/residue: 0.7226 time to fit residues: 920.7179 Evaluate side-chains 723 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 548 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 95 GLN Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 217 MET Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 46 THR Chi-restraints excluded: chain h residue 83 TRP Chi-restraints excluded: chain h residue 98 THR Chi-restraints excluded: chain h residue 145 GLU Chi-restraints excluded: chain h residue 149 GLU Chi-restraints excluded: chain h residue 256 ILE Chi-restraints excluded: chain h residue 268 ASP Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain h residue 313 THR Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 70 MET Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain R residue 18 THR Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 116 ASN Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 5 ILE Chi-restraints excluded: chain T residue 40 TYR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 82 TRP Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 132 ARG Chi-restraints excluded: chain U residue 51 ASN Chi-restraints excluded: chain U residue 55 THR Chi-restraints excluded: chain U residue 79 TYR Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 75 LYS Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 70 THR Chi-restraints excluded: chain Z residue 75 ILE Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 156 MET Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 184 THR Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain P residue 31 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 26 ASN Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 103 ASN Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 27 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 87 GLU Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain c residue 4 CYS Chi-restraints excluded: chain c residue 15 SER Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 115 ILE Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 53 VAL Chi-restraints excluded: chain e residue 59 CYS Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 67 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 212 optimal weight: 5.9990 chunk 567 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 370 optimal weight: 7.9990 chunk 155 optimal weight: 30.0000 chunk 630 optimal weight: 5.9990 chunk 523 optimal weight: 5.9990 chunk 292 optimal weight: 0.1980 chunk 52 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 113 GLN f 88 GLN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN T 134 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN ** Y 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 83109 Z= 0.230 Angle : 0.634 10.767 121016 Z= 0.323 Chirality : 0.038 0.264 15038 Planarity : 0.004 0.085 8535 Dihedral : 23.979 179.727 34048 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.73 % Allowed : 22.95 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.09 % Twisted Proline : 0.52 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.12), residues: 4767 helix: -1.13 (0.14), residues: 1331 sheet: -1.60 (0.19), residues: 718 loop : -1.76 (0.12), residues: 2718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP h 259 HIS 0.007 0.001 HIS G 51 PHE 0.024 0.001 PHE E 24 TYR 0.023 0.001 TYR C 133 ARG 0.010 0.000 ARG O 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 590 time to evaluate : 4.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 HIS cc_start: 0.8058 (p90) cc_final: 0.7799 (p90) REVERT: B 164 ASN cc_start: 0.7825 (t0) cc_final: 0.7172 (t0) REVERT: B 176 TRP cc_start: 0.8470 (t60) cc_final: 0.8192 (t60) REVERT: b 46 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6780 (pt0) REVERT: C 99 ASN cc_start: 0.8308 (t0) cc_final: 0.8085 (t0) REVERT: C 103 MET cc_start: 0.7363 (tmm) cc_final: 0.6622 (tmm) REVERT: C 122 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7101 (tm-30) REVERT: C 191 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.6001 (p0) REVERT: D 72 ASP cc_start: 0.8153 (t0) cc_final: 0.7921 (t0) REVERT: D 221 ASP cc_start: 0.7345 (m-30) cc_final: 0.7109 (m-30) REVERT: D 269 PHE cc_start: 0.8843 (m-10) cc_final: 0.8551 (m-10) REVERT: d 13 ARG cc_start: 0.8020 (mmm-85) cc_final: 0.7818 (mmm-85) REVERT: d 47 LYS cc_start: 0.8329 (ttmt) cc_final: 0.7702 (ttmt) REVERT: d 59 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7423 (pt) REVERT: E 32 ASP cc_start: 0.8521 (p0) cc_final: 0.8013 (p0) REVERT: E 87 TYR cc_start: 0.7148 (m-80) cc_final: 0.6856 (m-80) REVERT: E 119 CYS cc_start: 0.8487 (m) cc_final: 0.8076 (m) REVERT: E 120 TYR cc_start: 0.7458 (t80) cc_final: 0.7240 (t80) REVERT: E 127 MET cc_start: 0.8768 (mmm) cc_final: 0.8523 (mmm) REVERT: E 179 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7336 (mm-40) REVERT: E 207 HIS cc_start: 0.8142 (t70) cc_final: 0.7863 (t-170) REVERT: f 95 GLN cc_start: 0.8756 (pp30) cc_final: 0.8364 (pp30) REVERT: h 140 TYR cc_start: 0.7827 (t80) cc_final: 0.7350 (t80) REVERT: h 149 GLU cc_start: -0.1209 (OUTLIER) cc_final: -0.1734 (tm-30) REVERT: h 217 MET cc_start: 0.7047 (mmt) cc_final: 0.5598 (mmt) REVERT: h 268 ASP cc_start: 0.5030 (OUTLIER) cc_final: 0.4796 (m-30) REVERT: I 72 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7101 (t80) REVERT: K 20 PHE cc_start: 0.7672 (m-80) cc_final: 0.7174 (m-10) REVERT: K 26 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7539 (t0) REVERT: L 38 LYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6164 (ptpp) REVERT: L 49 MET cc_start: 0.6955 (mmt) cc_final: 0.6593 (mmt) REVERT: Q 52 LYS cc_start: 0.6920 (mmmt) cc_final: 0.6585 (mmtt) REVERT: Q 54 HIS cc_start: 0.7777 (m170) cc_final: 0.7286 (m90) REVERT: Q 111 MET cc_start: 0.0712 (mtt) cc_final: 0.0049 (mtt) REVERT: R 22 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8159 (p) REVERT: T 28 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7027 (m-10) REVERT: T 40 TYR cc_start: 0.5396 (OUTLIER) cc_final: 0.1803 (t80) REVERT: T 126 PHE cc_start: 0.3400 (t80) cc_final: 0.2919 (t80) REVERT: T 132 ARG cc_start: 0.2310 (OUTLIER) cc_final: -0.0033 (tpp80) REVERT: W 81 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8707 (mmtm) REVERT: F 155 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7937 (tp30) REVERT: M 87 MET cc_start: 0.9326 (mmt) cc_final: 0.8920 (mmm) REVERT: M 157 ASN cc_start: 0.8702 (t0) cc_final: 0.7934 (t0) REVERT: M 161 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: M 166 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7718 (p) REVERT: M 199 GLU cc_start: 0.8076 (mp0) cc_final: 0.7262 (mp0) REVERT: O 121 GLN cc_start: 0.8302 (mp10) cc_final: 0.7391 (mp10) REVERT: X 39 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.6747 (m-30) REVERT: X 72 TYR cc_start: 0.7806 (m-10) cc_final: 0.7479 (m-10) REVERT: X 93 LEU cc_start: 0.8437 (tp) cc_final: 0.8202 (tp) REVERT: X 113 GLN cc_start: 0.7940 (mm-40) cc_final: 0.6625 (mm-40) REVERT: Y 4 MET cc_start: 0.8757 (mmt) cc_final: 0.8404 (mmt) REVERT: Y 24 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7799 (pt0) REVERT: Y 62 VAL cc_start: 0.9510 (t) cc_final: 0.9230 (m) REVERT: Y 111 MET cc_start: 0.8766 (ptt) cc_final: 0.8250 (ptp) REVERT: Y 112 ASP cc_start: 0.8802 (p0) cc_final: 0.8077 (p0) REVERT: c 88 ASP cc_start: 0.7208 (t70) cc_final: 0.6981 (t70) REVERT: c 99 GLU cc_start: 0.7275 (tm-30) cc_final: 0.6960 (tm-30) REVERT: e 17 ARG cc_start: 0.8072 (ptp-170) cc_final: 0.7819 (mtp85) REVERT: e 36 LYS cc_start: 0.7745 (mmmt) cc_final: 0.7239 (mttm) outliers start: 197 outliers final: 146 residues processed: 725 average time/residue: 0.7079 time to fit residues: 896.1080 Evaluate side-chains 716 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 554 time to evaluate : 4.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 ASP Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 103 HIS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 83 TRP Chi-restraints excluded: chain h residue 98 THR Chi-restraints excluded: chain h residue 149 GLU Chi-restraints excluded: chain h residue 268 ASP Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain h residue 313 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 168 GLN Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 70 MET Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 116 ASN Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 28 PHE Chi-restraints excluded: chain T residue 40 TYR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 82 TRP Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 129 LEU Chi-restraints excluded: chain T residue 132 ARG Chi-restraints excluded: chain U residue 51 ASN Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 75 LYS Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 156 MET Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 161 GLN Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 31 ASP Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 103 ASN Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 24 GLN Chi-restraints excluded: chain Y residue 27 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain c residue 4 CYS Chi-restraints excluded: chain c residue 15 SER Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 53 VAL Chi-restraints excluded: chain e residue 59 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 608 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 359 optimal weight: 8.9990 chunk 460 optimal weight: 9.9990 chunk 356 optimal weight: 30.0000 chunk 531 optimal weight: 5.9990 chunk 352 optimal weight: 30.0000 chunk 628 optimal weight: 10.0000 chunk 393 optimal weight: 1.9990 chunk 383 optimal weight: 9.9990 chunk 290 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 88 GLN G 148 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN K 75 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS ** T 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 94 HIS ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 83109 Z= 0.306 Angle : 0.679 10.444 121016 Z= 0.346 Chirality : 0.040 0.340 15038 Planarity : 0.005 0.087 8535 Dihedral : 23.977 179.899 34048 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 5.17 % Allowed : 23.10 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.09 % Twisted Proline : 0.52 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.12), residues: 4767 helix: -1.07 (0.14), residues: 1322 sheet: -1.69 (0.19), residues: 716 loop : -1.76 (0.12), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 55 HIS 0.010 0.001 HIS G 51 PHE 0.019 0.002 PHE E 24 TYR 0.025 0.002 TYR C 133 ARG 0.010 0.001 ARG Z 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 565 time to evaluate : 4.