Starting phenix.real_space_refine on Sat Apr 13 18:04:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1s_9572/04_2024/5h1s_9572.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1s_9572/04_2024/5h1s_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_9572/04_2024/5h1s_9572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1s_9572/04_2024/5h1s_9572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1s_9572/04_2024/5h1s_9572.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5h1s_9572/04_2024/5h1s_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-dev-5288/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: 35.16, per 1000 atoms: 0.39 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: 41.53 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: 30.53 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: 134.08 Time building geometry restraints manager: 44.81 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: 54617 35.82 - 71.65: 7691 71.65 - 107.47: 962 107.47 - 143.29: 62 143.29 - 179.11: 74 Dihedral angle restraints: 63406 sinusoidal: 54070 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 63403 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: 1.670 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: 0.060 Extract box with map and model: 9.460 Check model and map are aligned: 1.030 Set scattering table: 0.650 Process input model: 307.150 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.210 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:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 324.110 ------------------------------------------------------------------------------- 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 : 25.452 179.115 57409 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 : 3.857 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: L 237 ILE cc_start: 0.7561 (mt) cc_final: 0.7324 (mt) REVERT: M 87 ILE cc_start: 0.8423 (tp) cc_final: 0.8212 (tt) REVERT: N 134 MET cc_start: 0.7237 (mmm) cc_final: 0.7031 (mmm) REVERT: N 143 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6819 (mt) REVERT: P 124 GLU cc_start: 0.6130 (mm-30) cc_final: 0.5791 (mm-30) REVERT: R 205 GLU cc_start: 0.6920 (pm20) cc_final: 0.6579 (pm20) REVERT: S 17 ILE cc_start: 0.9280 (mm) cc_final: 0.9046 (mt) REVERT: T 102 GLU cc_start: 0.5871 (mm-30) cc_final: 0.5641 (tt0) REVERT: T 113 LYS cc_start: 0.5166 (OUTLIER) cc_final: 0.4438 (mptt) REVERT: T 140 ARG cc_start: 0.8128 (tpp80) cc_final: 0.5810 (tpm170) REVERT: U 164 MET cc_start: 0.5756 (mmm) cc_final: 0.4988 (ptm) REVERT: V 120 ILE cc_start: 0.7530 (pt) cc_final: 0.7307 (mt) REVERT: W 164 THR cc_start: 0.7010 (p) cc_final: 0.6696 (p) REVERT: W 173 ARG cc_start: 0.5649 (OUTLIER) cc_final: 0.3727 (mmp-170) REVERT: X 81 ILE cc_start: 0.8643 (mm) cc_final: 0.8387 (mt) REVERT: X 111 LYS cc_start: 0.8069 (tttt) cc_final: 0.7649 (ttmt) REVERT: X 145 GLU cc_start: 0.4996 (OUTLIER) cc_final: 0.3506 (mp0) REVERT: X 162 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6889 (ptm160) REVERT: Y 128 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8708 (m) REVERT: c 41 ASN cc_start: 0.7123 (t0) cc_final: 0.6713 (t0) REVERT: d 116 SER cc_start: 0.8724 (p) cc_final: 0.8524 (p) REVERT: f 70 LYS cc_start: 0.9065 (ttpt) cc_final: 0.8738 (tttt) REVERT: f 71 GLN cc_start: 0.7353 (mt0) cc_final: 0.7061 (mt0) REVERT: F 121 ASN cc_start: 0.7441 (OUTLIER) cc_final: 0.6799 (m110) REVERT: F 143 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8161 (ttt-90) REVERT: F 169 GLN cc_start: 0.7239 (mt0) cc_final: 0.6942 (mt0) REVERT: F 178 ASP cc_start: 0.6727 (p0) cc_final: 0.6390 (p0) REVERT: G 152 MET cc_start: 0.7895 (tpp) cc_final: 0.6791 (tpt) REVERT: G 232 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8368 (tpt90) REVERT: G 255 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8325 (mp) REVERT: H 124 LYS cc_start: 0.6287 (tttt) cc_final: 0.5940 (mmtt) REVERT: h 71 ASP cc_start: 0.7724 (t0) cc_final: 0.7298 (t0) outliers start: 89 outliers final: 36 residues processed: 1198 average time/residue: 1.0022 time to fit residues: 1915.7369 Evaluate side-chains 888 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 842 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 107 HIS Chi-restraints excluded: chain L residue 217 LEU Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 163 ARG Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain T residue 93 PHE Chi-restraints excluded: chain T residue 103 TYR Chi-restraints excluded: chain T residue 113 LYS Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 176 ILE Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain W residue 170 THR Chi-restraints excluded: chain W residue 173 ARG Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 126 GLU Chi-restraints excluded: chain X residue 128 TYR Chi-restraints excluded: chain X residue 133 LYS Chi-restraints excluded: chain X residue 145 GLU Chi-restraints excluded: chain X residue 162 ARG Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 128 THR Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 131 LYS Chi-restraints excluded: chain Z residue 120 ARG Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 258 ARG Chi-restraints excluded: chain c residue 13 LEU Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 232 ARG Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 255 LEU Chi-restraints excluded: chain H residue 186 ARG Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain J residue 77 PHE 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: 5.9990 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: 10.0000 chunk 358 optimal weight: 0.7980 chunk 558 optimal weight: 0.9980 overall best weight: 1.3596 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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** b 18 ASN ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 95 HIS e 145 ASN ** f 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN F 229 HIS G 71 ASN G 94 ASN G 153 ASN G 181 ASN G 222 ASN ** H 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN H 188 GLN I 168 ASN I 183 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 99032 Z= 0.231 Angle : 0.818 14.977 148663 Z= 0.417 Chirality : 0.042 0.422 18994 Planarity : 0.007 0.141 7537 Dihedral : 25.993 179.077 50727 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.93 % Favored : 87.51 % Rotamer: Outliers : 5.55 % Allowed : 14.92 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.16 % 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: -3.98 (0.13), residues: 3218 helix: -1.34 (0.17), residues: 849 sheet: -3.32 (0.19), residues: 473 loop : -3.23 (0.12), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP G 197 HIS 0.015 0.002 HIS Q 149 PHE 0.034 0.003 PHE T 124 TYR 0.029 0.003 TYR N 157 ARG 0.024 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 1109 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 955 time to evaluate : 3.858 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: L 207 MET cc_start: 0.8541 (mmt) cc_final: 0.8187 (mmt) REVERT: L 237 ILE cc_start: 0.7445 (mt) cc_final: 0.7221 (mt) REVERT: M 24 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6811 (pt) REVERT: N 97 ARG cc_start: 0.8748 (mtp180) cc_final: 0.8537 (mtm-85) REVERT: N 225 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6874 (mm) REVERT: R 206 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7679 (pp) REVERT: R 220 TYR cc_start: 0.8647 (m-10) cc_final: 0.8373 (m-80) REVERT: S 17 ILE cc_start: 0.9145 (mm) cc_final: 0.8792 (mt) REVERT: S 25 ARG cc_start: 0.8365 (ttt180) cc_final: 0.7998 (ttt180) REVERT: T 113 LYS cc_start: 0.5759 (OUTLIER) cc_final: 