Starting phenix.real_space_refine (version: 1.21rc1) on Sun Oct 15 06:06:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqc_22433/10_2023/7jqc_22433.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqc_22433/10_2023/7jqc_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_22433/10_2023/7jqc_22433.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqc_22433/10_2023/7jqc_22433.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqc_22433/10_2023/7jqc_22433.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jqc_22433/10_2023/7jqc_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-1.21rc1-5097/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: 29.36, per 1000 atoms: 0.38 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: 32.40 Conformation dependent library (CDL) restraints added in 4.2 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: 23.26 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: 54.39 Time building geometry restraints manager: 34.88 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: 44092 35.99 - 71.98: 2013 71.98 - 107.97: 181 107.97 - 143.96: 17 143.96 - 179.95: 30 Dihedral angle restraints: 46333 sinusoidal: 32434 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 46330 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.380 Construct map_model_manager: 0.060 Extract box with map and model: 9.880 Check model and map are aligned: 0.880 Set scattering table: 0.530 Process input model: 196.780 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.220 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 215.810 ------------------------------------------------------------------------------- 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 : 17.610 179.955 37367 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 *********************** 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 : 4.432 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 outliers start: 21 outliers final: 9 residues processed: 918 average time/residue: 0.7865 time to fit residues: 1199.7042 Evaluate side-chains 599 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 590 time to evaluate : 4.438 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.5598 time to fit residues: 14.8206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E 207 HIS 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 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 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 ASN ** M 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 ASN O 5 GLN P 5 HIS P 62 GLN ** 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 84 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1753 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= 0.310 Angle : 0.730 9.972 121016 Z= 0.375 Chirality : 0.042 0.263 15038 Planarity : 0.006 0.089 8535 Dihedral : 17.342 179.948 27408 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.45 % Favored : 91.53 % Rotamer: Outliers : 2.93 % Allowed : 17.57 % Favored : 79.50 % 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: -3.51 (0.11), residues: 4767 helix: -2.76 (0.11), residues: 1340 sheet: -1.77 (0.19), residues: 682 loop : -2.28 (0.11), residues: 2745 *********************** 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 763 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 641 time to evaluate : 4.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 70 residues processed: 714 average time/residue: 0.7684 time to fit residues: 939.8387 Evaluate side-chains 626 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 556 time to evaluate : 4.418 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 0.5914 time to fit residues: 84.8330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 329 optimal weight: 20.0000 chunk 183 optimal weight: 3.9990 chunk 492 optimal weight: 5.9990 chunk 403 optimal weight: 2.9990 chunk 163 optimal weight: 30.0000 chunk 593 optimal weight: 2.9990 chunk 640 optimal weight: 10.0000 chunk 528 optimal weight: 10.0000 chunk 588 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 475 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 104 HIS ** h 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN J 168 GLN ** 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 48 ASN ** 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 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** ** W 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 ASN P 62 GLN P 90 HIS X 32 HIS ** Y 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 87 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 83109 Z= 0.256 Angle : 0.670 9.206 121016 Z= 0.344 Chirality : 0.040 0.255 15038 Planarity : 0.005 0.076 8535 Dihedral : 17.215 179.698 27408 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 2.64 % Allowed : 19.56 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.09 % Twisted Proline : 1.03 % Twisted General : 0.15 % 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: -2.98 (0.11), residues: 4767 helix: -2.02 (0.13), residues: 1340 sheet: -1.69 (0.19), residues: 688 loop : -2.06 (0.11), residues: 2739 *********************** 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 735 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 625 time to evaluate : 4.482 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 outliers start: 110 outliers final: 49 residues processed: 699 average time/residue: 0.7216 time to fit residues: 873.6058 Evaluate side-chains 603 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 554 time to evaluate : 4.467 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.5805 time to fit residues: 59.1473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 586 optimal weight: 5.9990 chunk 445 optimal weight: 40.0000 chunk 307 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 283 optimal weight: 2.9990 chunk 398 optimal weight: 0.6980 chunk 595 optimal weight: 7.9990 chunk 630 optimal weight: 9.9990 chunk 311 optimal weight: 20.0000 chunk 564 optimal weight: 0.3980 chunk 169 optimal weight: 0.4980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 64 ASN D 267 GLN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS f 88 GLN G 148 ASN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 187 HIS h 181 ASN h 188 HIS h 191 HIS J 64 ASN ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 77 GLN ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** W 