Starting phenix.real_space_refine on Fri Dec 15 07:28:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1s_9572/12_2023/5h1s_9572.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1s_9572/12_2023/5h1s_9572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1s_9572/12_2023/5h1s_9572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1s_9572/12_2023/5h1s_9572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1s_9572/12_2023/5h1s_9572.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1s_9572/12_2023/5h1s_9572.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3018 5.49 5 S 98 5.16 5 C 45355 2.51 5 N 16981 2.21 5 O 25373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L ARG 126": "NH1" <-> "NH2" Residue "L ARG 168": "NH1" <-> "NH2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 174": "NH1" <-> "NH2" Residue "L ARG 175": "NH1" <-> "NH2" Residue "L ARG 179": "NH1" <-> "NH2" Residue "L ARG 194": "NH1" <-> "NH2" Residue "L ARG 198": "NH1" <-> "NH2" Residue "L ARG 205": "NH1" <-> "NH2" Residue "L ARG 212": "NH1" <-> "NH2" Residue "L ARG 242": "NH1" <-> "NH2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M ARG 30": "NH1" <-> "NH2" Residue "M ARG 31": "NH1" <-> "NH2" Residue "M ARG 34": "NH1" <-> "NH2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 71": "NH1" <-> "NH2" Residue "M ARG 78": "NH1" <-> "NH2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "M ARG 107": "NH1" <-> "NH2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 97": "NH1" <-> "NH2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "N PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 127": "NH1" <-> "NH2" Residue "N PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 130": "OE1" <-> "OE2" Residue "N TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 175": "OE1" <-> "OE2" Residue "N ARG 192": "NH1" <-> "NH2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "N PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 223": "OE1" <-> "OE2" Residue "N TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 252": "NH1" <-> "NH2" Residue "O ARG 6": "NH1" <-> "NH2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 14": "NH1" <-> "NH2" Residue "O ARG 23": "NH1" <-> "NH2" Residue "O ARG 31": "NH1" <-> "NH2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "O ARG 52": "NH1" <-> "NH2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O ARG 59": "NH1" <-> "NH2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O ARG 67": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 116": "NH1" <-> "NH2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "O PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 15": "NH1" <-> "NH2" Residue "P ARG 19": "NH1" <-> "NH2" Residue "P ARG 27": "NH1" <-> "NH2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P ARG 32": "NH1" <-> "NH2" Residue "P ARG 43": "NH1" <-> "NH2" Residue "P ARG 48": "NH1" <-> "NH2" Residue "P ARG 73": "NH1" <-> "NH2" Residue "P ARG 74": "NH1" <-> "NH2" Residue "P ARG 96": "NH1" <-> "NH2" Residue "P ARG 106": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "P ARG 113": "NH1" <-> "NH2" Residue "P ARG 114": "NH1" <-> "NH2" Residue "P TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q ARG 53": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q ARG 61": "NH1" <-> "NH2" Residue "Q ARG 72": "NH1" <-> "NH2" Residue "Q ARG 77": "NH1" <-> "NH2" Residue "Q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "Q ARG 151": "NH1" <-> "NH2" Residue "Q ARG 160": "NH1" <-> "NH2" Residue "R ARG 116": "NH1" <-> "NH2" Residue "R ASP 121": "OD1" <-> "OD2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 144": "NH1" <-> "NH2" Residue "R ARG 152": "NH1" <-> "NH2" Residue "R ARG 160": "NH1" <-> "NH2" Residue "R ARG 161": "NH1" <-> "NH2" Residue "R ARG 172": "NH1" <-> "NH2" Residue "R ARG 182": "NH1" <-> "NH2" Residue "R ARG 184": "NH1" <-> "NH2" Residue "R ARG 185": "NH1" <-> "NH2" Residue "R ARG 228": "NH1" <-> "NH2" Residue "S ARG 6": "NH1" <-> "NH2" Residue "S TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 12": "NH1" <-> "NH2" Residue "S ARG 18": "NH1" <-> "NH2" Residue "S PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 25": "NH1" <-> "NH2" Residue "S ARG 30": "NH1" <-> "NH2" Residue "S ARG 33": "NH1" <-> "NH2" Residue "S ARG 48": "NH1" <-> "NH2" Residue "S ARG 50": "NH1" <-> "NH2" Residue "S ARG 52": "NH1" <-> "NH2" Residue "S ARG 55": "NH1" <-> "NH2" Residue "S ARG 58": "NH1" <-> "NH2" Residue "S ARG 59": "NH1" <-> "NH2" Residue "S ARG 64": "NH1" <-> "NH2" Residue "S ARG 70": "NH1" <-> "NH2" Residue "S ARG 72": "NH1" <-> "NH2" Residue "S TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "T PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 140": "NH1" <-> "NH2" Residue "T TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 207": "NH1" <-> "NH2" Residue "T ARG 213": "NH1" <-> "NH2" Residue "T ARG 218": "NH1" <-> "NH2" Residue "T TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 35": "NH1" <-> "NH2" Residue "U ARG 47": "NH1" <-> "NH2" Residue "U ARG 48": "NH1" <-> "NH2" Residue "U ARG 54": "NH1" <-> "NH2" Residue "U TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 119": "NH1" <-> "NH2" Residue "U ARG 121": "NH1" <-> "NH2" Residue "U ARG 127": "NH1" <-> "NH2" Residue "U ARG 137": "NH1" <-> "NH2" Residue "U ASP 143": "OD1" <-> "OD2" Residue "V TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 106": "NH1" <-> "NH2" Residue "V ARG 107": "NH1" <-> "NH2" Residue "V ARG 148": "NH1" <-> "NH2" Residue "V ARG 160": "NH1" <-> "NH2" Residue "V ARG 167": "NH1" <-> "NH2" Residue "V TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 146": "NH1" <-> "NH2" Residue "W ARG 156": "NH1" <-> "NH2" Residue "W ARG 159": "NH1" <-> "NH2" Residue "W ASP 169": "OD1" <-> "OD2" Residue "W ASP 172": "OD1" <-> "OD2" Residue "W ARG 173": "NH1" <-> "NH2" Residue "X ARG 70": "NH1" <-> "NH2" Residue "X ARG 76": "NH1" <-> "NH2" Residue "X ARG 95": "NH1" <-> "NH2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 131": "OD1" <-> "OD2" Residue "X ARG 151": "NH1" <-> "NH2" Residue "Y ARG 73": "NH1" <-> "NH2" Residue "Y ARG 97": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Z ARG 69": "NH1" <-> "NH2" Residue "Z PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 97": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "Z ARG 111": "NH1" <-> "NH2" Residue "Z ARG 114": "NH1" <-> "NH2" Residue "Z ARG 131": "NH1" <-> "NH2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 50": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 234": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 253": "NH1" <-> "NH2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 268": "NH1" <-> "NH2" Residue "c ARG 20": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ARG 32": "NH1" <-> "NH2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c ARG 45": "NH1" <-> "NH2" Residue "c TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 112": "NH1" <-> "NH2" Residue "d ARG 114": "NH1" <-> "NH2" Residue "d ARG 121": "NH1" <-> "NH2" Residue "d ARG 126": "NH1" <-> "NH2" Residue "d ARG 127": "NH1" <-> "NH2" Residue "d ARG 132": "NH1" <-> "NH2" Residue "d ARG 146": "NH1" <-> "NH2" Residue "e ARG 101": "NH1" <-> "NH2" Residue "e ARG 103": "NH1" <-> "NH2" Residue "e ARG 112": "NH1" <-> "NH2" Residue "e ARG 113": "NH1" <-> "NH2" Residue "e ARG 114": "NH1" <-> "NH2" Residue "e ARG 128": "NH1" <-> "NH2" Residue "e ARG 131": "NH1" <-> "NH2" Residue "f ARG 41": "NH1" <-> "NH2" Residue "f ARG 45": "NH1" <-> "NH2" Residue "f ARG 52": "NH1" <-> "NH2" Residue "f ARG 55": "NH1" <-> "NH2" Residue "f ARG 57": "NH1" <-> "NH2" Residue "f ARG 59": "NH1" <-> "NH2" Residue "F PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F ARG 147": "NH1" <-> "NH2" Residue "F ARG 154": "NH1" <-> "NH2" Residue "F ARG 166": "NH1" <-> "NH2" Residue "F PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "F ARG 274": "NH1" <-> "NH2" Residue "F ARG 291": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G ARG 97": "NH1" <-> "NH2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G ARG 125": "NH1" <-> "NH2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "G ARG 146": "NH1" <-> "NH2" Residue "G ARG 158": "NH1" <-> "NH2" Residue "G PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 221": "NH1" <-> "NH2" Residue "G ARG 224": "NH1" <-> "NH2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 258": "NH1" <-> "NH2" Residue "H ARG 56": "NH1" <-> "NH2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "H ARG 133": "NH1" <-> "NH2" Residue "H ARG 145": "NH1" <-> "NH2" Residue "H ARG 155": "NH1" <-> "NH2" Residue "H ARG 163": "NH1" <-> "NH2" Residue "H ARG 165": "NH1" <-> "NH2" Residue "H TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 187": "OE1" <-> "OE2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 42": "NH1" <-> "NH2" Residue "I ARG 78": "NH1" <-> "NH2" Residue "I ARG 91": "NH1" <-> "NH2" Residue "I ARG 93": "NH1" <-> "NH2" Residue "I ARG 99": "NH1" <-> "NH2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "I ARG 109": "NH1" <-> "NH2" Residue "I ARG 135": "NH1" <-> "NH2" Residue "I ARG 154": "NH1" <-> "NH2" Residue "I ARG 176": "NH1" <-> "NH2" Residue "I ARG 189": "NH1" <-> "NH2" Residue "I ARG 192": "NH1" <-> "NH2" Residue "I ARG 203": "NH1" <-> "NH2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "g ARG 116": "NH1" <-> "NH2" Residue "a ARG 46": "NH1" <-> "NH2" Residue "a GLU 47": "OE1" <-> "OE2" Residue "a GLU 71": "OE1" <-> "OE2" Residue "h ARG 50": "NH1" <-> "NH2" Residue "h ARG 63": "NH1" <-> "NH2" Residue "h ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 90825 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 60117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2799, 60117 Classifications: {'RNA': 2799} Modifications used: {'rna2p_pur': 169, 'rna2p_pyr': 67, 'rna3p_pur': 1459, 'rna3p_pyr': 1104} Link IDs: {'rna2p': 236, 'rna3p': 2562} Chain breaks: 2 Chain: "C" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2187 Classifications: {'RNA': 102} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 54, 'rna3p_pyr': 36} Link IDs: {'rna2p': 12, 'rna3p': 89} Chain: "B" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2500 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 60, 'rna3p_pyr': 50} Link IDs: {'rna2p': 7, 'rna3p': 109} Chain: "L" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1184 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 9, 'TRANS': 137} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "N" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1342 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain: "O" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1067 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain: "P" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 947 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "R" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 953 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "S" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 996 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain: "T" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1171 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 13, 'TRANS': 133} Chain: "U" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1149 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "V" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 740 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "W" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "X" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 810 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "Y" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 605 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "Z" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "E" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1904 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "b" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 378 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "c" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "d" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "e" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 563 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "f" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 304 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "F" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1620 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 9, 'TRANS': 202} Chain: "G" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1655 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 13, 'TRANS': 196} Chain: "H" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1351 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "I" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1353 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain: "J" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 423 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "g" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 345 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "a" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 300 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "h" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 368 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 8, 'TRANS': 37} Time building chain proxies: 38.57, per 1000 atoms: 0.42 Number of scatterers: 90825 At special positions: 0 Unit cell: (203.52, 229.12, 221.44, 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 98 16.00 P 3018 15.00 O 25373 8.00 N 16981 7.00 C 45355 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS f 48 " - pdb=" SG CYS f 64 " distance=2.05 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 Atom "ATOM 24850 O4' A A1160 .*. O " rejected from bonding due to valence issues. Atom "ATOM 42991 O5' G A2011 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.71 Conformation dependent library (CDL) restraints added in 3.9 seconds 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5994 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 39 sheets defined 28.3% alpha, 12.9% beta 795 base pairs and 1450 stacking pairs defined. Time for finding SS restraints: 31.53 Creating SS restraints... Processing helix chain 'L' and resid 123 through 132 Processing helix chain 'L' and resid 166 through 171 Processing helix chain 'L' and resid 187 through 195 Processing helix chain 'L' and resid 197 through 208 removed outlier: 3.624A pdb=" N ARG L 205 " --> pdb=" O GLU L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 218 removed outlier: 3.727A pdb=" N ARG L 215 " --> pdb=" O GLY L 211 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 109 Processing helix chain 'M' and resid 110 through 116 removed outlier: 3.523A pdb=" N VAL M 114 " --> pdb=" O PHE M 110 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU M 116 " --> pdb=" O LYS M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 120 removed outlier: 3.722A pdb=" N SER N 119 " --> pdb=" O ARG N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 140 Processing helix chain 'N' and resid 160 through 166 Processing helix chain 'N' and resid 176 through 185 removed outlier: 4.033A pdb=" N SER N 180 " --> pdb=" O VAL N 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 229 Processing helix chain 'N' and resid 243 through 254 Processing helix chain 'O' and resid 44 through 59 Processing helix chain 'O' and resid 110 through 124 Processing helix chain 'P' and resid 23 through 42 Processing helix chain 'P' and resid 48 through 66 removed outlier: 3.702A pdb=" N TYR P 57 " --> pdb=" O ALA P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 