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 104 ARG cc_start: 0.8612 (ptt90) cc_final: 0.8318 (ptt90) REVERT: B 164 ASN cc_start: 0.7858 (t0) cc_final: 0.7203 (t0) REVERT: B 176 TRP cc_start: 0.8500 (t60) cc_final: 0.8188 (t60) REVERT: b 46 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: C 99 ASN cc_start: 0.8357 (t0) cc_final: 0.8126 (t0) REVERT: C 103 MET cc_start: 0.7425 (tmm) cc_final: 0.6689 (tmm) REVERT: C 122 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7133 (tm-30) REVERT: C 191 ASP cc_start: 0.6683 (OUTLIER) cc_final: 0.5968 (p0) REVERT: D 72 ASP cc_start: 0.8136 (t0) cc_final: 0.7906 (t0) REVERT: D 133 TYR cc_start: 0.7631 (m-80) cc_final: 0.7334 (m-80) REVERT: D 221 ASP cc_start: 0.7346 (m-30) cc_final: 0.7119 (m-30) REVERT: D 269 PHE cc_start: 0.8872 (m-10) cc_final: 0.8632 (m-10) REVERT: E 87 TYR cc_start: 0.7161 (m-80) cc_final: 0.6860 (m-80) REVERT: E 119 CYS cc_start: 0.8538 (m) cc_final: 0.8126 (m) REVERT: E 127 MET cc_start: 0.8782 (mmm) cc_final: 0.8537 (mmm) REVERT: E 179 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7411 (mm-40) REVERT: E 207 HIS cc_start: 0.8138 (t70) cc_final: 0.7845 (t-170) REVERT: h 140 TYR cc_start: 0.7845 (t80) cc_final: 0.7337 (t80) REVERT: h 149 GLU cc_start: -0.0861 (OUTLIER) cc_final: -0.1403 (tm-30) REVERT: h 268 ASP cc_start: 0.5155 (OUTLIER) cc_final: 0.4953 (m-30) REVERT: I 72 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.7107 (t80) REVERT: J 181 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8435 (mm-40) REVERT: K 20 PHE cc_start: 0.7888 (m-80) cc_final: 0.7429 (m-10) REVERT: K 26 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.7621 (t0) REVERT: L 5 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8480 (mmmt) REVERT: L 38 LYS cc_start: 0.6743 (OUTLIER) cc_final: 0.6203 (ptpp) REVERT: L 49 MET cc_start: 0.7027 (mmt) cc_final: 0.6569 (mmt) REVERT: Q 52 LYS cc_start: 0.6949 (mmmt) cc_final: 0.6629 (mmtt) REVERT: Q 54 HIS cc_start: 0.7768 (m170) cc_final: 0.7346 (m90) REVERT: Q 111 MET cc_start: 0.0760 (mtt) cc_final: 0.0274 (mtt) REVERT: R 22 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.8142 (p) REVERT: S 48 ASN cc_start: 0.8391 (t0) cc_final: 0.7807 (t0) REVERT: T 40 TYR cc_start: 0.5390 (OUTLIER) cc_final: 0.1806 (t80) REVERT: T 132 ARG cc_start: 0.2259 (OUTLIER) cc_final: -0.0033 (tpp80) REVERT: W 64 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: W 81 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8728 (mmtt) REVERT: F 155 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7925 (tp30) REVERT: F 166 SER cc_start: 0.9312 (OUTLIER) cc_final: 0.8625 (m) REVERT: M 87 MET cc_start: 0.9324 (mmt) cc_final: 0.8895 (mmm) REVERT: M 157 ASN cc_start: 0.8767 (t0) cc_final: 0.8041 (t0) REVERT: M 161 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: M 166 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7496 (p) REVERT: M 199 GLU cc_start: 0.8096 (mp0) cc_final: 0.7243 (mp0) REVERT: O 121 GLN cc_start: 0.8335 (mp10) cc_final: 0.7439 (mp10) REVERT: X 39 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: X 72 TYR cc_start: 0.7840 (m-10) cc_final: 0.7447 (m-10) REVERT: X 93 LEU cc_start: 0.8484 (tp) cc_final: 0.8195 (tp) REVERT: Y 4 MET cc_start: 0.8784 (mmt) cc_final: 0.8487 (mmt) REVERT: Y 111 MET cc_start: 0.8849 (ptt) cc_final: 0.8271 (ptp) REVERT: Y 112 ASP cc_start: 0.8817 (p0) cc_final: 0.8048 (p0) REVERT: c 99 GLU cc_start: 0.7303 (tm-30) cc_final: 0.7006 (tm-30) REVERT: e 17 ARG cc_start: 0.8132 (ptp-170) cc_final: 0.7911 (mtp85) REVERT: e 36 LYS cc_start: 0.7791 (mmmt) cc_final: 0.7244 (mttm) outliers start: 215 outliers final: 173 residues processed: 717 average time/residue: 0.7034 time to fit residues: 883.7726 Evaluate side-chains 732 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 544 time to evaluate : 4.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 ASP Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 103 HIS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 45 VAL Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain d residue 21 THR Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 46 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 116 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 190 ILE Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 83 TRP Chi-restraints excluded: chain h residue 98 THR Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 149 GLU Chi-restraints excluded: chain h residue 150 TRP Chi-restraints excluded: chain h residue 164 ILE Chi-restraints excluded: chain h residue 256 ILE Chi-restraints excluded: chain h residue 268 ASP Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain h residue 313 THR Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 70 MET Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 41 MET Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 111 ILE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 116 ASN Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 40 TYR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 82 TRP Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 132 ARG Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 21 PHE Chi-restraints excluded: chain U residue 51 ASN Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 75 LYS Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 75 ILE Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 156 MET Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 161 GLN Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 184 THR Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 113 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 31 ASP Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 103 ASN Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 27 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain c residue 4 CYS Chi-restraints excluded: chain c residue 15 SER Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 102 VAL Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 53 VAL Chi-restraints excluded: chain e residue 59 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 388 optimal weight: 6.9990 chunk 250 optimal weight: 0.9980 chunk 375 optimal weight: 20.0000 chunk 189 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 399 optimal weight: 0.6980 chunk 428 optimal weight: 30.0000 chunk 310 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 493 optimal weight: 9.