0.5523 (mptt) REVERT: T 140 ARG cc_start: 0.7781 (tpp80) cc_final: 0.5681 (tpm170) REVERT: T 200 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.6253 (p90) REVERT: T 229 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6841 (p0) REVERT: U 97 ASN cc_start: 0.6759 (p0) cc_final: 0.6552 (p0) REVERT: U 164 MET cc_start: 0.5414 (mmm) cc_final: 0.4962 (ptm) REVERT: W 64 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7935 (mp) REVERT: W 168 VAL cc_start: 0.7479 (t) cc_final: 0.7162 (t) REVERT: W 173 ARG cc_start: 0.6034 (OUTLIER) cc_final: 0.4156 (mmp-170) REVERT: X 73 LYS cc_start: 0.6972 (pmtt) cc_final: 0.6333 (pmtt) REVERT: X 81 ILE cc_start: 0.8448 (mm) cc_final: 0.8210 (mm) REVERT: X 150 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7639 (t80) REVERT: Y 90 HIS cc_start: 0.7101 (t70) cc_final: 0.6749 (t-170) REVERT: Y 103 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9087 (pt) REVERT: Z 68 LEU cc_start: 0.8404 (mp) cc_final: 0.8202 (mt) REVERT: d 115 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7199 (mmm) REVERT: f 61 ILE cc_start: 0.8809 (pt) cc_final: 0.8547 (pt) REVERT: f 70 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8699 (ttpt) REVERT: f 71 GLN cc_start: 0.7128 (mt0) cc_final: 0.6800 (mt0) REVERT: F 121 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7151 (m110) REVERT: F 170 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6711 (pm20) REVERT: G 232 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8036 (tpt90) REVERT: G 235 ASN cc_start: 0.7938 (p0) cc_final: 0.7272 (p0) REVERT: G 256 ASN cc_start: 0.8185 (m-40) cc_final: 0.7877 (m-40) REVERT: H 64 LYS cc_start: 0.5360 (ptmm) cc_final: 0.5113 (pttp) REVERT: H 136 MET cc_start: 0.5801 (tmm) cc_final: 0.5307 (tmm) REVERT: h 71 ASP cc_start: 0.7535 (t0) cc_final: 0.7303 (t0) REVERT: h 82 LEU cc_start: 0.8350 (tp) cc_final: 0.8116 (tp) outliers start: 154 outliers final: 77 residues processed: 1017 average time/residue: 0.9483 time to fit residues: 1580.4513 Evaluate side-chains 912 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 821 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 18 GLU Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 163 ARG Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 232 VAL Chi-restraints excluded: chain O residue 92 TYR Chi-restraints excluded: chain O residue 131 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 115 ILE Chi-restraints excluded: chain T residue 113 LYS Chi-restraints excluded: chain T residue 117 PRO Chi-restraints excluded: chain T residue 144 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 164 VAL Chi-restraints excluded: chain T residue 172 ILE Chi-restraints excluded: chain T residue 200 TYR Chi-restraints excluded: chain T residue 206 TYR Chi-restraints excluded: chain T residue 229 ASP Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain V residue 128 ILE Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain V residue 185 SER Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 147 VAL Chi-restraints excluded: chain W residue 170 THR Chi-restraints excluded: chain W residue 173 ARG Chi-restraints excluded: chain X residue 67 LYS Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 128 TYR Chi-restraints excluded: chain X residue 150 TYR Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 131 LYS Chi-restraints excluded: chain Z residue 142 ARG Chi-restraints excluded: chain Z residue 151 SER Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain c residue 13 LEU Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain d residue 115 MET Chi-restraints excluded: chain e residue 130 ASN Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 145 ARG Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 232 ARG Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 168 ASN Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain h residue 70 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 310 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 464 optimal weight: 5.9990 chunk 380 optimal weight: 0.9990 chunk 154 optimal weight: 10.0000 chunk 559 optimal weight: 0.9990 chunk 604 optimal weight: 2.9990 chunk 498 optimal weight: 0.4980 chunk 554 optimal weight: 5.9990 chunk 190 optimal weight: 10.0000 chunk 448 optimal weight: 6.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 219 ASN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 ASN R 178 HIS S 47 HIS ** S 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 153 ASN T 189 GLN ** T 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 132 ASN V 183 ASN Y 104 GLN E 26 ASN E 84 ASN ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 18 ASN c 36 GLN c 38 ASN ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN ** H 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 GLN I 183 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 99032 Z= 0.199 Angle : 0.714 12.881 148663 Z= 0.367 Chirality : 0.039 0.372 18994 Planarity : 0.006 0.141 7537 Dihedral : 25.642 179.576 50664 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.40 % Allowed : 11.50 % Favored : 88.10 % Rotamer: Outliers : 6.41 % Allowed : 18.20 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.58 % Twisted General : 0.16 % 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: -3.41 (0.13), residues: 3218 helix: -0.88 (0.17), residues: 861 sheet: -2.79 (0.20), residues: 498 loop : -2.91 (0.13), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP G 197 HIS 0.018 0.002 HIS S 83 PHE 0.025 0.002 PHE G 178 TYR 0.022 0.002 TYR b 11 ARG 0.012 0.001 ARG E 268 *********************** REFINEMENT MACRO_CYCLE 3 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 1036 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 858 time to evaluate : 3.862 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: L 207 MET cc_start: 0.8588 (mmt) cc_final: 0.8104 (mmt) REVERT: L 225 LYS cc_start: 0.7964 (ptmm) cc_final: 0.7577 (tttt) REVERT: N 97 ARG cc_start: 0.8700 (mtp180) cc_final: 0.8253 (mtp180) REVERT: N 225 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6715 (mm) REVERT: O 17 MET cc_start: 0.7828 (mmt) cc_final: 0.7614 (mmm) REVERT: O 91 GLU cc_start: 0.5300 (OUTLIER) cc_final: 0.4916 (mm-30) REVERT: P 13 HIS cc_start: 0.7445 (m90) cc_final: 0.7195 (m90) REVERT: P 40 LYS cc_start: 0.7569 (ttmm) cc_final: 0.7310 (tttp) REVERT: R 220 TYR cc_start: 0.8605 (m-10) cc_final: 0.8367 (m-10) REVERT: S 17 ILE cc_start: 0.9049 (mm) cc_final: 0.8750 (mt) REVERT: S 44 VAL cc_start: 0.9132 (t) cc_final: 0.8830 (m) REVERT: S 80 LYS cc_start: 0.8361 (mttt) cc_final: 0.8116 (mttt) REVERT: S 114 GLU cc_start: 0.6684 (tt0) cc_final: 0.6439 (tt0) REVERT: T 140 ARG cc_start: 0.7810 (tpp80) cc_final: 0.5846 (tpm170) REVERT: T 200 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.6426 (p90) REVERT: U 97 ASN cc_start: 0.6908 (p0) cc_final: 0.6670 (p0) REVERT: U 138 ASP cc_start: 0.5950 (t0) cc_final: 0.5750 (t0) REVERT: U 164 MET cc_start: 0.5536 (mmm) cc_final: 0.5095 (ptm) REVERT: W 64 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7911 (mp) REVERT: W 173 ARG cc_start: 0.5882 (mtp-110) cc_final: 0.4081 (mmp-170) REVERT: X 73 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6876 (pmtt) REVERT: X 81 ILE cc_start: 0.8500 (mm) cc_final: 0.8256 (mm) REVERT: Y 90 HIS cc_start: 0.7209 (t70) cc_final: 0.6830 (t-170) REVERT: Y 131 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7194 (tmtm) REVERT: Z 68 LEU cc_start: 0.8387 (mp) cc_final: 0.8174 (mt) REVERT: E 212 LYS cc_start: 0.8639 (mttt) cc_final: 0.8405 (mttp) REVERT: b 34 LEU cc_start: 0.8793 (tt) cc_final: 0.8478 (tp) REVERT: f 70 LYS cc_start: 0.8913 (ttpt) cc_final: 0.8672 (ttpt) REVERT: f 72 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8115 (ttp80) REVERT: F 121 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7146 (m110) REVERT: F 170 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7235 (pt0) REVERT: F 185 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7687 (tt) REVERT: G 232 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7350 (tpt90) REVERT: G 235 ASN cc_start: 0.7722 (p0) cc_final: 0.7427 (p0) REVERT: h 50 ARG cc_start: 0.8614 (mmt90) cc_final: 0.7633 (mtt-85) REVERT: h 71 ASP cc_start: 0.7591 (t0) cc_final: 0.7294 (t0) REVERT: h 82 LEU cc_start: 0.8360 (tp) cc_final: 0.8118 (tp) outliers start: 178 outliers final: 104 residues processed: 942 average time/residue: 0.9214 time to fit residues: 1440.9337 Evaluate side-chains 901 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 787 time to evaluate : 3.