80 Processing helix chain 'P' and resid 82 through 91 removed outlier: 4.140A pdb=" N VAL P 86 " --> pdb=" O GLU P 82 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS P 87 " --> pdb=" O LYS P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 97 removed outlier: 3.766A pdb=" N ARG P 96 " --> pdb=" O GLU P 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 65 removed outlier: 4.304A pdb=" N ALA Q 55 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 116 through 132 Processing helix chain 'Q' and resid 150 through 162 removed outlier: 4.074A pdb=" N ALA Q 154 " --> pdb=" O GLY Q 150 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS Q 162 " --> pdb=" O ALA Q 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 138 Processing helix chain 'R' and resid 175 through 178 Processing helix chain 'R' and resid 226 through 230 Processing helix chain 'S' and resid 8 through 21 removed outlier: 3.968A pdb=" N ARG S 12 " --> pdb=" O TYR S 8 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE S 17 " --> pdb=" O ARG S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 71 removed outlier: 4.634A pdb=" N GLN S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 88 removed outlier: 3.641A pdb=" N HIS S 83 " --> pdb=" O SER S 79 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 104 removed outlier: 4.458A pdb=" N ILE S 102 " --> pdb=" O ALA S 98 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU S 103 " --> pdb=" O GLN S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'T' and resid 104 through 111 Processing helix chain 'U' and resid 42 through 53 removed outlier: 3.605A pdb=" N ALA U 46 " --> pdb=" O SER U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 68 removed outlier: 3.687A pdb=" N LEU U 67 " --> pdb=" O MET U 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 85 removed outlier: 3.879A pdb=" N ILE U 76 " --> pdb=" O ALA U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 88 No H-bonds generated for 'chain 'U' and resid 86 through 88' Processing helix chain 'U' and resid 153 through 161 removed outlier: 4.025A pdb=" N ALA U 159 " --> pdb=" O LYS U 155 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 113 No H-bonds generated for 'chain 'V' and resid 111 through 113' Processing helix chain 'V' and resid 121 through 132 removed outlier: 4.084A pdb=" N ASN V 132 " --> pdb=" O ILE V 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 144 through 149 Processing helix chain 'V' and resid 183 through 192 removed outlier: 4.075A pdb=" N LYS V 190 " --> pdb=" O GLU V 186 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE V 191 " --> pdb=" O LEU V 187 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 54 Processing helix chain 'X' and resid 148 through 165 removed outlier: 4.216A pdb=" N ALA X 152 " --> pdb=" O ASN X 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 111 through 114 Processing helix chain 'Y' and resid 122 through 133 Processing helix chain 'Y' and resid 134 through 142 Processing helix chain 'Z' and resid 72 through 96 removed outlier: 3.557A pdb=" N ARG Z 94 " --> pdb=" O LEU Z 90 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER Z 95 " --> pdb=" O ARG Z 91 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA Z 96 " --> pdb=" O LEU Z 92 " (cutoff:3.500A) Processing helix chain 'Z' and resid 100 through 105 Processing helix chain 'Z' and resid 105 through 127 removed outlier: 3.888A pdb=" N ALA Z 113 " --> pdb=" O ARG Z 109 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG Z 114 " --> pdb=" O LYS Z 110 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN Z 126 " --> pdb=" O ARG Z 122 " (cutoff:3.500A) Processing helix chain 'Z' and resid 129 through 142 Processing helix chain 'E' and resid 193 through 199 removed outlier: 3.557A pdb=" N VAL E 196 " --> pdb=" O ASN E 193 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN E 198 " --> pdb=" O GLY E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 211 Processing helix chain 'b' and resid 9 through 39 removed outlier: 3.628A pdb=" N LYS b 13 " --> pdb=" O SER b 9 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA b 27 " --> pdb=" O LYS b 23 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA b 28 " --> pdb=" O GLY b 24 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU b 29 " --> pdb=" O TYR b 25 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS b 30 " --> pdb=" O TRP b 26 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA b 31 " --> pdb=" O ALA b 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 101 through 110 removed outlier: 3.612A pdb=" N THR d 108 " --> pdb=" O SER d 104 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 117 removed outlier: 3.502A pdb=" N SER d 116 " --> pdb=" O ARG d 112 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR d 117 " --> pdb=" O LEU d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 117 through 131 removed outlier: 3.696A pdb=" N GLY d 131 " --> pdb=" O ARG d 127 " (cutoff:3.500A) Processing helix chain 'e' and resid 95 through 99 Processing helix chain 'e' and resid 125 through 132 Processing helix chain 'e' and resid 141 through 146 Processing helix chain 'f' and resid 66 through 70 Processing