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 ASN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN ** c 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 83109 Z= 0.176 Angle : 0.607 10.581 121016 Z= 0.309 Chirality : 0.037 0.267 15038 Planarity : 0.004 0.079 8535 Dihedral : 23.915 179.333 34048 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.42 % Allowed : 24.03 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.09 % Twisted Proline : 0.52 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.12), residues: 4767 helix: -0.85 (0.14), residues: 1323 sheet: -1.53 (0.19), residues: 738 loop : -1.62 (0.12), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 55 HIS 0.009 0.001 HIS f 76 PHE 0.027 0.001 PHE E 24 TYR 0.019 0.001 TYR B 156 ARG 0.006 0.000 ARG G 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 601 time to evaluate : 4.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 ASN cc_start: 0.7793 (t0) cc_final: 0.7340 (t0) REVERT: B 176 TRP cc_start: 0.8497 (t60) cc_final: 0.8210 (t60) REVERT: b 46 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6749 (pt0) REVERT: C 71 LEU cc_start: 0.8694 (mt) cc_final: 0.8447 (mt) REVERT: C 99 ASN cc_start: 0.8293 (t0) cc_final: 0.8083 (t0) REVERT: C 103 MET cc_start: 0.7349 (tmm) cc_final: 0.6589 (tmm) REVERT: C 191 ASP cc_start: 0.6682 (OUTLIER) cc_final: 0.6162 (p0) REVERT: D 133 TYR cc_start: 0.7508 (m-80) cc_final: 0.7230 (m-80) REVERT: D 221 ASP cc_start: 0.7357 (m-30) cc_final: 0.7113 (m-30) REVERT: D 269 PHE cc_start: 0.8813 (m-10) cc_final: 0.8560 (m-10) REVERT: d 31 ARG cc_start: 0.9096 (tpt90) cc_final: 0.8863 (tpt90) REVERT: d 59 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7470 (pt) REVERT: E 32 ASP cc_start: 0.8506 (p0) cc_final: 0.8001 (p0) REVERT: E 87 TYR cc_start: 0.7176 (m-80) cc_final: 0.6877 (m-80) REVERT: E 119 CYS cc_start: 0.8562 (m) cc_final: 0.7888 (m) REVERT: E 124 ARG cc_start: 0.8079 (ptt90) cc_final: 0.7719 (ptt90) REVERT: E 127 MET cc_start: 0.8761 (mmm) cc_final: 0.8545 (mmm) REVERT: E 152 PHE cc_start: 0.7904 (m-80) cc_final: 0.7622 (m-80) REVERT: E 179 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7355 (mm-40) REVERT: E 207 HIS cc_start: 0.8148 (t70) cc_final: 0.7903 (t-170) REVERT: h 140 TYR cc_start: 0.7776 (t80) cc_final: 0.7286 (t80) REVERT: h 147 HIS cc_start: 0.4360 (p-80) cc_final: 0.3981 (p90) REVERT: h 149 GLU cc_start: -0.1294 (OUTLIER) cc_final: -0.1673 (tm-30) REVERT: h 217 MET cc_start: 0.6940 (mmt) cc_final: 0.5541 (mmt) REVERT: h 268 ASP cc_start: 0.5384 (OUTLIER) cc_final: 0.5115 (m-30) REVERT: I 72 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.7164 (t80) REVERT: K 20 PHE cc_start: 0.7517 (m-80) cc_final: 0.6959 (m-10) REVERT: K 26 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7609 (t0) REVERT: L 38 LYS cc_start: 0.6680 (OUTLIER) cc_final: 0.6087 (ptpp) REVERT: L 49 MET cc_start: 0.6849 (mmt) cc_final: 0.6443 (mmt) REVERT: L 91 PRO cc_start: 0.8455 (Cg_endo) cc_final: 0.8253 (Cg_exo) REVERT: Q 52 LYS cc_start: 0.6896 (mmmt) cc_final: 0.6564 (mmtt) REVERT: Q 54 HIS cc_start: 0.7795 (m170) cc_final: 0.7273 (m90) REVERT: Q 65 LYS cc_start: 0.7647 (ptpp) cc_final: 0.7444 (ptpp) REVERT: Q 89 MET cc_start: 0.6423 (tpt) cc_final: 0.6181 (tpp) REVERT: Q 93 MET cc_start: 0.2715 (mpp) cc_final: 0.1919 (mpp) REVERT: R 22 VAL cc_start: 0.8300 (OUTLIER) cc_final: 0.8093 (p) REVERT: S 47 ARG cc_start: 0.8238 (ppt170) cc_final: 0.7903 (ptp90) REVERT: S 48 ASN cc_start: 0.8339 (t0) cc_final: 0.7874 (t0) REVERT: T 40 TYR cc_start: 0.5305 (OUTLIER) cc_final: 0.2206 (t80) REVERT: T 126 PHE cc_start: 0.3740 (t80) cc_final: 0.3345 (t80) REVERT: W 64 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6390 (mm-30) REVERT: W 81 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8688 (mmtm) REVERT: F 155 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7839 (tp30) REVERT: F 166 SER cc_start: 0.9301 (OUTLIER) cc_final: 0.8638 (m) REVERT: M 1 MET cc_start: 0.3948 (ttt) cc_final: 0.3679 (tpt) REVERT: M 87 MET cc_start: 0.9316 (mmt) cc_final: 0.8903 (mmm) REVERT: M 157 ASN cc_start: 0.8674 (t0) cc_final: 0.7903 (t0) REVERT: M 166 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7520 (p) REVERT: M 199 GLU cc_start: 0.8145 (mp0) cc_final: 0.7345 (mp0) REVERT: O 48 LYS cc_start: 0.8773 (tppt) cc_final: 0.8535 (tppt) REVERT: O 121 GLN cc_start: 0.8268 (mp10) cc_final: 0.7504 (mp10) REVERT: O 124 ASP cc_start: 0.8275 (m-30) cc_final: 0.7954 (m-30) REVERT: X 39 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.6710 (m-30) REVERT: X 72 TYR cc_start: 0.7683 (m-10) cc_final: 0.7344 (m-10) REVERT: X 93 LEU cc_start: 0.8410 (tp) cc_final: 0.8208 (tp) REVERT: X 113 GLN cc_start: 0.7961 (mm-40) cc_final: 0.6948 (mm-40) REVERT: Y 4 MET cc_start: 0.8671 (mmt) cc_final: 0.8330 (mmt) REVERT: Y 18 GLU cc_start: 0.7569 (pp20) cc_final: 0.7365 (pp20) REVERT: Y 62 VAL cc_start: 0.9507 (t) cc_final: 0.9209 (m) REVERT: Y 70 ASN cc_start: 0.8279 (m-40) cc_final: 0.7847 (m110) REVERT: Y 111 MET cc_start: 0.8671 (ptt) cc_final: 0.8084 (ptp) REVERT: Y 112 ASP cc_start: 0.8724 (p0) cc_final: 0.7876 (p0) REVERT: c 99 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6934 (tm-30) REVERT: e 17 ARG cc_start: 0.8039 (ptp-170) cc_final: 0.7769 (mtp85) REVERT: e 36 LYS cc_start: 0.7714 (mmmt) cc_final: 0.7286 (mttm) REVERT: e 51 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8369 (tt0) outliers start: 184 outliers final: 136 residues processed: 727 average time/residue: 0.7160 time to fit residues: 909.5582 Evaluate side-chains 717 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 566 time to evaluate : 4.