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 159 ASP Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 163 ARG Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 232 VAL Chi-restraints excluded: chain O residue 91 GLU Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 131 PHE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 69 SER Chi-restraints excluded: chain P residue 85 ILE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 5 LYS Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain T residue 117 PRO Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 144 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 156 ILE Chi-restraints excluded: chain T residue 162 LEU Chi-restraints excluded: chain T residue 164 VAL Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 200 TYR Chi-restraints excluded: chain T residue 206 TYR Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 170 THR Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 73 LYS Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 128 TYR Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain X residue 146 ASN Chi-restraints excluded: chain X residue 150 TYR Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 131 LYS Chi-restraints excluded: chain Z residue 151 SER Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain c residue 13 LEU Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain d residue 124 LEU Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 232 ARG Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 108 MET Chi-restraints excluded: chain a residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 552 optimal weight: 3.9990 chunk 420 optimal weight: 0.9980 chunk 290 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 267 optimal weight: 10.0000 chunk 375 optimal weight: 0.9990 chunk 561 optimal weight: 6.9990 chunk 594 optimal weight: 2.9990 chunk 293 optimal weight: 9.9990 chunk 532 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 219 ASN M 3 GLN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 57 ASN R 150 GLN R 211 HIS S 83 HIS ** T 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 153 ASN ** T 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 183 ASN Z 75 GLN E 124 ASN ** E 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 99032 Z= 0.303 Angle : 0.757 14.232 148663 Z= 0.386 Chirality : 0.042 0.326 18994 Planarity : 0.006 0.164 7537 Dihedral : 25.525 179.353 50647 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.49 % Favored : 87.10 % Rotamer: Outliers : 7.28 % Allowed : 20.07 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.16 % 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: -3.30 (0.13), residues: 3218 helix: -0.75 (0.17), residues: 869 sheet: -2.66 (0.21), residues: 481 loop : -2.90 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP h 70 HIS 0.050 0.002 HIS R 178 PHE 0.022 0.002 PHE I 108 TYR 0.026 0.002 TYR R 221 ARG 0.010 0.001 ARG E 25 *********************** REFINEMENT MACRO_CYCLE 4 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 996 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 794 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 207 MET cc_start: 0.8526 (mmt) cc_final: 0.7901 (mmt) REVERT: L 225 LYS cc_start: 0.8038 (ptmm) cc_final: 0.7603 (tttt) REVERT: L 243 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7331 (t70) REVERT: N 97 ARG cc_start: 0.8758 (mtp180) cc_final: 0.8286 (mtp180) REVERT: O 132 ILE cc_start: 0.8138 (mm) cc_final: 0.7932 (mt) REVERT: Q 117 VAL cc_start: 0.8558 (t) cc_final: 0.8294 (t) REVERT: R 173 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.6973 (mt0) REVERT: R 220 TYR cc_start: 0.8787 (m-10) cc_final: 0.8523 (m-10) REVERT: R 221 TYR cc_start: 0.8707 (p90) cc_final: 0.8454 (p90) REVERT: S 17 ILE cc_start: 0.9157 (mm) cc_final: 0.8813 (mt) REVERT: S 25 ARG cc_start: 0.8116 (ttt180) cc_final: 0.7745 (ttt180) REVERT: T 140 ARG cc_start: 0.7708 (tpp80) cc_final: 0.6266 (tpm170) REVERT: T 156 ILE cc_start: 0.8349 (mt) cc_final: 0.8127 (pt) REVERT: T 200 TYR cc_start: 0.7947 (OUTLIER) cc_final: 0.6828 (p90) REVERT: U 97 ASN cc_start: 0.7006 (p0) cc_final: 0.6756 (p0) REVERT: U 102 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7725 (mtmm) REVERT: U 164 MET cc_start: 0.5900 (mmm) cc_final: 0.5117 (ptm) REVERT: W 57 LYS cc_start: 0.8138 (mttm) cc_final: 0.7934 (mttm) REVERT: W 64 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7944 (mp) REVERT: W 137 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6772 (tt) REVERT: W 173 ARG cc_start: 0.6084 (mtp-110) cc_final: 0.4116 (mmp-170) REVERT: X 81 ILE cc_start: 0.8579 (mm) cc_final: 0.8303 (mt) REVERT: X 150 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7597 (t80) REVERT: Y 90 HIS cc_start: 0.7282 (t70) cc_final: 0.6911 (t-170) REVERT: E 212 LYS cc_start: 0.8483 (mttt) cc_final: 0.8256 (mttp) REVERT: E 232 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6367 (mp0) REVERT: b 34 LEU cc_start: 0.8784 (tt) cc_final: 0.8531 (tp) REVERT: f 70 LYS cc_start: 0.8896 (ttpt) cc_final: 0.8688 (ttpt) REVERT: f 72 ARG cc_start: 0.8610 (ttp80) cc_final: 0.8219 (ttp80) REVERT: F 121 ASN cc_start: 0.8096 (OUTLIER) cc_final: 0.7772 (m110) REVERT: F 170 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7258 (pt0) REVERT: F 185 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8024 (tt) REVERT: G 232 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7581 (tpt90) REVERT: G 235 ASN cc_start: 0.8131 (p0) cc_final: 0.7801 (p0) REVERT: G 256 ASN cc_start: 0.8047 (m-40) cc_final: 0.7637 (m-40) REVERT: h 82 LEU cc_start: 0.8276 (tp) cc_final: 0.8050 (tp) outliers start: 202 outliers final: 138 residues processed: 891 average time/residue: 0.9695 time to fit residues: 1442.8063 Evaluate side-chains 909 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 760 time to evaluate : 3.