helix chain 'F' and resid 150 through 160 removed outlier: 3.900A pdb=" N ALA F 160 " --> pdb=" O HIS F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 215 Processing helix chain 'G' and resid 79 through 95 removed outlier: 3.508A pdb=" N GLY G 87 " --> pdb=" O VAL G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 169 removed outlier: 3.923A pdb=" N LEU G 159 " --> pdb=" O LYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 198 Processing helix chain 'G' and resid 213 through 218 Processing helix chain 'G' and resid 248 through 259 Processing helix chain 'H' and resid 57 through 64 removed outlier: 3.594A pdb=" N TYR H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 74 removed outlier: 4.110A pdb=" N LEU H 69 " --> pdb=" O MET H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 81 Processing helix chain 'H' and resid 99 through 114 removed outlier: 3.525A pdb=" N THR H 114 " --> pdb=" O LEU H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 160 Processing helix chain 'H' and resid 195 through 199 removed outlier: 3.843A pdb=" N ILE H 198 " --> pdb=" O LYS H 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL H 199 " --> pdb=" O PRO H 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 195 through 199' Processing helix chain 'H' and resid 217 through 225 Processing helix chain 'I' and resid 99 through 122 removed outlier: 3.910A pdb=" N GLY I 106 " --> pdb=" O ASN I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 190 Processing helix chain 'J' and resid 70 through 75 removed outlier: 3.751A pdb=" N ARG J 75 " --> pdb=" O ALA J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 93 removed outlier: 3.968A pdb=" N LYS J 93 " --> pdb=" O PRO J 89 " (cutoff:3.500A) Processing helix chain 'g' and resid 80 through 84 Processing helix chain 'g' and resid 89 through 121 removed outlier: 4.127A pdb=" N SER g 94 " --> pdb=" O LEU g 90 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR g 117 " --> pdb=" O ARG g 113 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA g 121 " --> pdb=" O THR g 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 56 through 62 removed outlier: 3.606A pdb=" N LYS h 61 " --> pdb=" O ALA h 57 " (cutoff:3.500A) Processing helix chain 'h' and resid 68 through 74 removed outlier: 3.513A pdb=" N ILE h 72 " --> pdb=" O ALA h 68 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG h 74 " --> pdb=" O TRP h 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 115 through 118 removed outlier: 6.373A pdb=" N TYR L 115 " --> pdb=" O ILE L 154 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL L 156 " --> pdb=" O TYR L 115 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL L 117 " --> pdb=" O VAL L 156 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL L 153 " --> pdb=" O LYS L 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'L' and resid 175 through 176 removed outlier: 3.808A pdb=" N ARG L 175 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 91 through 93 removed outlier: 4.376A pdb=" N ASP M 88 " --> pdb=" O GLY M 91 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ILE M 86 " --> pdb=" O PRO M 93 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA M 83 " --> pdb=" O VAL M 63 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG M 59 " --> pdb=" O ILE M 87 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL M 38 " --> pdb=" O ILE M 24 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE M 24 " --> pdb=" O VAL M 38 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU M 18 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA M 46 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA M 16 " --> pdb=" O ALA M 46 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ARG M 17 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL M 10 " --> pdb=" O ARG M 17 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU M 19 " --> pdb=" O LEU M 8 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA M 84 " --> pdb=" O HIS M 7 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN M 9 " --> pdb=" O ALA M 84 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE M 86 " --> pdb=" O ASN M 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 102 through 106 removed outlier: 6.258A pdb=" N ILE O 102 " --> pdb=" O ALA O 36 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA O 36 " --> pdb=" O ILE O 102 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR O 104 " --> pdb=" O LEU O 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 40 through 43 Processing sheet with id=AA6, first strand: chain 'P' and resid 44 through 47 removed outlier: 4.056A pdb=" N ARG P 106 " --> pdb=" O GLU P 124 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 44 through 47 removed outlier: 4.220A pdb=" N MET P 120 " --> pdb=" O THR P 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 93 through 99 removed outlier: 5.813A pdb=" N THR Q 94 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP Q 88 " --> pdb=" O THR Q 94 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU Q 73 " --> pdb=" O ASP Q 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 192 through 197 removed outlier: 6.317A pdb=" N THR R 180 " --> pdb=" O ARG R 172 