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 ASP Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 103 HIS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 43 ASN Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain h residue 83 TRP Chi-restraints excluded: chain h residue 98 THR Chi-restraints excluded: chain h residue 149 GLU Chi-restraints excluded: chain h residue 268 ASP Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain h residue 313 THR Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 91 VAL Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 26 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 80 ASP Chi-restraints excluded: chain Q residue 70 MET Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 116 ASN Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain T residue 40 TYR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 82 TRP Chi-restraints excluded: chain T residue 107 LEU Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 117 ILE Chi-restraints excluded: chain T residue 132 ARG Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 21 PHE Chi-restraints excluded: chain U residue 51 ASN Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 156 MET Chi-restraints excluded: chain M residue 166 THR Chi-restraints excluded: chain M residue 184 THR Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain P residue 31 ASP Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain P residue 145 THR Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain c residue 4 CYS Chi-restraints excluded: chain c residue 15 SER Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain e residue 43 ILE Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 51 GLN Chi-restraints excluded: chain e residue 53 VAL Chi-restraints excluded: chain e residue 59 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 571 optimal weight: 9.9990 chunk 602 optimal weight: 3.9990 chunk 549 optimal weight: 8.9990 chunk 585 optimal weight: 9.9990 chunk 601 optimal weight: 0.9980 chunk 352 optimal weight: 20.0000 chunk 255 optimal weight: 10.0000 chunk 459 optimal weight: 10.0000 chunk 179 optimal weight: 6.9990 chunk 529 optimal weight: 0.3980 chunk 553 optimal weight: 0.9980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 88 GLN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 83109 Z= 0.178 Angle : 0.603 13.974 121016 Z= 0.305 Chirality : 0.036 0.269 15038 Planarity : 0.004 0.082 8535 Dihedral : 23.825 179.839 34048 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 4.23 % Allowed : 24.66 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.09 % Twisted Proline : 0.52 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.12), residues: 4767 helix: -0.70 (0.14), residues: 1338 sheet: -1.44 (0.19), residues: 741 loop : -1.56 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 55 HIS 0.006 0.001 HIS G 51 PHE 0.032 0.001 PHE O 17 TYR 0.021 0.001 TYR H 156 ARG 0.006 0.000 ARG d 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 604 time to evaluate : 4.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 ASN cc_start: 0.7785 (t0) cc_final: 0.7314 (t0) REVERT: B 176 TRP cc_start: 0.8510 (t60) cc_final: 0.8239 (t60) REVERT: b 46 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6741 (pt0) REVERT: C 71 LEU cc_start: 0.8700 (mt) cc_final: 0.8458 (mt) REVERT: C 99 ASN cc_start: 0.8267 (t0) cc_final: 0.8045 (t0) REVERT: C 103 MET cc_start: 0.7367 (tmm) cc_final: 0.6599 (tmm) REVERT: C 172 MET cc_start: 0.8524 (mtm) cc_final: 0.8262 (mtt) REVERT: C 191 ASP cc_start: 0.6660 (OUTLIER) cc_final: 0.6026 (p0) REVERT: D 133 TYR cc_start: 0.7469 (m-80) cc_final: 0.7188 (m-80) REVERT: D 221 ASP cc_start: 0.7385 (m-30) cc_final: 0.7125 (m-30) REVERT: D 269 PHE cc_start: 0.8835 (m-10) cc_final: 0.8610 (m-10) REVERT: d 31 ARG cc_start: 0.9084 (tpt90) cc_final: 0.8833 (tpt90) REVERT: d 54 ASP cc_start: 0.7402 (p0) cc_final: 0.6857 (p0) REVERT: E 32 ASP cc_start: 0.8506 (p0) cc_final: 0.7972 (p0) REVERT: E 87 TYR cc_start: 0.7200 (m-80) cc_final: 0.6911 (m-80) REVERT: E 119 CYS cc_start: 0.8530 (m) cc_final: 0.7922 (m) REVERT: E 120 TYR cc_start: 0.7229 (t80) cc_final: 0.6813 (t80) REVERT: E 124 ARG cc_start: 0.8042 (ptt90) cc_final: 0.7619 (ptt90) REVERT: E 127 MET cc_start: 0.8765 (mmm) cc_final: 0.8531 (mmm) REVERT: E 179 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7399 (mm-40) REVERT: E 206 ASP cc_start: 0.7594 (OUTLIER) cc_final: 0.7194 (p0) REVERT: E 207 HIS cc_start: 0.8124 (t70) cc_final: 0.7886 (t-170) REVERT: h 21 ILE cc_start: 0.1195 (mt) cc_final: 0.0733 (mt) REVERT: h 140 TYR cc_start: 0.7715 (t80) cc_final: 0.7245 (t80) REVERT: h 147 HIS cc_start: 0.4176 (p-80) cc_final: 0.3793 (p90) REVERT: h 149 GLU cc_start: -0.1269 (OUTLIER) cc_final: -0.1680 (tm-30) REVERT: h 217 MET cc_start: 0.7077 (mmt) cc_final: 0.5674 (mmt) REVERT: I 72 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.7014 (t80) REVERT: I 76 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6982 (mt0) REVERT: K 20 PHE