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 163 ARG Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain N residue 225 LEU Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 232 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 131 PHE Chi-restraints excluded: chain P residue 44 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 90 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 131 CYS Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 173 GLN Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 93 PHE Chi-restraints excluded: chain T residue 124 PHE Chi-restraints excluded: chain T residue 144 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 162 LEU Chi-restraints excluded: chain T residue 164 VAL Chi-restraints excluded: chain T residue 166 THR Chi-restraints excluded: chain T residue 172 ILE Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 200 TYR Chi-restraints excluded: chain T residue 206 TYR Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 89 HIS Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 108 ILE Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain V residue 185 SER Chi-restraints excluded: chain W residue 51 TRP Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 137 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 170 THR Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 128 TYR Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain X residue 146 ASN Chi-restraints excluded: chain X residue 150 TYR Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 131 LYS Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain Z residue 142 ARG Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain c residue 13 LEU Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain e residue 150 LEU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 229 HIS Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 148 TRP Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 232 ARG Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 172 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 108 MET Chi-restraints excluded: chain a residue 59 MET Chi-restraints excluded: chain h residue 66 LYS Chi-restraints excluded: chain h residue 90 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 495 optimal weight: 0.3980 chunk 337 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 442 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 chunk 507 optimal weight: 7.9990 chunk 410 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 303 optimal weight: 0.2980 chunk 533 optimal weight: 0.1980 chunk 150 optimal weight: 30.0000 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 219 ASN ** N 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 101 ASN R 150 GLN R 211 HIS ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN E 228 HIS ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 99032 Z= 0.175 Angle : 0.670 11.840 148663 Z= 0.342 Chirality : 0.037 0.295 18994 Planarity : 0.005 0.109 7537 Dihedral : 25.411 179.468 50645 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.81 % Favored : 88.88 % Rotamer: Outliers : 6.09 % Allowed : 21.98 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.16 % 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: -3.02 (0.14), residues: 3218 helix: -0.45 (0.17), residues: 855 sheet: -2.39 (0.21), residues: 500 loop : -2.78 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 20 HIS 0.010 0.001 HIS R 178 PHE 0.021 0.002 PHE G 208 TYR 0.020 0.002 TYR c 54 ARG 0.010 0.001 ARG H 145 *********************** REFINEMENT MACRO_CYCLE 5 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 962 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 793 time to evaluate : 3.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 207 MET cc_start: 0.8618 (mmt) cc_final: 0.8043 (mmt) REVERT: L 225 LYS cc_start: 0.7970 (ptmm) cc_final: 0.7588 (tttt) REVERT: L 243 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7185 (t70) REVERT: N 97 ARG cc_start: 0.8769 (mtp180) cc_final: 0.8259 (mtp180) REVERT: N 100 ARG cc_start: 0.8894 (mmp80) cc_final: 0.8611 (tpp-160) REVERT: N 163 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6883 (mmp-170) REVERT: O 54 MET cc_start: 0.6752 (mtm) cc_final: 0.6550 (mtm) REVERT: Q 117 VAL cc_start: 0.8492 (t) cc_final: 0.8238 (t) REVERT: R 150 GLN cc_start: 0.7719 (tt0) cc_final: 0.7487 (tt0) REVERT: R 221 TYR cc_start: 0.8648 (p90) cc_final: 0.8431 (p90) REVERT: S 17 ILE cc_start: 0.9093 (mm) cc_final: 0.8766 (mt) REVERT: S 96 ILE cc_start: 0.6296 (mm) cc_final: 0.5856 (tt) REVERT: T 140 ARG cc_start: 0.7688 (tpp80) cc_final: 0.7211 (mmm160) REVERT: T 200 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.6719 (p90) REVERT: U 97 ASN cc_start: 0.6885 (p0) cc_final: 0.6588 (p0) REVERT: U 102 LYS cc_start: 0.7941 (mtmm) cc_final: 0.7690 (mtmm) REVERT: U 164 MET cc_start: 0.5768 (mmm) cc_final: 0.5056 (ptm) REVERT: W 64 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7888 (mp) REVERT: X 81 ILE cc_start: 0.8560 (mm) cc_final: 0.8346 (mm) REVERT: Y 90 HIS cc_start: 0.7195 (t70) cc_final: 0.6800 (t-170) REVERT: b 34 LEU cc_start: 0.8782 (tt) cc_final: 0.8553 (tp) REVERT: c 28 ARG cc_start: 0.6241 (ptt90) cc_final: 0.5798 (mtm110) REVERT: f 72 ARG cc_start: 0.8494 (ttp80) cc_final: 0.8251 (ttp-110) REVERT: F 121 ASN cc_start: 0.7982 (m-40) cc_final: 0.7772 (m110) REVERT: F 170 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: F 178 ASP cc_start: 0.6584 (p0) cc_final: 0.6382 (p0) REVERT: F 185 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7793 (tt) REVERT: G 232 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8085 (tpt90) REVERT: G 256 ASN cc_start: 0.7986 (m-40) cc_final: 0.7559 (m-40) REVERT: h 82 LEU cc_start: 0.8262 (tp) cc_final: 0.8001 (tp) outliers start: 169 outliers final: 112 residues processed: 879 average time/residue: 0.9128 time to fit residues: 1336.8284 Evaluate side-chains 843 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 724 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 163 ARG Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain O residue 83 MET Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 131 PHE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 90 PHE Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 5 LYS Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 PHE Chi-restraints excluded: chain T residue 124 PHE Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 162 LEU Chi-restraints excluded: chain T residue 164 VAL Chi-restraints excluded: chain T residue 172 ILE Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 200 TYR Chi-restraints excluded: chain T residue 206 TYR Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 185 SER Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 170 THR Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain X residue 150 TYR Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 126 LEU Chi-restraints excluded: chain Y residue 131 LYS Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain Z residue 136 LEU Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 13 LEU Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain d residue 136 CYS Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 229 HIS Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 148 TRP Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 232 ARG Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 114 ASN Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain h residue 66 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 200 optimal weight: 6.9990 chunk 535 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 349 optimal weight: 0.0170 chunk 146 optimal weight: 10.0000 chunk 595 optimal weight: 8.9990 chunk 493 optimal weight: 4.9990 chunk 275 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 312 optimal weight: 6.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 189 GLN ** T 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 163 ASN W 59 ASN W 133 ASN E 26 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 88 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 99032 Z= 0.411 Angle : 0.823 14.167 148663 Z= 0.416 Chirality : 0.045 0.337 18994 Planarity : 0.007 0.096 7537 Dihedral : 25.425 179.173 50641 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.90 % Favored : 86.73 % Rotamer: Outliers : 8.43 % Allowed : 20.97 % Favored : 70.