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG R 172 " --> pdb=" O THR R 180 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG R 182 " --> pdb=" O ILE R 170 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ASP R 147 " --> pdb=" O VAL R 169 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE R 148 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU R 154 " --> pdb=" O ILE R 203 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE R 203 " --> pdb=" O GLU R 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 132 through 136 removed outlier: 4.903A pdb=" N LEU T 163 " --> pdb=" O VAL T 126 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL T 128 " --> pdb=" O VAL T 161 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL T 161 " --> pdb=" O VAL T 128 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 141 through 144 removed outlier: 6.892A pdb=" N HIS T 183 " --> pdb=" O THR T 222 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 197 through 199 removed outlier: 3.786A pdb=" N LYS T 199 " --> pdb=" O ARG T 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'U' and resid 32 through 35 removed outlier: 3.538A pdb=" N ILE U 32 " --> pdb=" O LEU U 136 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU U 136 " --> pdb=" O ILE U 32 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE U 134 " --> pdb=" O THR U 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'U' and resid 32 through 35 removed outlier: 3.538A pdb=" N ILE U 32 " --> pdb=" O LEU U 136 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU U 136 " --> pdb=" O ILE U 32 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE U 134 " --> pdb=" O THR U 34 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'U' and resid 111 through 117 Processing sheet with id=AB7, first strand: chain 'V' and resid 115 through 118 removed outlier: 6.786A pdb=" N THR V 137 " --> pdb=" O GLN V 116 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU V 135 " --> pdb=" O PRO V 118 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS V 173 " --> pdb=" O THR V 164 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR V 164 " --> pdb=" O LYS V 173 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR V 175 " --> pdb=" O VAL V 162 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL V 162 " --> pdb=" O TYR V 175 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N MET V 177 " --> pdb=" O ARG V 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'W' and resid 129 through 130 removed outlier: 3.818A pdb=" N LYS W 91 " --> pdb=" O ILE W 100 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'W' and resid 107 through 108 Processing sheet with id=AC1, first strand: chain 'W' and resid 150 through 151 Processing sheet with id=AC2, first strand: chain 'X' and resid 92 through 94 removed outlier: 6.670A pdb=" N ILE X 115 " --> pdb=" O ILE X 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 122 through 124 Processing sheet with id=AC4, first strand: chain 'Y' and resid 83 through 84 Processing sheet with id=AC5, first strand: chain 'Y' and resid 104 through 110 removed outlier: 3.709A pdb=" N LYS Y 106 " --> pdb=" O LEU Y 119 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 76 through 78 removed outlier: 3.998A pdb=" N THR E 76 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 137 through 140 removed outlier: 4.313A pdb=" N ASN E 139 " --> pdb=" O THR E 187 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 159 through 164 removed outlier: 3.994A pdb=" N THR E 169 " --> pdb=" O ILE E 161 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS E 163 " --> pdb=" O SER E 167 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU E 176 " --> pdb=" O LEU E 172 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 13 through 15 Processing sheet with id=AD1, first strand: chain 'e' and resid 103 through 104 removed outlier: 3.855A pdb=" N ARG e 103 " --> pdb=" O VAL e 111 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'f' and resid 52 through 56 Processing sheet with id=AD3, first strand: chain 'F' and resid 258 through 264 removed outlier: 5.395A pdb=" N LYS F 260 " --> pdb=" O GLY F 201 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLY F 201 " --> pdb=" O LYS F 260 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ARG F 262 " --> pdb=" O ILE F 199 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE F 199 " --> pdb=" O ARG F 262 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR F 202 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU F 289 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LYS F 96 " --> pdb=" O GLY F 116 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLY F 116 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY F 98 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL F 114 " --> pdb=" O GLY F 98 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL F 110 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 122 through 127 removed outlier: 3.516A pdb=" N ILE F 122 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLN F 138 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL F 126 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA F 136 " --> pdb=" O VAL F 