cc_start: 0.7623 (m-80) cc_final: 0.7047 (m-10) REVERT: K 26 ASP cc_start: 0.8010 (t0) cc_final: 0.7647 (t0) REVERT: K 124 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.7399 (t-90) REVERT: L 38 LYS cc_start: 0.6636 (OUTLIER) cc_final: 0.5963 (ptpp) REVERT: L 49 MET cc_start: 0.6854 (mmt) cc_final: 0.6376 (mmt) REVERT: Q 34 MET cc_start: 0.7456 (mmt) cc_final: 0.7086 (mmm) REVERT: Q 52 LYS cc_start: 0.6911 (mmmt) cc_final: 0.6631 (mmtt) REVERT: Q 54 HIS cc_start: 0.7818 (m170) cc_final: 0.7286 (m90) REVERT: Q 89 MET cc_start: 0.6275 (tpt) cc_final: 0.5994 (tpp) REVERT: Q 93 MET cc_start: 0.2618 (mpp) cc_final: 0.1897 (mpp) REVERT: R 22 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.8106 (p) REVERT: S 47 ARG cc_start: 0.8261 (ppt170) cc_final: 0.7940 (ptp90) REVERT: S 48 ASN cc_start: 0.8349 (t0) cc_final: 0.7866 (t0) REVERT: T 40 TYR cc_start: 0.5418 (OUTLIER) cc_final: 0.2572 (t80) REVERT: T 55 ARG cc_start: 0.3746 (OUTLIER) cc_final: 0.1237 (tpt90) REVERT: T 126 PHE cc_start: 0.3749 (t80) cc_final: 0.3357 (t80) REVERT: W 64 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6201 (mm-30) REVERT: W 81 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8706 (mmtm) REVERT: F 155 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7621 (tp30) REVERT: F 166 SER cc_start: 0.9311 (OUTLIER) cc_final: 0.8655 (m) REVERT: M 1 MET cc_start: 0.3941 (ttt) cc_final: 0.3651 (tpt) REVERT: M 87 MET cc_start: 0.9315 (mmt) cc_final: 0.8887 (mmm) REVERT: M 157 ASN cc_start: 0.8639 (t0) cc_final: 0.7904 (t0) REVERT: M 199 GLU cc_start: 0.8137 (mp0) cc_final: 0.7349 (mp0) REVERT: O 48 LYS cc_start: 0.8834 (tppt) cc_final: 0.8546 (tppt) REVERT: O 121 GLN cc_start: 0.8256 (mp10) cc_final: 0.7491 (mp10) REVERT: O 124 ASP cc_start: 0.8269 (m-30) cc_final: 0.7951 (m-30) REVERT: P 87 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7907 (p0) REVERT: X 20 GLN cc_start: 0.7580 (pt0) cc_final: 0.7176 (mp10) REVERT: X 39 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.6711 (m-30) REVERT: X 72 TYR cc_start: 0.7644 (m-10) cc_final: 0.7305 (m-10) REVERT: X 113 GLN cc_start: 0.7935 (mm-40) cc_final: 0.6967 (mm-40) REVERT: Y 4 MET cc_start: 0.8658 (mmt) cc_final: 0.8303 (mmt) REVERT: Y 70 ASN cc_start: 0.8262 (m-40) cc_final: 0.7810 (m110) REVERT: Y 112 ASP cc_start: 0.8737 (p0) cc_final: 0.8290 (p0) REVERT: c 81 ILE cc_start: 0.8889 (mm) cc_final: 0.8544 (pt) REVERT: c 88 ASP cc_start: 0.7032 (t70) cc_final: 0.6824 (t0) REVERT: c 99 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6879 (tm-30) REVERT: e 17 ARG cc_start: 0.7977 (ptp-170) cc_final: 0.7705 (mtp85) REVERT: e 36 LYS cc_start: 0.7677 (mmmt) cc_final: 0.7344 (mttm) REVERT: e 51 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8301 (tt0) outliers start: 176 outliers final: 137 residues processed: 725 average time/residue: 0.7516 time to fit residues: 953.9664 Evaluate side-chains 734 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 581 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 ASP Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 103 HIS Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain H residue 56 ASN Chi-restraints excluded: chain h residue 83 TRP Chi-restraints excluded: chain h residue 98 THR Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 149 GLU Chi-restraints excluded: chain h residue 218 LEU Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain h residue 313 THR Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 124 HIS Chi-restraints excluded: chain K residue 137 VAL Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 70 MET Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 116 ASN Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 40 TYR Chi-restraints excluded: chain T residue 55 ARG Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 82 TRP Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 132 ARG Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 21 PHE Chi-restraints excluded: chain U residue 51 ASN Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 75 ILE Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain Z residue 117 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 156 MET Chi-restraints excluded: chain M residue 160 ILE Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 103 ASN Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 27 ILE Chi-restraints excluded: chain Y residue 33 VAL Chi-restraints excluded: chain Y residue 35 VAL Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain c residue 4 CYS Chi-restraints excluded: chain c residue 15 SER Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 51 GLN Chi-restraints excluded: chain e residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 583 optimal weight: 5.9990 chunk 384 optimal weight: 9.9990 chunk 619 optimal weight: 2.9990 chunk 377 optimal weight: 0.6980 chunk 293 optimal weight: 3.9990 chunk 430 optimal weight: 5.9990 chunk 649 optimal weight: 8.9990 chunk 597 optimal weight: 6.9990 chunk 517 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 399 optimal weight: 0.7980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 88 GLN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN ** K 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 83109 Z= 0.183 Angle : 0.603 11.906 121016 Z= 0.305 Chirality : 0.036 0.263 15038 Planarity : 0.004 0.077 8535 Dihedral : 23.790 179.797 34048 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.89 % Allowed : 25.23 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.09 % Twisted Proline : 0.52 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.12), residues: 4767 helix: -0.65 (0.14), residues: 1343 sheet: -1.40 (0.19), residues: 719 loop : -1.48 (0.12), residues: 2705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 69 HIS 0.007 0.001 HIS G 51 PHE 0.024 0.001 PHE E 24 TYR 0.018 0.001 TYR U 65 ARG 0.007 0.000 ARG H 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9534 Ramachandran restraints generated. 