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.16 % 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: -3.21 (0.13), residues: 3218 helix: -0.70 (0.17), residues: 871 sheet: -2.42 (0.21), residues: 506 loop : -2.89 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP O 65 HIS 0.012 0.002 HIS P 13 PHE 0.039 0.003 PHE I 108 TYR 0.026 0.002 TYR X 82 ARG 0.018 0.001 ARG O 56 *********************** REFINEMENT MACRO_CYCLE 6 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 992 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 758 time to evaluate : 3.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 207 MET cc_start: 0.8568 (mmt) cc_final: 0.7765 (mmt) REVERT: L 243 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7413 (t70) REVERT: N 163 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6935 (mmp-170) REVERT: N 239 LYS cc_start: 0.5198 (pttt) cc_final: 0.4939 (pttm) REVERT: R 220 TYR cc_start: 0.8815 (m-10) cc_final: 0.8560 (m-10) REVERT: R 221 TYR cc_start: 0.8811 (p90) cc_final: 0.8512 (p90) REVERT: S 17 ILE cc_start: 0.9196 (mm) cc_final: 0.8832 (mt) REVERT: T 140 ARG cc_start: 0.7831 (tpp80) cc_final: 0.7150 (tpt90) REVERT: T 200 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7103 (p90) REVERT: U 50 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9063 (tp) REVERT: U 164 MET cc_start: 0.6240 (mmm) cc_final: 0.5282 (ptm) REVERT: W 64 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7831 (mp) REVERT: W 74 THR cc_start: 0.7106 (p) cc_final: 0.6843 (p) REVERT: X 81 ILE cc_start: 0.8643 (mm) cc_final: 0.8232 (mt) REVERT: X 123 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8691 (t) REVERT: X 150 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7553 (t80) REVERT: Y 90 HIS cc_start: 0.7139 (t70) cc_final: 0.6804 (t-170) REVERT: E 232 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6148 (mp0) REVERT: f 72 ARG cc_start: 0.8730 (ttp80) cc_final: 0.8419 (ttp80) REVERT: F 121 ASN cc_start: 0.8148 (m-40) cc_final: 0.7933 (m110) REVERT: F 170 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7350 (pt0) REVERT: G 256 ASN cc_start: 0.8170 (m-40) cc_final: 0.7937 (m-40) REVERT: h 74 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7799 (ptp-170) REVERT: h 82 LEU cc_start: 0.8601 (tp) cc_final: 0.8393 (tp) outliers start: 234 outliers final: 174 residues processed: 882 average time/residue: 0.8850 time to fit residues: 1307.3713 Evaluate side-chains 912 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 728 time to evaluate : 3.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 159 ASP Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 208 LEU Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 163 ARG Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 212 ILE Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain N residue 231 SER Chi-restraints excluded: chain N residue 232 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 131 PHE Chi-restraints excluded: chain P residue 35 THR Chi-restraints excluded: chain P residue 44 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 69 SER Chi-restraints excluded: chain P residue 89 LEU Chi-restraints excluded: chain P residue 90 PHE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 75 VAL Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 131 CYS Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 177 ILE Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 43 LEU Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 PHE Chi-restraints excluded: chain T residue 124 PHE Chi-restraints excluded: chain T residue 144 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 162 LEU Chi-restraints excluded: chain T residue 164 VAL Chi-restraints excluded: chain T residue 172 ILE Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 200 TYR Chi-restraints excluded: chain T residue 206 TYR Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 101 SER Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain V residue 185 SER Chi-restraints excluded: chain W residue 59 ASN Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 170 THR Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain X residue 146 ASN Chi-restraints excluded: chain X residue 150 TYR Chi-restraints excluded: chain Y residue 78 THR Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 131 LYS Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 11 TYR Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 13 LEU Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 38 ASN Chi-restraints excluded: chain c residue 44 SER Chi-restraints excluded: chain d residue 136 CYS Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 126 THR Chi-restraints excluded: chain e residue 135 LEU Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain e residue 150 LEU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 229 HIS Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 148 TRP Chi-restraints excluded: chain G residue 178 PHE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 232 ARG Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 54 VAL Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 114 ASN Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain I residue 195 GLU Chi-restraints excluded: chain I residue 204 TYR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain g residue 88 GLN Chi-restraints excluded: chain g residue 96 LEU Chi-restraints excluded: chain h residue 62 THR Chi-restraints excluded: chain h residue 66 LYS Chi-restraints excluded: chain h residue 74 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 573 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 339 optimal weight: 2.9990 chunk 434 optimal weight: 0.7980 chunk 336 optimal weight: 0.8980 chunk 500 optimal weight: 0.5980 chunk 332 optimal weight: 0.8980 chunk 592 optimal weight: 9.9990 chunk 370 optimal weight: 5.9990 chunk 361 optimal weight: 2.9990 chunk 273 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 170 GLN ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 153 ASN ** T 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN E 91 HIS E 124 ASN ** f 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 99032 Z= 0.185 Angle : 0.683 14.282 148663 Z= 0.349 Chirality : 0.038 0.351 18994 Planarity : 0.005 0.088 7537 Dihedral : 25.352 179.642 50641 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.91 % Favored : 88.78 % Rotamer: Outliers : 5.91 % Allowed : 24.72 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.16 % 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: -2.96 (0.14), residues: 3218 helix: -0.47 (0.17), residues: 859 sheet: -2.25 (0.21), residues: 508 loop : -2.73 (0.13), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP W 51 HIS 0.011 0.001 HIS O 13 PHE 0.018 0.002 PHE I 108 TYR 0.020 0.002 TYR X 82 ARG 0.017 0.001 ARG O 82 *********************** REFINEMENT MACRO_CYCLE 7 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 924 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 760 time to evaluate : 3.