35 ASN ** M 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 157 ASN ** O 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 62 GLN ** 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 83109 Z= 0.167 Angle : 0.603 9.241 121016 Z= 0.309 Chirality : 0.037 0.272 15038 Planarity : 0.004 0.068 8535 Dihedral : 16.970 179.898 27408 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.26 % Allowed : 21.68 % Favored : 76.06 % 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: -2.58 (0.12), residues: 4767 helix: -1.50 (0.13), residues: 1349 sheet: -1.60 (0.19), residues: 702 loop : -1.87 (0.11), residues: 2716 *********************** 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 739 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 645 time to evaluate : 4.361 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 outliers start: 94 outliers final: 48 residues processed: 702 average time/residue: 0.7438 time to fit residues: 902.0664 Evaluate side-chains 614 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 566 time to evaluate : 4.351 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.5929 time to fit residues: 58.8880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 524 optimal weight: 0.4980 chunk 357 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 469 optimal weight: 20.0000 chunk 260 optimal weight: 0.0770 chunk 537 optimal weight: 50.0000 chunk 435 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 321 optimal weight: 9.9990 chunk 565 optimal weight: 2.9990 chunk 159 optimal weight: 40.0000 overall best weight: 4.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 45 ASN C 148 ASN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** 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** Z 94 HIS Z 106 GLN M 98 ASN ** M 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 83109 Z= 0.233 Angle : 0.632 12.293 121016 Z= 0.322 Chirality : 0.038 0.276 15038 Planarity : 0.005 0.094 8535 Dihedral : 16.944 179.501 27408 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 2.24 % Allowed : 23.22 % Favored : 74.55 % 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: -2.42 (0.12), residues: 4767 helix: -1.25 (0.14), residues: 1340 sheet: -1.59 (0.19), residues: 707 loop : -1.81 (0.12), residues: 2720 *********************** 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 706 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 613 time to evaluate : 4.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 57 residues processed: 671 average time/residue: 0.7726 time to fit residues: 910.0090 Evaluate side-chains 619 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 562 time to evaluate : 4.386 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.5822 time to fit residues: 68.9424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 212 optimal weight: 7.9990 chunk 567 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 370 optimal weight: 10.0000 chunk 155 optimal weight: 30.0000 chunk 630 optimal weight: 9.9990 chunk 523 optimal weight: 5.9990 chunk 292 optimal weight: 0.0170 chunk 52 optimal weight: 10.0000 chunk 208 optimal weight: 9.9990 chunk 331 optimal weight: 30.0000 overall best weight: 6.8026 ------------------------------------------------------------------------------- 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** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN J 155 ASN ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 GLN ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 11 HIS T 101 ASN ** 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 98 ASN M 142 HIS P 62 GLN ** X 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 83109 Z= 0.323 Angle : 0.699 11.610 121016 Z= 0.356 Chirality : 0.041 0.371 15038 Planarity : 0.005 0.092 8535 Dihedral : 17.140 179.573 27408 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 2.74 % Allowed : 23.84 % Favored : 73.42 % 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: -2.47 (0.12), residues: 4767 helix: -1.27 (0.14), residues: 1332 sheet: -1.71 (0.19), residues: 725 loop : -1.81 (0.12), residues: 2710 *********************** 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 688 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 574 time to evaluate : 4.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 114 outliers final: 67 residues processed: 650 average time/residue: 0.7296 time to fit residues: 826.8944 Evaluate side-chains 597 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 530 time to evaluate : 4.485 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.5983 time to fit residues: 80.7696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 608 optimal weight: 7.9990 chunk 71 optimal weight: 20.0000 chunk 359 optimal weight: 20.0000 chunk 460 optimal weight: 10.0000 chunk 356 optimal weight: 7.9990 chunk 531 optimal weight: 4.9990 chunk 352 optimal weight: 9.9990 chunk 628 optimal weight: 3.9990 chunk 393 optimal weight: 9.9990 chunk 383 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 88 GLN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN K 75 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 42 HIS ** 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 P 62 GLN c 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3034 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= 0.305 Angle : 0.691 11.026 121016 Z= 0.351 Chirality : 0.041 0.546 15038 Planarity : 0.005 0.089 8535 Dihedral : 17.168 179.663 27408 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 1.78 % Allowed : 25.11 % Favored : 73.11 % 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: -2.43 (0.12), residues: 4767 helix: -1.18 (0.14), residues: 1329 sheet: -1.76 (0.18), residues: 719 loop : -1.80 (0.12), residues: 2719 *********************** 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 650 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 576 time to evaluate : 4.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 47 residues processed: 617 average time/residue: 0.7487 time to fit residues: 804.4270 Evaluate side-chains 585 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 538 time to evaluate : 4.554 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.6182 time to fit residues: 60.5470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 388 optimal weight: 8.9990 chunk 250 optimal weight: 2.9990 chunk 375 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 399 optimal weight: 0.4980 chunk 428 optimal weight: 20.0000 chunk 310 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 493 optimal weight: 5.