4767 Oldfield, 0 Emsley, 4767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 603 time to evaluate : 4.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 ASN cc_start: 0.7774 (t0) cc_final: 0.7077 (t0) REVERT: B 176 TRP cc_start: 0.8547 (t60) cc_final: 0.8278 (t60) REVERT: b 46 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6732 (pt0) REVERT: C 99 ASN cc_start: 0.8268 (t0) cc_final: 0.8045 (t0) REVERT: C 172 MET cc_start: 0.8442 (mtm) cc_final: 0.8220 (mtt) REVERT: C 191 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6036 (p0) REVERT: D 133 TYR cc_start: 0.7533 (m-80) cc_final: 0.7254 (m-80) REVERT: D 221 ASP cc_start: 0.7383 (m-30) cc_final: 0.7120 (m-30) REVERT: D 224 THR cc_start: 0.8670 (m) cc_final: 0.8078 (p) REVERT: D 269 PHE cc_start: 0.8838 (m-10) cc_final: 0.8617 (m-10) REVERT: d 21 THR cc_start: 0.8702 (t) cc_final: 0.8298 (p) REVERT: d 31 ARG cc_start: 0.9078 (tpt90) cc_final: 0.8821 (tpt90) REVERT: d 54 ASP cc_start: 0.7324 (p0) cc_final: 0.6717 (p0) REVERT: E 32 ASP cc_start: 0.8507 (p0) cc_final: 0.7973 (p0) REVERT: E 87 TYR cc_start: 0.7278 (m-80) cc_final: 0.7014 (m-80) REVERT: E 119 CYS cc_start: 0.8379 (m) cc_final: 0.7827 (m) REVERT: E 120 TYR cc_start: 0.7140 (t80) cc_final: 0.6754 (t80) REVERT: E 124 ARG cc_start: 0.8025 (ptt90) cc_final: 0.7598 (ptt90) REVERT: E 127 MET cc_start: 0.8691 (mmm) cc_final: 0.8479 (mmm) REVERT: E 157 MET cc_start: 0.7709 (tpp) cc_final: 0.7254 (tpt) REVERT: E 179 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7423 (mm-40) REVERT: E 206 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7354 (p0) REVERT: E 207 HIS cc_start: 0.8111 (t70) cc_final: 0.7872 (t-170) REVERT: h 21 ILE cc_start: 0.1029 (mt) cc_final: 0.0812 (mt) REVERT: h 140 TYR cc_start: 0.7722 (t80) cc_final: 0.7268 (t80) REVERT: h 147 HIS cc_start: 0.4103 (p-80) cc_final: 0.3746 (p90) REVERT: h 149 GLU cc_start: -0.1339 (OUTLIER) cc_final: -0.1677 (tm-30) REVERT: h 217 MET cc_start: 0.7109 (mmt) cc_final: 0.5720 (mmt) REVERT: I 72 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.7155 (t80) REVERT: K 20 PHE cc_start: 0.7427 (m-80) cc_final: 0.6847 (m-10) REVERT: K 26 ASP cc_start: 0.8114 (t0) cc_final: 0.7670 (t0) REVERT: K 124 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.7315 (t-90) REVERT: L 38 LYS cc_start: 0.6444 (OUTLIER) cc_final: 0.5786 (ptpp) REVERT: Q 34 MET cc_start: 0.7444 (mmt) cc_final: 0.7082 (mmm) REVERT: Q 52 LYS cc_start: 0.6883 (mmmt) cc_final: 0.6645 (mmtt) REVERT: Q 54 HIS cc_start: 0.7728 (m170) cc_final: 0.7224 (m90) REVERT: Q 89 MET cc_start: 0.6259 (tpt) cc_final: 0.5972 (tpp) REVERT: Q 93 MET cc_start: 0.2772 (mpp) cc_final: 0.2195 (mpp) REVERT: R 22 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.8098 (p) REVERT: S 47 ARG cc_start: 0.8255 (ppt170) cc_final: 0.7944 (ptp90) REVERT: S 48 ASN cc_start: 0.8347 (t0) cc_final: 0.7868 (t0) REVERT: T 40 TYR cc_start: 0.5381 (OUTLIER) cc_final: 0.2852 (t80) REVERT: T 55 ARG cc_start: 0.3667 (OUTLIER) cc_final: 0.1180 (tpt90) REVERT: T 126 PHE cc_start: 0.3751 (t80) cc_final: 0.3363 (t80) REVERT: W 64 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6392 (mm-30) REVERT: W 81 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8705 (mmtm) REVERT: F 155 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7574 (tp30) REVERT: F 166 SER cc_start: 0.9308 (OUTLIER) cc_final: 0.8653 (m) REVERT: M 1 MET cc_start: 0.3830 (ttt) cc_final: 0.3595 (tpt) REVERT: M 87 MET cc_start: 0.9307 (mmt) cc_final: 0.8893 (mmm) REVERT: M 157 ASN cc_start: 0.8676 (t0) cc_final: 0.7915 (t0) REVERT: M 199 GLU cc_start: 0.8134 (mp0) cc_final: 0.7354 (mp0) REVERT: O 48 LYS cc_start: 0.8825 (tppt) cc_final: 0.8551 (tppt) REVERT: O 65 ASN cc_start: 0.7747 (t0) cc_final: 0.7471 (t0) REVERT: O 121 GLN cc_start: 0.8247 (mp10) cc_final: 0.7490 (mp10) REVERT: O 124 ASP cc_start: 0.8270 (m-30) cc_final: 0.7948 (m-30) REVERT: P 87 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8048 (p0) REVERT: X 20 GLN cc_start: 0.7577 (pt0) cc_final: 0.7182 (mp10) REVERT: X 39 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.6668 (m-30) REVERT: X 72 TYR cc_start: 0.7642 (m-10) cc_final: 0.7133 (m-10) REVERT: X 113 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7214 (mm-40) REVERT: Y 4 MET cc_start: 0.8660 (mmt) cc_final: 0.8296 (mmt) REVERT: Y 70 ASN cc_start: 0.8135 (m-40) cc_final: 0.7766 (m110) REVERT: Y 112 ASP cc_start: 0.8635 (p0) cc_final: 0.7904 (p0) REVERT: c 88 ASP cc_start: 0.7104 (t70) cc_final: 0.6890 (t0) REVERT: c 99 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6858 (tm-30) REVERT: e 17 ARG cc_start: 0.7973 (ptp-170) cc_final: 0.7705 (mtp85) REVERT: e 36 LYS cc_start: 0.7643 (mmmt) cc_final: 0.7353 (mttm) REVERT: e 51 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8209 (tt0) outliers start: 162 outliers final: 134 residues processed: 710 average time/residue: 0.7298 time to fit residues: 904.8720 Evaluate side-chains 731 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 582 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 42 ASP Chi-restraints excluded: chain a residue 51 ASP Chi-restraints excluded: chain a residue 