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 225 LYS cc_start: 0.8052 (ptmm) cc_final: 0.7691 (tttt) REVERT: L 243 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7313 (t70) REVERT: N 163 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6856 (mmp-170) REVERT: R 143 ILE cc_start: 0.8895 (mm) cc_final: 0.8670 (mt) REVERT: R 220 TYR cc_start: 0.8628 (m-10) cc_final: 0.8370 (m-10) REVERT: R 221 TYR cc_start: 0.8734 (p90) cc_final: 0.8416 (p90) REVERT: S 17 ILE cc_start: 0.9149 (mm) cc_final: 0.8812 (mt) REVERT: S 96 ILE cc_start: 0.6399 (mm) cc_final: 0.5995 (tt) REVERT: T 140 ARG cc_start: 0.7583 (tpp80) cc_final: 0.7204 (mmm160) REVERT: T 200 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.6686 (p90) REVERT: U 70 TYR cc_start: 0.8668 (m-80) cc_final: 0.8355 (m-80) REVERT: U 164 MET cc_start: 0.6075 (mmm) cc_final: 0.5253 (ptm) REVERT: W 64 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7813 (mp) REVERT: W 74 THR cc_start: 0.6829 (p) cc_final: 0.6610 (p) REVERT: Y 90 HIS cc_start: 0.7213 (t70) cc_final: 0.6854 (t-170) REVERT: Z 86 GLU cc_start: 0.5710 (mt-10) cc_final: 0.5350 (mt-10) REVERT: E 84 ASN cc_start: 0.8620 (t0) cc_final: 0.8402 (t0) REVERT: E 128 LEU cc_start: 0.8131 (tp) cc_final: 0.7903 (tp) REVERT: E 232 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6015 (mp0) REVERT: c 28 ARG cc_start: 0.6422 (ptt90) cc_final: 0.5820 (mtm110) REVERT: f 72 ARG cc_start: 0.8717 (ttp80) cc_final: 0.8498 (ttp-110) REVERT: G 256 ASN cc_start: 0.8067 (m-40) cc_final: 0.7596 (m-40) REVERT: h 82 LEU cc_start: 0.8454 (tp) cc_final: 0.8223 (tp) outliers start: 164 outliers final: 131 residues processed: 844 average time/residue: 0.9144 time to fit residues: 1289.3431 Evaluate side-chains 850 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 714 time to evaluate : 3.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 170 GLN Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 163 ARG Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain N residue 212 ILE Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain O residue 83 MET Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 131 PHE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 44 ILE Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 90 PHE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 131 CYS Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 115 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 124 PHE Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 162 LEU Chi-restraints excluded: chain T residue 164 VAL Chi-restraints excluded: chain T residue 166 THR Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 200 TYR Chi-restraints excluded: chain T residue 206 TYR Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 SER Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 170 THR Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain X residue 150 TYR Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 131 LYS Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Z residue 92 LEU Chi-restraints excluded: chain Z residue 128 VAL Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 13 LEU Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 44 SER Chi-restraints excluded: chain d residue 136 CYS Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 138 VAL Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain e residue 150 LEU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 229 HIS Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 148 TRP Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 232 ARG Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain h residue 66 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 366 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 354 optimal weight: 0.1980 chunk 178 optimal weight: 7.9990 chunk 116 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 403 optimal weight: 0.9980 chunk 293 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 465 optimal weight: 1.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN E 26 ASN E 193 ASN ** f 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 99032 Z= 0.274 Angle : 0.719 15.044 148663 Z= 0.365 Chirality : 0.040 0.388 18994 Planarity : 0.006 0.084 7537 Dihedral : 25.306 179.323 50641 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.37 % Allowed : 12.09 % Favored : 87.54 % Rotamer: Outliers : 7.17 % Allowed : 24.11 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.94 % Twisted General : 0.16 % 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: -2.94 (0.14), residues: 3218 helix: -0.47 (0.17), residues: 859 sheet: -2.20 (0.22), residues: 494 loop : -2.72 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 110 HIS 0.012 0.002 HIS O 13 PHE 0.025 0.002 PHE I 108 TYR 0.025 0.002 TYR X 82 ARG 0.017 0.001 ARG M 23 *********************** REFINEMENT MACRO_CYCLE 8 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 937 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 738 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 207 MET cc_start: 0.8612 (mmt) cc_final: 0.7783 (mmt) REVERT: L 225 LYS cc_start: 0.8159 (ptmm) cc_final: 0.7697 (tttt) REVERT: L 243 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7335 (t70) REVERT: N 163 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6884 (mmp-170) REVERT: P 54 MET cc_start: 0.5956 (tpp) cc_final: 0.5641 (tpp) REVERT: Q 87 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8188 (pt) REVERT: S 17 ILE cc_start: 0.9180 (mm) cc_final: 0.8840 (mt) REVERT: S 52 ARG cc_start: 0.7801 (mtp-110) cc_final: 0.7593 (mmm160) REVERT: S 96 ILE cc_start: 0.6255 (mm) cc_final: 0.5880 (tt) REVERT: T 129 ILE cc_start: 0.8300 (mm) cc_final: 0.8033 (mt) REVERT: T 140 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7323 (mmm160) REVERT: T 200 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.6980 (p90) REVERT: U 50 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.8997 (tp) REVERT: U 70 TYR cc_start: 0.8657 (m-80) cc_final: 0.8353 (m-80) REVERT: U 101 SER cc_start: 0.8765 (t) cc_final: 0.8561 (t) REVERT: U 164 MET cc_start: 0.6048 (mmm) cc_final: 0.5208 (ptm) REVERT: W 64 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7832 (mp) REVERT: W 74 THR cc_start: 0.6902 (p) cc_final: 0.6689 (p) REVERT: X 150 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7594 (t80) REVERT: Y 90 HIS cc_start: 0.7218 (t70) cc_final: 0.6869 (t-170) REVERT: E 44 ILE cc_start: 0.8388 (mp) cc_final: 0.8084 (mp) REVERT: E 128 LEU cc_start: 0.7953 (tp) cc_final: 0.7749 (tp) REVERT: E 232 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6077 (mp0) REVERT: c 28 ARG cc_start: 0.6723 (ptt90) cc_final: 0.6036 (mtm110) REVERT: f 72 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8432 (ttp-110) REVERT: F 170 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7107 (pm20) REVERT: F 185 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.7971 (tt) REVERT: G 197 TRP cc_start: 0.7011 (OUTLIER) cc_final: 0.6695 (t60) REVERT: G 256 ASN cc_start: 0.8133 (m-40) cc_final: 0.7686 (m-40) REVERT: h 74 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7802 (ptp-170) REVERT: h 82 LEU cc_start: 0.8573 (tp) cc_final: 0.8354 (tp) outliers start: 199 outliers final: 154 residues processed: 839 average time/residue: 0.9209 time to fit residues: 1295.5549 Evaluate side-chains 895 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 729 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 122 LEU Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 243 ASP Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 163 ARG Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain N residue 212 ILE Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 131 PHE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 44 ILE Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 90 PHE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 87 ILE Chi-restraints excluded: chain Q residue 99 SER Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 131 CYS Chi-restraints excluded: chain R residue 126 LEU Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 216 LYS Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 124 PHE Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 162 LEU Chi-restraints excluded: chain T residue 164 VAL Chi-restraints excluded: chain T residue 166 THR Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 200 TYR Chi-restraints excluded: chain T residue 206 TYR Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 233 SER Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 