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 ASN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** J 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN K 113 GLN ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 GLN ** U 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 62 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: 0.7934 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 83109 Z= 0.223 Angle : 0.640 11.186 121016 Z= 0.326 Chirality : 0.039 0.535 15038 Planarity : 0.004 0.084 8535 Dihedral : 17.047 179.665 27408 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 1.08 % Allowed : 26.05 % Favored : 72.87 % 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: -2.26 (0.12), residues: 4767 helix: -1.00 (0.14), residues: 1336 sheet: -1.57 (0.19), residues: 718 loop : -1.74 (0.12), residues: 2713 *********************** 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 640 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 595 time to evaluate : 4.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 26 residues processed: 615 average time/residue: 0.7424 time to fit residues: 796.6169 Evaluate side-chains 582 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 556 time to evaluate : 4.585 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.5991 time to fit residues: 34.6247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 571 optimal weight: 6.9990 chunk 602 optimal weight: 5.9990 chunk 549 optimal weight: 0.7980 chunk 585 optimal weight: 10.0000 chunk 601 optimal weight: 4.9990 chunk 352 optimal weight: 20.0000 chunk 255 optimal weight: 4.9990 chunk 459 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 529 optimal weight: 10.0000 chunk 553 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 64 ASN ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 ASN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** Z 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 161 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 83109 Z= 0.240 Angle : 0.652 13.215 121016 Z= 0.331 Chirality : 0.039 0.531 15038 Planarity : 0.005 0.088 8535 Dihedral : 17.031 179.680 27408 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.87 % Allowed : 26.65 % Favored : 72.48 % 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: -2.22 (0.12), residues: 4767 helix: -0.97 (0.14), residues: 1351 sheet: -1.54 (0.19), residues: 721 loop : -1.72 (0.12), residues: 2695 *********************** 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 611 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 575 time to evaluate : 4.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 21 residues processed: 595 average time/residue: 0.7479 time to fit residues: 775.6065 Evaluate side-chains 570 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 549 time to evaluate : 4.632 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.6288 time to fit residues: 29.7565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 583 optimal weight: 9.9990 chunk 384 optimal weight: 6.9990 chunk 619 optimal weight: 0.9990 chunk 377 optimal weight: 0.3980 chunk 293 optimal weight: 6.9990 chunk 430 optimal weight: 0.0070 chunk 649 optimal weight: 8.9990 chunk 597 optimal weight: 3.9990 chunk 517 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 399 optimal weight: 5.9990 overall best weight: 1.8804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 64 ASN ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 ASN C 157 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS G 114 ASN ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN J 168 GLN ** K 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 GLN ** 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 83109 Z= 0.158 Angle : 0.610 13.622 121016 Z= 0.308 Chirality : 0.036 0.369 15038 Planarity : 0.004 0.082 8535 Dihedral : 16.820 179.006 27408 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.43 % Allowed : 26.94 % Favored : 72.63 % 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: -1.98 (0.12), residues: 4767 helix: -0.74 (0.14), residues: 1340 sheet: -1.40 (0.19), residues: 718 loop : -1.58 (0.12), residues: 2709 ********************** 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 644 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 626 time to evaluate : 4.441 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 outliers start: 18 outliers final: 12 residues processed: 633 average time/residue: 0.7504 time to fit residues: 824.0591 Evaluate side-chains 590 residues out of total 4167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 578 time to evaluate : 4.463 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5881 time to fit residues: 18.6023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 317 optimal weight: 5.9990 chunk 410 optimal weight: 7.9990 chunk 550 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 chunk 476 optimal weight: 3.9990 chunk 76 optimal weight: 20.0000 chunk 143 optimal weight: 20.0000 chunk 518 optimal weight: 20.0000 chunk 216 optimal weight: 3.9990 chunk 531 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 64 ASN ** a 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 ASN C 157 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 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** S 74 GLN ** T 105 ASN ** 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 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.095175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.073519 restraints weight = 319381.605| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.83 r_work: 0.3388 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 83109 Z= 0.240 Angle : 0.644 16.203 121016 Z= 0.326 Chirality : 0.038 0.306 15038 Planarity : 0.005 0.085 8535 Dihedral : 16.857 179.685 27408 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.41 % Allowed : 27.88 % Favored : 71.71 % 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: -1.99 (0.12), residues: 4767 helix: -0.76 (0.14), residues: 1354 sheet: -1.35 (0.19), residues: 727 loop : -1.61 (0.12), residues: 2686 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16235.25 seconds wall clock time: 289 minutes 27.83 seconds (17367.83 seconds total)