103 HIS Chi-restraints excluded: chain a residue 109 TYR Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain b residue 8 ASN Chi-restraints excluded: chain b residue 46 GLU Chi-restraints excluded: chain b residue 60 ASP Chi-restraints excluded: chain b residue 64 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain E residue 11 PHE Chi-restraints excluded: chain E residue 17 PHE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain g residue 109 ASP Chi-restraints excluded: chain h residue 83 TRP Chi-restraints excluded: chain h residue 98 THR Chi-restraints excluded: chain h residue 142 VAL Chi-restraints excluded: chain h residue 149 GLU Chi-restraints excluded: chain h residue 218 LEU Chi-restraints excluded: chain h residue 309 VAL Chi-restraints excluded: chain h residue 313 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 72 PHE Chi-restraints excluded: chain I residue 76 GLN Chi-restraints excluded: chain I residue 165 ASN Chi-restraints excluded: chain I residue 166 VAL Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 64 ASN Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 105 ASP Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain K residue 12 THR Chi-restraints excluded: chain K residue 14 VAL Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 124 HIS Chi-restraints excluded: chain L residue 38 LYS Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain Q residue 55 SER Chi-restraints excluded: chain Q residue 70 MET Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain R residue 22 VAL Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 24 LEU Chi-restraints excluded: chain S residue 40 ILE Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 85 VAL Chi-restraints excluded: chain S residue 113 SER Chi-restraints excluded: chain S residue 116 ASN Chi-restraints excluded: chain S residue 120 THR Chi-restraints excluded: chain T residue 4 VAL Chi-restraints excluded: chain T residue 40 TYR Chi-restraints excluded: chain T residue 55 ARG Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 81 ASP Chi-restraints excluded: chain T residue 82 TRP Chi-restraints excluded: chain T residue 111 LEU Chi-restraints excluded: chain T residue 132 ARG Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 51 ASN Chi-restraints excluded: chain U residue 113 VAL Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 60 THR Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 95 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 36 VAL Chi-restraints excluded: chain W residue 64 GLU Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 38 THR Chi-restraints excluded: chain Z residue 50 THR Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain Z residue 102 THR Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 156 MET Chi-restraints excluded: chain M residue 184 THR Chi-restraints excluded: chain M residue 197 ASN Chi-restraints excluded: chain M residue 206 ASP Chi-restraints excluded: chain M residue 225 ILE Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain O residue 7 GLU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 120 VAL Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 60 VAL Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 87 ASP Chi-restraints excluded: chain P residue 102 LEU Chi-restraints excluded: chain P residue 134 VAL Chi-restraints excluded: chain P residue 138 ASN Chi-restraints excluded: chain X residue 21 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 39 ASP Chi-restraints excluded: chain X residue 52 THR Chi-restraints excluded: chain X residue 53 ILE Chi-restraints excluded: chain X residue 103 ASN Chi-restraints excluded: chain X residue 119 LEU Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain Y residue 102 ILE Chi-restraints excluded: chain c residue 4 CYS Chi-restraints excluded: chain c residue 15 SER Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain c residue 100 VAL Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 130 LEU Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 51 GLN Chi-restraints excluded: chain e residue 53 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 317 optimal weight: 10.0000 chunk 410 optimal weight: 5.9990 chunk 550 optimal weight: 0.9980 chunk 158 optimal weight: 20.0000 chunk 476 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 518 optimal weight: 20.0000 chunk 216 optimal weight: 0.4980 chunk 531 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN K 27 GLN ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.095962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.074243 restraints weight = 317533.511| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.80 r_work: 0.3407 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 83109 Z= 0.192 Angle : 0.605 11.861 121016 Z= 0.306 Chirality : 0.036 0.258 15038 Planarity : 0.004 0.082 8535 Dihedral : 23.768 179.564 34048 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.97 % Allowed : 25.31 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.58 % Cis-general : 0.09 % Twisted Proline : 0.52 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.12), residues: 4767 helix: -0.58 (0.14), residues: 1335 sheet: -1.38 (0.19), residues: 717 loop : -1.46 (0.12), residues: 2715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 69 HIS 0.006 0.001 HIS K 124 PHE 0.029 0.001 PHE e 79 TYR 0.018 0.001 TYR U 65 ARG 0.017 0.000 ARG h 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17020.34 seconds wall clock time: 302 minutes 38.67 seconds (18158.67 seconds total)