52 GLN Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain V residue 185 SER Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 170 THR Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 136 SER Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain X residue 146 ASN Chi-restraints excluded: chain X residue 150 TYR Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 131 LYS Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 183 ASN Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 13 LEU Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain c residue 35 THR Chi-restraints excluded: chain c residue 44 SER Chi-restraints excluded: chain d residue 136 CYS Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 138 VAL Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain e residue 150 LEU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 229 HIS Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 148 TRP Chi-restraints excluded: chain G residue 197 TRP Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 232 ARG Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 257 GLN Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 113 ILE Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain h residue 66 LYS Chi-restraints excluded: chain h residue 74 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 539 optimal weight: 0.9990 chunk 567 optimal weight: 6.9990 chunk 518 optimal weight: 5.9990 chunk 552 optimal weight: 0.0980 chunk 332 optimal weight: 0.0770 chunk 240 optimal weight: 6.9990 chunk 433 optimal weight: 4.9990 chunk 169 optimal weight: 6.9990 chunk 499 optimal weight: 6.9990 chunk 522 optimal weight: 7.9990 chunk 550 optimal weight: 0.9980 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 150 GLN ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN F 138 GLN ** H 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 99032 Z= 0.186 Angle : 0.664 11.950 148663 Z= 0.337 Chirality : 0.037 0.403 18994 Planarity : 0.005 0.082 7537 Dihedral : 25.247 179.019 50641 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.88 % Favored : 88.84 % Rotamer: Outliers : 6.20 % Allowed : 25.15 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.29 % Twisted General : 0.16 % 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: -2.74 (0.14), residues: 3218 helix: -0.29 (0.18), residues: 845 sheet: -2.08 (0.22), residues: 496 loop : -2.59 (0.13), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Y 110 HIS 0.010 0.001 HIS O 13 PHE 0.019 0.002 PHE I 108 TYR 0.021 0.002 TYR X 82 ARG 0.013 0.001 ARG O 56 *********************** REFINEMENT MACRO_CYCLE 9 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 934 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 762 time to evaluate : 3.795 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: L 207 MET cc_start: 0.8578 (mmt) cc_final: 0.7738 (mmt) REVERT: L 225 LYS cc_start: 0.8126 (ptmm) cc_final: 0.7693 (tttt) REVERT: N 163 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6979 (mmp-170) REVERT: S 17 ILE cc_start: 0.9161 (mm) cc_final: 0.8839 (mt) REVERT: T 140 ARG cc_start: 0.7693 (tpp80) cc_final: 0.7329 (mmm160) REVERT: T 200 TYR cc_start: 0.7660 (OUTLIER) cc_final: 0.6657 (p90) REVERT: T 229 ASP cc_start: 0.7556 (p0) cc_final: 0.7189 (p0) REVERT: U 50 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.8997 (tp) REVERT: U 70 TYR cc_start: 0.8658 (m-80) cc_final: 0.8364 (m-80) REVERT: U 164 MET cc_start: 0.5962 (mmm) cc_final: 0.5192 (ptm) REVERT: W 64 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7756 (mp) REVERT: X 150 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7545 (t80) REVERT: X 155 ARG cc_start: 0.7319 (ttp80) cc_final: 0.7099 (ttp80) REVERT: X 162 ARG cc_start: 0.6957 (ttp80) cc_final: 0.6755 (ttp80) REVERT: Y 90 HIS cc_start: 0.7151 (t70) cc_final: 0.6782 (t-170) REVERT: E 128 LEU cc_start: 0.7896 (tp) cc_final: 0.7674 (tp) REVERT: E 232 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6010 (mp0) REVERT: c 28 ARG cc_start: 0.6492 (ptt90) cc_final: 0.5835 (mtm110) REVERT: F 185 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7894 (tt) REVERT: G 232 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7897 (tpt90) REVERT: G 256 ASN cc_start: 0.8050 (m-40) cc_final: 0.7527 (m-40) REVERT: h 74 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7812 (ptp-170) outliers start: 172 outliers final: 139 residues processed: 854 average time/residue: 0.9071 time to fit residues: 1295.5398 Evaluate side-chains 874 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 726 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 146 ILE Chi-restraints excluded: chain N residue 163 ARG Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain N residue 212 ILE Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 131 PHE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 44 ILE Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 90 PHE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 131 CYS Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 115 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 PHE Chi-restraints excluded: chain T residue 124 PHE Chi-restraints excluded: chain T residue 144 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 162 LEU Chi-restraints excluded: chain T residue 164 VAL Chi-restraints excluded: chain T residue 166 THR Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 200 TYR Chi-restraints excluded: chain T residue 206 TYR Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain V residue 185 SER Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 170 THR Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain X residue 146 ASN Chi-restraints excluded: chain X residue 150 TYR Chi-restraints excluded: chain Y residue 86 ASN Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 131 LYS Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 225 ASP Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 13 LEU Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain d residue 136 CYS Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 138 VAL Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain e residue 150 LEU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 93 MET Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 229 HIS Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 148 TRP Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 232 ARG Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain h residue 66 LYS Chi-restraints excluded: chain h residue 74 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 362 optimal weight: 5.9990 chunk 584 optimal weight: 0.7980 chunk 356 optimal weight: 7.9990 chunk 277 optimal weight: 7.9990 chunk 406 optimal weight: 4.9990 chunk 612 optimal weight: 0.4980 chunk 563 optimal weight: 7.9990 chunk 487 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 104 GLN ** E 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN ** H 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 99032 Z= 0.271 Angle : 0.713 12.678 148663 Z= 0.361 Chirality : 0.040 0.361 18994 Planarity : 0.006 0.081 7537 Dihedral : 25.233 179.794 50641 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.03 % Favored : 87.63 % Rotamer: Outliers : 6.05 % Allowed : 25.30 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.16 % 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: -2.76 (0.14), residues: 3218 helix: -0.35 (0.18), residues: 854 sheet: -2.05 (0.22), residues: 493 loop : -2.61 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Y 110 HIS 0.013 0.002 HIS O 13 PHE 0.019 0.002 PHE J 73 TYR 0.021 0.002 TYR S 78 ARG 0.011 0.001 ARG G 146 ********************** REFINEMENT MACRO_CYCLE 10 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 887 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 719 time to evaluate : 3.866 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: L 207 MET cc_start: 0.8623 (mmt) cc_final: 0.7899 (mmt) REVERT: L 225 LYS cc_start: 0.8156 (ptmm) cc_final: 0.7626 (tttt) REVERT: N 163 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6995 (mmp-170) REVERT: S 17 ILE cc_start: 0.9144 (mm) cc_final: 0.8807 (mt) REVERT: S 52 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7533 (mmm160) REVERT: T 140 ARG cc_start: 0.7766 (tpp80) cc_final: 0.7334 (mmm160) REVERT: T 200 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.6818 (p90) REVERT: U 50 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9033 (tp) REVERT: U 70 TYR cc_start: 0.8671 (m-80) cc_final: 0.8352 (m-80) REVERT: U 164 MET cc_start: 0.6275 (mmm) cc_final: 0.5111 (ptm) REVERT: W 64 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7778 (mp) REVERT: W 173 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.4123 (mmp-170) REVERT: X 150 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7746 (t80) REVERT: Y 90 HIS cc_start: 0.7131 (t70) cc_final: 0.6761 (t-170) REVERT: E 232 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6064 (mp0) REVERT: c 28 ARG cc_start: 0.6823 (ptt90) cc_final: 0.5982 (mtm110) REVERT: F 185 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7969 (tt) REVERT: G 197 TRP cc_start: 0.7012 (OUTLIER) cc_final: 0.6695 (t60) REVERT: G 232 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7896 (tpt90) REVERT: G 256 ASN cc_start: 0.8129 (m-40) cc_final: 0.7652 (m-40) REVERT: h 74 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7791 (ptp-170) outliers start: 168 outliers final: 147 residues processed: 806 average time/residue: 0.9074 time to fit residues: 1227.1973 Evaluate side-chains 867 residues out of total 2775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 709 time to evaluate : 3.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 213 LEU Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain M residue 6 THR Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 21 CYS Chi-restraints excluded: chain M residue 24 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 163 ARG Chi-restraints excluded: chain N residue 196 LEU Chi-restraints excluded: chain N residue 212 ILE Chi-restraints excluded: chain N residue 217 PHE Chi-restraints excluded: chain O residue 20 ILE Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain O residue 131 PHE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 44 ILE Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 90 PHE Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 131 CYS Chi-restraints excluded: chain R residue 128 LYS Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 149 VAL Chi-restraints excluded: chain R residue 178 HIS Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain S residue 4 VAL Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 93 PHE Chi-restraints excluded: chain T residue 124 PHE Chi-restraints excluded: chain T residue 144 THR Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 162 LEU Chi-restraints excluded: chain T residue 164 VAL Chi-restraints excluded: chain T residue 166 THR Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 200 TYR Chi-restraints excluded: chain T residue 206 TYR Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 233 SER Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 50 ILE Chi-restraints excluded: chain U residue 52 GLN Chi-restraints excluded: chain U residue 53 ILE Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain U residue 82 SER Chi-restraints excluded: chain U residue 125 ILE Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain V residue 159 VAL Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 171 THR Chi-restraints excluded: chain V residue 185 SER Chi-restraints excluded: chain W residue 64 LEU Chi-restraints excluded: chain W residue 89 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 170 THR Chi-restraints excluded: chain W residue 173 ARG Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain X residue 146 ASN Chi-restraints excluded: chain X residue 150 TYR Chi-restraints excluded: chain Y residue 86 ASN Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 131 LYS Chi-restraints excluded: chain Y residue 137 VAL Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain Z residue 152 LEU Chi-restraints excluded: chain E residue 33 ARG Chi-restraints excluded: chain E residue 49 HIS Chi-restraints excluded: chain E residue 58 TYR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 94 ASP Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 232 GLU Chi-restraints excluded: chain E residue 255 SER Chi-restraints excluded: chain b residue 29 LEU Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain c residue 13 LEU Chi-restraints excluded: chain c residue 16 THR Chi-restraints excluded: chain c residue 34 ILE Chi-restraints excluded: chain d residue 136 CYS Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain e residue 98 SER Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 138 VAL Chi-restraints excluded: chain e residue 142 ASP Chi-restraints excluded: chain e residue 150 LEU Chi-restraints excluded: chain e residue 153 LEU Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain F residue 90 ILE Chi-restraints excluded: chain F residue 144 LEU Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 199 ILE Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 229 HIS Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 235 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 148 TRP Chi-restraints excluded: chain G residue 197 TRP Chi-restraints excluded: chain G residue 223 ILE Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 232 ARG Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain I residue 65 VAL Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 157 ILE Chi-restraints excluded: chain I residue 190 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain h residue 66 LYS Chi-restraints excluded: chain h residue 74 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 387 optimal weight: 1.9990 chunk 519 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 449 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 chunk 488 optimal weight: 7.9990 chunk 204 optimal weight: 6.9990 chunk 501 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 133 GLN ** T 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 46 GLN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117270 restraints weight = 153259.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.117501 restraints weight = 84837.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.119769 restraints weight = 66227.553| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 99032 Z= 0.305 Angle : 0.739 15.269 148663 Z= 0.373 Chirality : 0.041 0.413 18994 Planarity : 0.006 0.082 7537 Dihedral : 25.247 179.141 50641 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 12.12 % Favored : 87.54 % Rotamer: Outliers : 6.13 % Allowed : 25.23 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.16 % 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: -2.82 (0.14), residues: 3218 helix: -0.37 (0.18), residues: 853 sheet: -2.13 (0.22), residues: 493 loop : -2.65 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP W 51 HIS 0.014 0.002 HIS O 13 PHE 0.027 0.002 PHE S 81 TYR 0.021 0.002 TYR S 78 ARG 0.021 0.001 ARG P 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19845.51 seconds wall clock time: 349 minutes 40.80 seconds (20980.80 seconds total)