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 208 through 209 Processing sheet with id=AD6, first strand: chain 'H' and resid 119 through 120 removed outlier: 3.568A pdb=" N VAL H 89 " --> pdb=" O VAL H 142 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 55 through 59 Processing sheet with id=AD8, first strand: chain 'I' and resid 80 through 84 Processing sheet with id=AD9, first strand: chain 'I' and resid 123 through 126 Processing sheet with id=AE1, first strand: chain 'I' and resid 135 through 139 Processing sheet with id=AE2, first strand: chain 'J' and resid 51 through 52 Processing sheet with id=AE3, first strand: chain 'a' and resid 50 through 51 removed outlier: 5.809A pdb=" N LYS a 50 " --> pdb=" O VAL a 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 785 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1985 hydrogen bonds 3078 hydrogen bond angles 0 basepair planarities 795 basepair parallelities 1450 stacking parallelities Total time for adding SS restraints: 133.73 Time building geometry restraints manager: 45.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 17327 1.33 - 1.46: 42497 1.46 - 1.59: 34733 1.59 - 1.72: 4302 1.72 - 1.85: 173 Bond restraints: 99032 Sorted by residual: bond pdb=" C6 A C 95 " pdb=" N1 A C 95 " ideal model delta sigma weight residual 1.351 1.849 -0.498 2.00e-02 2.50e+03 6.19e+02 bond pdb=" N3 A C 95 " pdb=" C4 A C 95 " ideal model delta sigma weight residual 1.344 1.805 -0.461 2.00e-02 2.50e+03 5.30e+02 bond pdb=" C2 A C 95 " pdb=" N3 A C 95 " ideal model delta sigma weight residual 1.331 1.757 -0.426 2.00e-02 2.50e+03 4.53e+02 bond pdb=" N1 A C 95 " pdb=" C2 A C 95 " ideal model delta sigma weight residual 1.339 1.762 -0.423 2.00e-02 2.50e+03 4.48e+02 bond pdb=" C5 A C 95 " pdb=" C6 A C 95 " ideal model delta sigma weight residual 1.406 1.791 -0.385 2.00e-02 2.50e+03 3.70e+02 ... (remaining 99027 not shown) Histogram of bond angle deviations from ideal: 88.83 - 98.99: 19 98.99 - 109.15: 40120 109.15 - 119.30: 61658 119.30 - 129.46: 44464 129.46 - 139.62: 2402 Bond angle restraints: 148663 Sorted by residual: angle pdb=" N ASP X 131 " pdb=" CA ASP X 131 " pdb=" C ASP X 131 " ideal model delta sigma weight residual 111.36 121.85 -10.49 1.09e+00 8.42e-01 9.26e+01 angle pdb=" C LEU N 196 " pdb=" N PRO N 197 " pdb=" CD PRO N 197 " ideal model delta sigma weight residual 125.00 88.83 36.17 4.10e+00 5.95e-02 7.78e+01 angle pdb=" N LYS X 132 " pdb=" CA LYS X 132 " pdb=" C LYS X 132 " ideal model delta sigma weight residual 110.20 122.96 -12.76 1.58e+00 4.01e-01 6.53e+01 angle pdb=" N GLY X 129 " pdb=" CA GLY X 129 " pdb=" C GLY X 129 " ideal model delta sigma weight residual 112.34 95.90 16.44 2.04e+00 2.40e-01 6.49e+01 angle pdb=" N LYS X 73 " pdb=" CA LYS X 73 " pdb=" C LYS X 73 " ideal model delta sigma weight residual 111.36 120.06 -8.70 1.09e+00 8.42e-01 6.37e+01 ... (remaining 148658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 53366 35.82 - 71.65: 6682 71.65 - 107.47: 962 107.47 - 143.29: 62 143.29 - 179.11: 74 Dihedral angle restraints: 61146 sinusoidal: 51810 harmonic: 9336 Sorted by residual: dihedral pdb=" C4' C A2210 " pdb=" C3' C A2210 " pdb=" C2' C A2210 " pdb=" C1' C A2210 " ideal model delta sinusoidal sigma weight residual -35.00 36.37 -71.37 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' C A1651 " pdb=" C3' C A1651 " pdb=" C2' C A1651 " pdb=" C1' C A1651 " ideal model delta sinusoidal sigma weight residual -35.00 36.32 -71.32 1 8.00e+00 1.56e-02 1.02e+02 dihedral pdb=" C4' C A1162 " pdb=" C3' C A1162 " pdb=" C2' C A1162 " pdb=" C1' C A1162 " ideal model delta sinusoidal sigma weight residual -35.00 36.32 -71.32 1 8.00e+00 1.56e-02 1.02e+02 ... (remaining 61143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 16470 0.093 - 0.186: 2320 0.186 - 0.279: 169 0.279 - 0.371: 32 0.371 - 0.464: 3 Chirality restraints: 18994 Sorted by residual: chirality pdb=" CA PRO T 175 " pdb=" N PRO T 175 " pdb=" C PRO T 175 " pdb=" CB PRO T 175 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" C3' G A1287 " pdb=" C4' G A1287 " pdb=" O3' G A1287 " pdb=" C2' G A1287 " both_signs ideal model delta sigma weight residual False -2.74 -2.29 -0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA LYS X 132 " pdb=" N LYS X 132 " pdb=" C LYS X 132 " pdb=" CB LYS X 132 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.74e+00 ... (remaining 18991 not shown) Planarity restraints: 7537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO T 116 " 0.146 5.00e-02 4.00e+02 2.17e-01 7.54e+01 pdb=" N PRO T 117 " -0.374 5.00e-02 4.00e+02 pdb=" CA PRO T 117 " 0.140 5.00e-02 4.00e+02 pdb=" CD PRO T 117 " 0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 196 " -0.136 5.00e-02 4.00e+02 2.15e-01 7.37e+01 pdb=" N PRO N 197 " 0.370 5.00e-02 4.00e+02 pdb=" CA PRO N 197 " -0.145 5.00e-02 4.00e+02 pdb=" CD PRO N 197 " -0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 154 " -0.122 5.00e-02 4.00e+02 1.93e-01 5.97e+01 pdb=" N PRO N 155 " 0.333 5.00e-02 4.00e+02 pdb=" CA PRO N 155 " -0.124 5.00e-02 4.00e+02 pdb=" CD PRO N 155 " -0.087 5.00e-02 4.00e+02 ... (remaining 7534 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 128 1.80 - 2.58: 2548 2.58 - 3.35: 113949 3.35 - 4.13: 284360 4.13 - 4.90: 419938 Nonbonded interactions: 820923 Sorted by model distance: nonbonded pdb=" C1' G A 836 " pdb=" NE2 GLN N 133 " model vdw 1.028 3.550 nonbonded pdb=" OP1 A A1236 " pdb=" NH2 ARG S 12 " model vdw 1.030 2.520 nonbonded pdb=" O4 U A1828 " pdb=" NH1 ARG E 152 " model vdw 1.063 2.520 nonbonded pdb=" OP1 G A1883 " pdb=" C TYR N 256 " model vdw 1.080 3.270 nonbonded pdb=" OP2 U A2106 " pdb=" NH2 ARG J 75 " model vdw 1.091 2.520 ... (remaining 820918 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 10.230 Check model and map are aligned: 1.000 Set scattering table: 0.670 Process input model: 312.700 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.260 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: 0.020 Load rotamer database and sin/cos tables:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 330.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 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 : 0.010 0.498 99032 Z= 0.605 Angle : 1.059 36.169 148663 Z= 0.590 Chirality : 0.066 0.464 18994 Planarity : 0.008 0.217 7537 Dihedral : 24.809 179.115 55149 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 46.50 Ramachandran Plot: Outliers : 1.55 % Allowed : 16.72 % Favored : 81.73 % Rotamer: Outliers : 3.21 % Allowed : 5.01 % Favored : 91.78 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.45 % 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: -4.90 (0.12), residues: 3218 helix: -2.17 (0.17), residues: 837 sheet: -3.66 (0.19), residues: 495 loop : -3.83 (0.11), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.005 TRP Y 110 HIS 0.018 0.003 HIS P 13 PHE 0.038 0.004 PHE Z 105 TYR 0.042 0.004 TYR O 92 ARG 0.021 0.002 ARG Y 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1234 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1145 time to evaluate : 4.078 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 outliers start: 89 outliers final: 36 residues processed: 1198 average time/residue: 1.0343 time to fit residues: 1975.2474 Evaluate side-chains 869 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 833 time to evaluate : 4.693 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 36 outliers final: 1 residues processed: 36 average time/residue: 0.8469 time to fit residues: 56.7121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 519 optimal weight: 1.9990 chunk 466 optimal weight: 0.9990 chunk 258 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 314 optimal weight: 0.0040 chunk 249 optimal weight: 2.9990 chunk 482 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 293 optimal weight: 9.9990 chunk 358 optimal weight: 0.7980 chunk 558 optimal weight: 0.9980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 157 ASN ** L 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 220 HIS M 49 ASN M 73 ASN M 82 ASN N 84 ASN O 13 HIS P 75 GLN P 101 ASN Q 149 HIS R 178 HIS R 202 ASN S 28 HIS S 47 HIS S 77 ASN S 99 GLN T 109 GLN T 133 GLN ** T 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 153 ASN ** T 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 106 ASN V 132 ASN W 68 HIS ** W 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 121 GLN W 130 HIS W 149 HIS X 102 HIS Y 90 HIS E 54 HIS E 84 ASN E 124 ASN E 149 GLN E 190 GLN ** E 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 36 GLN c 38 ASN ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 ASN ** f 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN F 169 GLN F 229 HIS G 71 ASN G 94 ASN G 153 ASN G 181 ASN G 222 ASN H 171 ASN I 168 ASN I 183 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 99032 Z= 0.223 Angle : 0.824 13.968 148663 Z= 0.419 Chirality : 0.042 0.408 18994 Planarity : 0.007 0.140 7537 Dihedral : 25.331 177.801 48351 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.53 % Allowed : 11.68 % Favored : 87.79 % Rotamer: Outliers : 4.83 % Allowed : 15.39 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.23 % 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: -3.90 (0.13), residues: 3218 helix: -1.34 (0.16), residues: 854 sheet: -3.16 (0.20), residues: 486 loop : -3.17 (0.12), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP G 197 HIS 0.012 0.002 HIS Q 149 PHE 0.033 0.003 PHE T 124 TYR 0.027 0.003 TYR N 157 ARG 0.013 0.001 ARG H 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 942 time to evaluate : 3.979 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: 134 outliers final: 66 residues processed: 989 average time/residue: 0.9573 time to fit residues: 1558.9639 Evaluate side-chains 854 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 788 time to evaluate : 3.830 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 1 residues processed: 66 average time/residue: 0.7343 time to fit residues: 93.9551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 310 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 464 optimal weight: 1.9990 chunk 380 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 559 optimal weight: 1.9990 chunk 604 optimal weight: 0.4980 chunk 498 optimal weight: 6.9990 chunk 554 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 448 optimal weight: 9.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: