Starting phenix.real_space_refine (version: dev) on Fri Dec 16 13:41:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlc_3525/12_2022/5mlc_3525.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlc_3525/12_2022/5mlc_3525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlc_3525/12_2022/5mlc_3525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlc_3525/12_2022/5mlc_3525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlc_3525/12_2022/5mlc_3525.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlc_3525/12_2022/5mlc_3525.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.068 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ASP 94": "OD1" <-> "OD2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D ASP 263": "OD1" <-> "OD2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 87": "OD1" <-> "OD2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 172": "NH1" <-> "NH2" Residue "E ASP 177": "OD1" <-> "OD2" Residue "E ASP 178": "OD1" <-> "OD2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 219": "NH1" <-> "NH2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "F PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F ARG 81": "NH1" <-> "NH2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 113": "NH1" <-> "NH2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ARG 134": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "F PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 196": "NH1" <-> "NH2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 211": "OD1" <-> "OD2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F ARG 224": "NH1" <-> "NH2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G GLU 34": "OE1" <-> "OE2" Residue "G ARG 117": "NH1" <-> "NH2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G ARG 193": "NH1" <-> "NH2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 195": "OE1" <-> "OE2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "I ASP 68": "OD1" <-> "OD2" Residue "I ARG 70": "NH1" <-> "NH2" Residue "L TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 136": "NH1" <-> "NH2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 174": "NH1" <-> "NH2" Residue "L ARG 175": "NH1" <-> "NH2" Residue "L PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 205": "NH1" <-> "NH2" Residue "L ARG 212": "NH1" <-> "NH2" Residue "L ASP 238": "OD1" <-> "OD2" Residue "L GLU 249": "OE1" <-> "OE2" Residue "M ARG 23": "NH1" <-> "NH2" Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 34": "NH1" <-> "NH2" Residue "M GLU 53": "OE1" <-> "OE2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M GLU 68": "OE1" <-> "OE2" Residue "M TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M ARG 107": "NH1" <-> "NH2" Residue "M PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 163": "NH1" <-> "NH2" Residue "N GLU 166": "OE1" <-> "OE2" Residue "N PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 238": "NH1" <-> "NH2" Residue "N TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 244": "OE1" <-> "OE2" Residue "N ARG 252": "NH1" <-> "NH2" Residue "N ASP 254": "OD1" <-> "OD2" Residue "N TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 14": "NH1" <-> "NH2" Residue "O ARG 26": "NH1" <-> "NH2" Residue "O ARG 31": "NH1" <-> "NH2" Residue "O ARG 45": "NH1" <-> "NH2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O ARG 59": "NH1" <-> "NH2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O ARG 77": "NH1" <-> "NH2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "P ARG 15": "NH1" <-> "NH2" Residue "P ARG 19": "NH1" <-> "NH2" Residue "P ARG 22": "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 TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 73": "NH1" <-> "NH2" Residue "P ARG 74": "NH1" <-> "NH2" Residue "P PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 106": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 49": "NH1" <-> "NH2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q GLU 69": "OE1" <-> "OE2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q ARG 72": "NH1" <-> "NH2" Residue "Q ASP 142": "OD1" <-> "OD2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "Q ARG 151": "NH1" <-> "NH2" Residue "Q ARG 160": "NH1" <-> "NH2" Residue "Q PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 144": "NH1" <-> "NH2" Residue "R ASP 147": "OD1" <-> "OD2" Residue "R ARG 152": "NH1" <-> "NH2" Residue "R ARG 160": "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 PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 212": "NH1" <-> "NH2" Residue "R ARG 218": "NH1" <-> "NH2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 223": "NH1" <-> "NH2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S ARG 6": "NH1" <-> "NH2" Residue "S ARG 12": "NH1" <-> "NH2" Residue "S ARG 13": "NH1" <-> "NH2" Residue "S ARG 14": "NH1" <-> "NH2" Residue "S ARG 18": "NH1" <-> "NH2" Residue "S ARG 25": "NH1" <-> "NH2" Residue "S ARG 33": "NH1" <-> "NH2" Residue "S ARG 41": "NH1" <-> "NH2" Residue "S ARG 48": "NH1" <-> "NH2" Residue "S ASP 51": "OD1" <-> "OD2" Residue "S ARG 52": "NH1" <-> "NH2" Residue "S ARG 59": "NH1" <-> "NH2" Residue "S ARG 70": "NH1" <-> "NH2" Residue "S ARG 72": "NH1" <-> "NH2" Residue "S TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 132": "NH1" <-> "NH2" Residue "T TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 140": "NH1" <-> "NH2" Residue "T ARG 146": "NH1" <-> "NH2" Residue "T PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 207": "NH1" <-> "NH2" Residue "T ARG 208": "NH1" <-> "NH2" Residue "T ARG 218": "NH1" <-> "NH2" Residue "U ARG 35": "NH1" <-> "NH2" Residue "U TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 48": "NH1" <-> "NH2" Residue "U ARG 56": "NH1" <-> "NH2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 117": "NH1" <-> "NH2" Residue "U ARG 119": "NH1" <-> "NH2" Residue "U ARG 127": "NH1" <-> "NH2" Residue "U ARG 137": "NH1" <-> "NH2" Residue "U GLU 150": "OE1" <-> "OE2" Residue "V TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 106": "NH1" <-> "NH2" Residue "V ARG 107": "NH1" <-> "NH2" Residue "V TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 141": "NH1" <-> "NH2" Residue "V ARG 148": "NH1" <-> "NH2" Residue "V PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 47": "NH1" <-> "NH2" Residue "W ARG 146": "NH1" <-> "NH2" Residue "W ARG 156": "NH1" <-> "NH2" Residue "W ARG 159": "NH1" <-> "NH2" Residue "X PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 155": "NH1" <-> "NH2" Residue "X ARG 162": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ARG 146": "NH1" <-> "NH2" Residue "Z PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 111": "NH1" <-> "NH2" Residue "Z ARG 131": "NH1" <-> "NH2" Residue "Z ARG 147": "NH1" <-> "NH2" Residue "2 ARG 7": "NH1" <-> "NH2" Residue "2 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 20": "NH1" <-> "NH2" Residue "3 ARG 28": "NH1" <-> "NH2" Residue "3 ARG 32": "NH1" <-> "NH2" Residue "3 TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 45": "NH1" <-> "NH2" Residue "3 ARG 49": "NH1" <-> "NH2" Residue "4 ARG 103": "NH1" <-> "NH2" Residue "4 ARG 105": "NH1" <-> "NH2" Residue "4 ARG 110": "NH1" <-> "NH2" Residue "4 PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 115": "NH1" <-> "NH2" Residue "4 ARG 117": "NH1" <-> "NH2" Residue "4 ARG 129": "NH1" <-> "NH2" Residue "4 ARG 149": "NH1" <-> "NH2" Residue "5 ARG 103": "NH1" <-> "NH2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 ARG 114": "NH1" <-> "NH2" Residue "5 ARG 128": "NH1" <-> "NH2" Residue "5 ARG 131": "NH1" <-> "NH2" Residue "5 ARG 140": "NH1" <-> "NH2" Residue "5 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 157": "NH1" <-> "NH2" Residue "6 ARG 8": "NH1" <-> "NH2" Residue "6 ARG 15": "NH1" <-> "NH2" Residue "6 ARG 18": "NH1" <-> "NH2" Residue "6 ARG 20": "NH1" <-> "NH2" Residue "6 ARG 22": "NH1" <-> "NH2" Residue "9 ARG 98": "NH1" <-> "NH2" Residue "9 ARG 107": "NH1" <-> "NH2" Residue "9 ARG 114": "NH1" <-> "NH2" Residue "9 ARG 195": "NH1" <-> "NH2" Residue "9 ARG 196": "NH1" <-> "NH2" Residue "9 ARG 215": "NH1" <-> "NH2" Residue "9 ARG 219": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 90647 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 59074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2750, 59074 Classifications: {'RNA': 2750} Modifications used: {'rna2p_pur': 246, 'rna2p_pyr': 112, 'rna3p_pur': 1355, 'rna3p_pyr': 1037} Link IDs: {'rna2p': 358, 'rna3p': 2391} Chain breaks: 5 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2564 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 59, 'rna3p_pyr': 53} Link IDs: {'rna2p': 8, 'rna3p': 111} Chain: "C" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 2001 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 51, 'rna3p_pyr': 35} Link IDs: {'rna2p': 7, 'rna3p': 85} Chain breaks: 1 Chain: "D" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1895 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 13, 'TRANS': 232} Chain: "E" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1669 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "F" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1617 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "G" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1387 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain: "H" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1386 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "I" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "L" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1489 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "M" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "N" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1385 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "O" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1075 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "P" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Q" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "R" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 915 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "S" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1003 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain: "T" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1017 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 124} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "U" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1165 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 145} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "V" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 734 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "W" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1018 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "X" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 866 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "Y" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 616 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "Z" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 788 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "2" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 341 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 489 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "4" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 471 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "5" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 575 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "6" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 305 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "9" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 881 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'TRANS': 106} Chain breaks: 1 Chain: "7" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 378 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "8" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 374 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 8, 'TRANS': 38} Time building chain proxies: 43.20, per 1000 atoms: 0.48 Number of scatterers: 90647 At special positions: 0 Unit cell: (207.956, 213.261, 217.505, 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 99 16.00 P 2963 15.00 O 25186 8.00 N 16983 7.00 C 45416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 6 11 " - pdb=" SG CYS 6 14 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 11 " - pdb=" SG CYS 6 27 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.07 Conformation dependent library (CDL) restraints added in 3.5 seconds 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6278 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 37 sheets defined 31.8% alpha, 14.0% beta 854 base pairs and 1446 stacking pairs defined. Time for finding SS restraints: 29.41 Creating SS restraints... Processing helix chain 'D' and resid 203 through 209 removed outlier: 3.892A pdb=" N LYS D 207 " --> pdb=" O ARG D 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 161 removed outlier: 3.889A pdb=" N ALA E 160 " --> pdb=" O HIS E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 216 Processing helix chain 'F' and resid 81 through 96 Processing helix chain 'F' and resid 153 through 169 removed outlier: 3.604A pdb=" N ARG F 157 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 198 removed outlier: 3.559A pdb=" N PHE F 190 " --> pdb=" O LYS F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 222 removed outlier: 4.496A pdb=" N ASN F 222 " --> pdb=" O LYS F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 242 removed outlier: 3.586A pdb=" N VAL F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 259 Processing helix chain 'G' and resid 17 through 26 removed outlier: 3.684A pdb=" N ASN G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 36 Processing helix chain 'G' and resid 56 through 60 removed outlier: 3.721A pdb=" N SER G 59 " --> pdb=" O GLY G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 74 Processing helix chain 'G' and resid 108 through 121 removed outlier: 3.663A pdb=" N TYR G 112 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 177 through 189 removed outlier: 3.743A pdb=" N ALA G 181 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR G 182 " --> pdb=" O ASP G 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 104 Processing helix chain 'H' and resid 104 through 121 removed outlier: 3.938A pdb=" N THR H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP H 113 " --> pdb=" O ARG H 109 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 192 removed outlier: 4.034A pdb=" N PHE H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE H 188 " --> pdb=" O PHE H 184 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TRP H 191 " --> pdb=" O THR H 187 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG H 192 " --> pdb=" O ILE H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 217 removed outlier: 3.645A pdb=" N ALA H 216 " --> pdb=" O GLU H 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 77 removed outlier: 4.104A pdb=" N LEU I 74 " --> pdb=" O ARG I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 removed outlier: 3.863A pdb=" N LEU I 81 " --> pdb=" O PHE I 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 74 removed outlier: 3.657A pdb=" N VAL L 68 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA L 73 " --> pdb=" O LYS L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 137 removed outlier: 3.663A pdb=" N THR L 130 " --> pdb=" O ARG L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 161 Processing helix chain 'L' and resid 166 through 171 Processing helix chain 'L' and resid 188 through 195 removed outlier: 3.709A pdb=" N ARG L 194 " --> pdb=" O GLN L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 206 removed outlier: 4.003A pdb=" N ILE L 200 " --> pdb=" O PRO L 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 217 removed outlier: 3.645A pdb=" N TYR L 216 " --> pdb=" O ARG L 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 108 removed outlier: 3.650A pdb=" N LEU M 106 " --> pdb=" O ALA M 103 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN M 108 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 116 removed outlier: 3.830A pdb=" N VAL M 114 " --> pdb=" O PHE M 110 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU M 116 " --> pdb=" O LYS M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 139 Processing helix chain 'N' and resid 161 through 166 removed outlier: 3.546A pdb=" N GLU N 166 " --> pdb=" O LEU N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 184 removed outlier: 3.590A pdb=" N LYS N 182 " --> pdb=" O LEU N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 196 Processing helix chain 'N' and resid 218 through 229 removed outlier: 3.816A pdb=" N GLU N 223 " --> pdb=" O GLY N 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 259 Processing helix chain 'O' and resid 22 through 26 removed outlier: 3.676A pdb=" N ASN O 25 " --> pdb=" O TYR O 22 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG O 26 " --> pdb=" O ARG O 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 22 through 26' Processing helix chain 'O' and resid 44 through 57 removed outlier: 3.759A pdb=" N ASN O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 125 removed outlier: 3.505A pdb=" N ARG O 116 " --> pdb=" O ASN O 112 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 42 removed outlier: 3.765A pdb=" N ARG P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA P 29 " --> pdb=" O ASP P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 53 Processing helix chain 'P' and resid 54 through 65 Processing helix chain 'P' and resid 69 through 81 removed outlier: 3.505A pdb=" N ARG P 74 " --> pdb=" O LEU P 70 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE P 79 " --> pdb=" O GLN P 75 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR P 81 " --> pdb=" O LEU P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 87 removed outlier: 3.666A pdb=" N VAL P 86 " --> pdb=" O GLU P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 92 removed outlier: 4.171A pdb=" N ALA P 91 " --> pdb=" O HIS P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 97 Processing helix chain 'P' and resid 113 through 117 removed outlier: 3.870A pdb=" N ASP P 116 " --> pdb=" O ARG P 113 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN P 117 " --> pdb=" O ARG P 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 113 through 117' Processing helix chain 'Q' and resid 50 through 65 removed outlier: 3.692A pdb=" N THR Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA Q 55 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE Q 60 " --> pdb=" O ARG Q 56 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS Q 63 " --> pdb=" O ARG Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 107 removed outlier: 3.853A pdb=" N SER Q 106 " --> pdb=" O GLN Q 102 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU Q 107 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 102 through 107' Processing helix chain 'Q' and resid 116 through 135 removed outlier: 3.640A pdb=" N GLU Q 125 " --> pdb=" O GLN Q 121 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA Q 128 " --> pdb=" O GLY Q 124 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU Q 132 " --> pdb=" O ALA Q 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 163 removed outlier: 4.184A pdb=" N GLY Q 163 " --> pdb=" O ALA Q 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 138 removed outlier: 3.571A pdb=" N ALA R 134 " --> pdb=" O ALA R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 178 Processing helix chain 'R' and resid 219 through 225 removed outlier: 3.776A pdb=" N LYS R 225 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 9 Processing helix chain 'S' and resid 10 through 22 removed outlier: 4.155A pdb=" N LYS S 16 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA S 21 " --> pdb=" O ILE S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 30 Processing helix chain 'S' and resid 31 through 70 removed outlier: 4.060A pdb=" N ILE S 40 " --> pdb=" O ALA S 36 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG S 41 " --> pdb=" O GLN S 37 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP S 51 " --> pdb=" O HIS S 47 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG S 55 " --> pdb=" O ASP S 51 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 88 removed outlier: 3.607A pdb=" N HIS S 83 " --> pdb=" O SER S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 93 through 104 Processing helix chain 'S' and resid 104 through 117 removed outlier: 3.728A pdb=" N ILE S 108 " --> pdb=" O ASN S 104 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE S 116 " --> pdb=" O TYR S 112 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS S 117 " --> pdb=" O ASN S 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 102 through 111 removed outlier: 4.217A pdb=" N ILE T 107 " --> pdb=" O TYR T 103 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN T 108 " --> pdb=" O ASN T 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 51 removed outlier: 4.118A pdb=" N VAL U 49 " --> pdb=" O LYS U 45 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP U 51 " --> pdb=" O ARG U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 68 removed outlier: 3.843A pdb=" N LEU U 67 " --> pdb=" O MET U 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 90 removed outlier: 3.839A pdb=" N ILE U 76 " --> pdb=" O ALA U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 118 through 120 No H-bonds generated for 'chain 'U' and resid 118 through 120' Processing helix chain 'U' and resid 142 through 149 removed outlier: 3.532A pdb=" N PHE U 148 " --> pdb=" O SER U 144 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 132 removed outlier: 3.515A pdb=" N LYS V 126 " --> pdb=" O GLU V 122 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA V 129 " --> pdb=" O ILE V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 156 Processing helix chain 'V' and resid 183 through 190 Processing helix chain 'X' and resid 149 through 166 Processing helix chain 'Y' and resid 122 through 132 removed outlier: 3.694A pdb=" N LEU Y 126 " --> pdb=" O SER Y 122 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 139 removed outlier: 3.810A pdb=" N VAL Y 137 " --> pdb=" O GLY Y 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 68 removed outlier: 4.528A pdb=" N LEU Z 65 " --> pdb=" O LYS Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 89 removed outlier: 4.341A pdb=" N ASN Z 77 " --> pdb=" O ASN Z 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY Z 85 " --> pdb=" O LEU Z 81 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU Z 86 " --> pdb=" O GLN Z 82 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU Z 87 " --> pdb=" O LEU Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 127 removed outlier: 3.580A pdb=" N GLY Z 106 " --> pdb=" O PRO Z 102 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL Z 118 " --> pdb=" O ARG Z 114 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU Z 125 " --> pdb=" O GLU Z 121 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN Z 126 " --> pdb=" O ARG Z 122 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 Processing helix chain '2' and resid 11 through 39 removed outlier: 3.705A pdb=" N ILE 2 19 " --> pdb=" O ILE 2 15 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP 2 20 " --> pdb=" O ARG 2 16 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA 2 35 " --> pdb=" O ALA 2 31 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS 2 36 " --> pdb=" O PHE 2 32 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER 2 37 " --> pdb=" O SER 2 33 " (cutoff:3.500A) Processing helix chain '4' and resid 104 through 113 Processing helix chain '4' and resid 113 through 120 removed outlier: 3.634A pdb=" N SER 4 119 " --> pdb=" O ARG 4 115 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR 4 120 " --> pdb=" O LEU 4 116 " (cutoff:3.500A) Processing helix chain '4' and resid 120 through 134 removed outlier: 3.666A pdb=" N LEU 4 126 " --> pdb=" O SER 4 122 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU 4 127 " --> pdb=" O GLY 4 123 " (cutoff:3.500A) Processing helix chain '5' and resid 98 through 102 Processing helix chain '5' and resid 125 through 134 removed outlier: 3.658A pdb=" N LYS 5 129 " --> pdb=" O ASN 5 125 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN 5 130 " --> pdb=" O THR 5 126 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG 5 131 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS 5 134 " --> pdb=" O ASN 5 130 " (cutoff:3.500A) Processing helix chain '5' and resid 142 through 150 Processing helix chain '9' and resid 90 through 113 removed outlier: 3.868A pdb=" N ASN 9 94 " --> pdb=" O LEU 9 90 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG 9 98 " --> pdb=" O ASN 9 94 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET 9 99 " --> pdb=" O THR 9 95 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU 9 100 " --> pdb=" O LYS 9 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS 9 101 " --> pdb=" O GLN 9 97 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER 9 112 " --> pdb=" O SER 9 108 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL 9 113 " --> pdb=" O ASN 9 109 " (cutoff:3.500A) Processing helix chain '9' and resid 194 through 231 removed outlier: 3.917A pdb=" N GLU 9 198 " --> pdb=" O ASP 9 194 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU 9 199 " --> pdb=" O ARG 9 195 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA 9 200 " --> pdb=" O ARG 9 196 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS 9 201 " --> pdb=" O LYS 9 197 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL 9 202 " --> pdb=" O GLU 9 198 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS 9 205 " --> pdb=" O LYS 9 201 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE 9 217 " --> pdb=" O ALA 9 213 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG 9 218 " --> pdb=" O VAL 9 214 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS 9 227 " --> pdb=" O LYS 9 223 " (cutoff:3.500A) Processing helix chain '9' and resid 237 through 253 Processing helix chain '9' and resid 253 through 270 removed outlier: 3.658A pdb=" N GLU 9 267 " --> pdb=" O GLN 9 263 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU 9 268 " --> pdb=" O LYS 9 264 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N MET 9 269 " --> pdb=" O GLU 9 265 " (cutoff:3.500A) Processing helix chain '7' and resid 100 through 128 removed outlier: 3.815A pdb=" N LYS 7 105 " --> pdb=" O GLU 7 101 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS 7 107 " --> pdb=" O LYS 7 103 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET 7 108 " --> pdb=" O ILE 7 104 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU 7 125 " --> pdb=" O ALA 7 121 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG 7 128 " --> pdb=" O SER 7 124 " (cutoff:3.500A) Processing helix chain '7' and resid 132 through 139 removed outlier: 3.878A pdb=" N MET 7 136 " --> pdb=" O PRO 7 132 " (cutoff:3.500A) Processing helix chain '8' and resid 55 through 62 removed outlier: 3.875A pdb=" N HIS 8 59 " --> pdb=" O GLY 8 55 " (cutoff:3.500A) Processing helix chain '8' and resid 68 through 73 removed outlier: 3.548A pdb=" N LYS 8 73 " --> pdb=" O ARG 8 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'D' and resid 97 through 101 removed outlier: 6.714A pdb=" N ILE D 87 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE D 77 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU D 89 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 125 through 127 removed outlier: 5.511A pdb=" N LEU D 160 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS D 171 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 261 through 264 removed outlier: 4.920A pdb=" N ARG E 262 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE E 199 " --> pdb=" O ARG E 262 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS E 96 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLY E 116 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY E 98 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL E 275 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE E 269 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET E 277 " --> pdb=" O MET E 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 123 through 127 removed outlier: 6.623A pdb=" N GLN E 138 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL E 126 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA E 136 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR E 141 " --> pdb=" O HIS E 167 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N HIS E 167 " --> pdb=" O TYR E 141 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ARG E 143 " --> pdb=" O MET E 165 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET E 165 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 205 through 209 removed outlier: 3.680A pdb=" N GLY E 207 " --> pdb=" O MET E 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 174 through 175 removed outlier: 3.685A pdb=" N THR F 248 " --> pdb=" O PHE F 208 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU F 229 " --> pdb=" O SER F 205 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE F 207 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 81 through 84 removed outlier: 3.717A pdb=" N GLY G 101 " --> pdb=" O THR G 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 170 through 173 Processing sheet with id=AB1, first strand: chain 'H' and resid 135 through 138 removed outlier: 3.647A pdb=" N ARG H 135 " --> pdb=" O SER H 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AB3, first strand: chain 'L' and resid 221 through 222 Processing sheet with id=AB4, first strand: chain 'L' and resid 172 through 176 Processing sheet with id=AB5, first strand: chain 'M' and resid 7 through 10 removed outlier: 3.736A pdb=" N VAL M 10 " --> pdb=" O ARG M 17 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG M 17 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA M 16 " --> pdb=" O ALA M 46 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA M 46 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU M 18 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL M 40 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE M 24 " --> pdb=" O VAL M 38 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL M 38 " --> pdb=" O ILE M 24 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL M 62 " --> pdb=" O VAL M 85 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL M 85 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA M 84 " --> pdb=" O HIS M 7 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASN M 9 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 69 through 70 removed outlier: 3.636A pdb=" N LEU M 69 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR R 180 " --> pdb=" O ARG R 172 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG R 172 " --> pdb=" O THR R 180 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG R 182 " --> pdb=" O ILE R 170 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE R 186 " --> pdb=" O LYS R 166 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N LYS R 166 " --> pdb=" O ILE R 186 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER R 163 " --> pdb=" O LEU R 153 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU R 153 " --> pdb=" O SER R 163 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP R 147 " --> pdb=" O VAL R 169 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE R 148 " --> pdb=" O VAL R 208 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL R 208 " --> pdb=" O ILE R 148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN R 150 " --> pdb=" O ILE R 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE R 206 " --> pdb=" O GLN R 150 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG R 152 " --> pdb=" O LYS R 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 211 through 214 Processing sheet with id=AB8, first strand: chain 'O' and resid 63 through 66 removed outlier: 6.669A pdb=" N LEU O 34 " --> pdb=" O LEU O 103 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU O 105 " --> pdb=" O TYR O 32 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR O 32 " --> pdb=" O GLU O 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 40 through 43 removed outlier: 3.644A pdb=" N TYR O 92 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 43 through 47 Processing sheet with id=AC2, first strand: chain 'Q' and resid 94 through 99 removed outlier: 3.977A pdb=" N ALA Q 96 " --> pdb=" O VAL Q 86 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU Q 73 " --> pdb=" O ASP Q 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 133 through 136 removed outlier: 3.688A pdb=" N LEU T 163 " --> pdb=" O VAL T 126 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL T 128 " --> pdb=" O VAL T 161 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL T 161 " --> pdb=" O VAL T 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 140 through 145 removed outlier: 3.551A pdb=" N ARG T 140 " --> pdb=" O ILE T 221 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG T 218 " --> pdb=" O GLU T 187 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N HIS T 183 " --> pdb=" O THR T 222 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP T 154 " --> pdb=" O VAL T 186 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 195 through 201 removed outlier: 4.515A pdb=" N TYR T 206 " --> pdb=" O LYS T 201 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 32 through 34 removed outlier: 3.773A pdb=" N ILE U 32 " --> pdb=" O LEU U 136 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU U 136 " --> pdb=" O ILE U 32 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N CYS U 130 " --> pdb=" O SER U 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 32 through 34 removed outlier: 3.773A pdb=" N ILE U 32 " --> pdb=" O LEU U 136 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU U 136 " --> pdb=" O ILE U 32 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG U 137 " --> pdb=" O ILE U 100 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE U 100 " --> pdb=" O ARG U 137 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 111 through 116 Processing sheet with id=AC9, first strand: chain 'V' and resid 117 through 118 removed outlier: 3.667A pdb=" N THR V 171 " --> pdb=" O ARG V 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG V 167 " --> pdb=" O THR V 171 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS V 161 " --> pdb=" O MET V 177 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 129 through 130 removed outlier: 3.624A pdb=" N LYS W 91 " --> pdb=" O ILE W 100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 110 through 111 removed outlier: 3.681A pdb=" N VAL W 111 " --> pdb=" O GLN W 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 148 through 151 Processing sheet with id=AD4, first strand: chain 'X' and resid 78 through 79 removed outlier: 6.684A pdb=" N ILE X 115 " --> pdb=" O ILE X 93 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 101 through 103 Processing sheet with id=AD6, first strand: chain 'Y' and resid 83 through 85 Processing sheet with id=AD7, first strand: chain 'Y' and resid 104 through 109 Processing sheet with id=AD8, first strand: chain '3' and resid 8 through 13 Processing sheet with id=AD9, first strand: chain '3' and resid 47 through 49 removed outlier: 3.954A pdb=" N LEU 3 48 " --> pdb=" O HIS 3 61 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '5' and resid 103 through 104 857 hydrogen bonds defined for protein. 2400 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2181 hydrogen bonds 3686 hydrogen bond angles 0 basepair planarities 854 basepair parallelities 1446 stacking parallelities Total time for adding SS restraints: 146.00 Time building geometry restraints manager: 42.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 17039 1.34 - 1.48: 44548 1.48 - 1.61: 36410 1.61 - 1.75: 534 1.75 - 1.89: 171 Bond restraints: 98702 Sorted by residual: bond pdb=" C ILE U 158 " pdb=" N ALA U 159 " ideal model delta sigma weight residual 1.333 1.845 -0.512 1.26e-02 6.30e+03 1.65e+03 bond pdb=" O3' C A1554 " pdb=" P G A1555 " ideal model delta sigma weight residual 1.607 1.330 0.277 1.50e-02 4.44e+03 3.41e+02 bond pdb=" C ASP W 169 " pdb=" N THR W 170 " ideal model delta sigma weight residual 1.331 1.580 -0.249 1.35e-02 5.49e+03 3.39e+02 bond pdb=" C PRO T 118 " pdb=" N PRO T 119 " ideal model delta sigma weight residual 1.334 1.709 -0.375 2.34e-02 1.83e+03 2.57e+02 bond pdb=" O3' U A1435 " pdb=" P U A1436 " ideal model delta sigma weight residual 1.607 1.439 0.168 1.50e-02 4.44e+03 1.25e+02 ... (remaining 98697 not shown) Histogram of bond angle deviations from ideal: 91.95 - 101.34: 2056 101.34 - 110.73: 50954 110.73 - 120.12: 57759 120.12 - 129.50: 35231 129.50 - 138.89: 1908 Bond angle restraints: 147908 Sorted by residual: angle pdb=" O3' A A 763 " pdb=" C3' A A 763 " pdb=" C2' A A 763 " ideal model delta sigma weight residual 109.50 128.71 -19.21 1.50e+00 4.44e-01 1.64e+02 angle pdb=" O3' G A 50 " pdb=" C3' G A 50 " pdb=" C2' G A 50 " ideal model delta sigma weight residual 109.50 126.57 -17.07 1.50e+00 4.44e-01 1.29e+02 angle pdb=" O3' G A1260 " pdb=" C3' G A1260 " pdb=" C2' G A1260 " ideal model delta sigma weight residual 113.70 98.75 14.95 1.50e+00 4.44e-01 9.94e+01 angle pdb=" N PRO T 117 " pdb=" CA PRO T 117 " pdb=" C PRO T 117 " ideal model delta sigma weight residual 110.70 122.86 -12.16 1.22e+00 6.72e-01 9.93e+01 angle pdb=" C4' A A1399 " pdb=" C3' A A1399 " pdb=" O3' A A1399 " ideal model delta sigma weight residual 109.40 124.13 -14.73 1.50e+00 4.44e-01 9.64e+01 ... (remaining 147903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 49518 35.98 - 71.97: 2791 71.97 - 107.95: 251 107.95 - 143.94: 26 143.94 - 179.92: 58 Dihedral angle restraints: 52644 sinusoidal: 42879 harmonic: 9765 Sorted by residual: dihedral pdb=" C5' U A1241 " pdb=" C4' U A1241 " pdb=" C3' U A1241 " pdb=" O3' U A1241 " ideal model delta sinusoidal sigma weight residual 147.00 80.06 66.94 1 8.00e+00 1.56e-02 9.13e+01 dihedral pdb=" O4' U A2090 " pdb=" C1' U A2090 " pdb=" N1 U A2090 " pdb=" C2 U A2090 " ideal model delta sinusoidal sigma weight residual 200.00 30.39 169.61 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' C A 557 " pdb=" C1' C A 557 " pdb=" N1 C A 557 " pdb=" C2 C A 557 " ideal model delta sinusoidal sigma weight residual 200.00 35.61 164.39 1 1.50e+01 4.44e-03 8.38e+01 ... (remaining 52641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 16134 0.167 - 0.334: 2679 0.334 - 0.501: 35 0.501 - 0.667: 17 0.667 - 0.834: 8 Chirality restraints: 18873 Sorted by residual: chirality pdb=" C3' G A1050 " pdb=" C4' G A1050 " pdb=" O3' G A1050 " pdb=" C2' G A1050 " both_signs ideal model delta sigma weight residual False -2.74 -1.91 -0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" C3' G A 50 " pdb=" C4' G A 50 " pdb=" O3' G A 50 " pdb=" C2' G A 50 " both_signs ideal model delta sigma weight residual False -2.74 -1.92 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C3' C A1048 " pdb=" C4' C A1048 " pdb=" O3' C A1048 " pdb=" C2' C A1048 " both_signs ideal model delta sigma weight residual False -2.74 -1.94 -0.81 2.00e-01 2.50e+01 1.63e+01 ... (remaining 18870 not shown) Planarity restraints: 7648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A2665 " 0.061 2.00e-02 2.50e+03 4.14e-02 3.86e+01 pdb=" N1 U A2665 " -0.036 2.00e-02 2.50e+03 pdb=" C2 U A2665 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U A2665 " 0.014 2.00e-02 2.50e+03 pdb=" N3 U A2665 " -0.068 2.00e-02 2.50e+03 pdb=" C4 U A2665 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U A2665 " 0.070 2.00e-02 2.50e+03 pdb=" C5 U A2665 " -0.016 2.00e-02 2.50e+03 pdb=" C6 U A2665 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Z 129 " -0.027 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C GLY Z 129 " 0.091 2.00e-02 2.50e+03 pdb=" O GLY Z 129 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS Z 130 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2707 " 0.067 2.00e-02 2.50e+03 3.03e-02 2.52e+01 pdb=" N9 A A2707 " -0.070 2.00e-02 2.50e+03 pdb=" C8 A A2707 " -0.009 2.00e-02 2.50e+03 pdb=" N7 A A2707 " 0.007 2.00e-02 2.50e+03 pdb=" C5 A A2707 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A A2707 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A A2707 " 0.017 2.00e-02 2.50e+03 pdb=" N1 A A2707 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A A2707 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A A2707 " -0.010 2.00e-02 2.50e+03 pdb=" C4 A A2707 " -0.009 2.00e-02 2.50e+03 ... (remaining 7645 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 17 2.13 - 2.83: 22277 2.83 - 3.52: 117876 3.52 - 4.21: 287499 4.21 - 4.90: 375258 Nonbonded interactions: 802927 Sorted by model distance: nonbonded pdb=" O4 U A 219 " pdb=" N1 A A 442 " model vdw 1.443 2.496 nonbonded pdb=" O2' A A 263 " pdb=" OP1 A A 265 " model vdw 1.445 2.440 nonbonded pdb=" O2' G A 49 " pdb=" CD LYS Z 130 " model vdw 1.554 3.440 nonbonded pdb=" O2' G A1438 " pdb=" O2' A A1623 " model vdw 1.694 2.440 nonbonded pdb=" N2 G A 81 " pdb=" O4 U A 102 " model vdw 1.707 2.520 ... (remaining 802922 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2963 5.49 5 S 99 5.16 5 C 45416 2.51 5 N 16983 2.21 5 O 25186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.080 Extract box with map and model: 15.970 Check model and map are aligned: 1.060 Convert atoms to be neutral: 0.600 Process input model: 324.990 Find NCS groups from input model: 1.720 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 349.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.008 0.512 98702 Z= 0.469 Angle : 1.223 19.211 147908 Z= 0.810 Chirality : 0.105 0.834 18873 Planarity : 0.007 0.074 7648 Dihedral : 18.654 179.924 46360 Min Nonbonded Distance : 1.443 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 3.00 % Allowed : 11.51 % Favored : 85.48 % Rotamer Outliers : 6.93 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.11), residues: 3362 helix: -1.94 (0.14), residues: 909 sheet: -2.63 (0.22), residues: 446 loop : -3.40 (0.11), residues: 2007 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 915 time to evaluate : 4.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 197 outliers final: 45 residues processed: 1043 average time/residue: 0.9783 time to fit residues: 1618.7094 Evaluate side-chains 777 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 732 time to evaluate : 4.109 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.7169 time to fit residues: 61.8472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 3.9990 chunk 472 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 319 optimal weight: 0.4980 chunk 252 optimal weight: 6.9990 chunk 489 optimal weight: 0.4980 chunk 189 optimal weight: 7.9990 chunk 297 optimal weight: 6.9990 chunk 364 optimal weight: 6.9990 chunk 566 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 ASN D 102 HIS E 301 ASN F 93 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 222 ASN G 22 ASN G 109 ASN H 53 ASN L 97 ASN ** L 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 9 ASN N 117 GLN N 133 GLN N 211 GLN O 12 GLN O 35 GLN P 26 GLN P 87 HIS P 101 ASN Q 93 HIS Q 108 ASN R 178 HIS ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 99 GLN S 106 ASN T 212 HIS U 97 ASN ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN W 59 ASN W 93 HIS W 95 HIS W 133 ASN X 68 ASN X 75 GLN X 85 GLN X 143 GLN ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN ** Y 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 61 HIS 5 95 HIS 5 118 GLN 9 97 GLN 9 109 ASN ** 7 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 98702 Z= 0.283 Angle : 0.776 17.332 147908 Z= 0.398 Chirality : 0.044 0.338 18873 Planarity : 0.006 0.092 7648 Dihedral : 17.156 179.687 39363 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.60 % Favored : 90.51 % Rotamer Outliers : 5.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.10 (0.13), residues: 3362 helix: -0.53 (0.16), residues: 910 sheet: -2.41 (0.20), residues: 576 loop : -2.84 (0.13), residues: 1876 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 795 time to evaluate : 4.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 85 residues processed: 881 average time/residue: 0.9579 time to fit residues: 1368.2282 Evaluate side-chains 793 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 708 time to evaluate : 4.022 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 0 residues processed: 85 average time/residue: 0.6628 time to fit residues: 110.4691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 471 optimal weight: 6.9990 chunk 385 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 567 optimal weight: 0.7980 chunk 613 optimal weight: 7.9990 chunk 505 optimal weight: 0.0370 chunk 562 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 455 optimal weight: 1.9990 overall best weight: 3.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 301 ASN F 222 ASN G 60 GLN G 70 ASN L 157 ASN ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN S 83 HIS S 104 ASN ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 126 GLN ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.087 98702 Z= 0.303 Angle : 0.741 15.559 147908 Z= 0.380 Chirality : 0.043 0.329 18873 Planarity : 0.006 0.094 7648 Dihedral : 16.900 179.999 39363 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.32 % Favored : 88.85 % Rotamer Outliers : 4.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.13), residues: 3362 helix: -0.30 (0.16), residues: 924 sheet: -2.23 (0.21), residues: 533 loop : -2.65 (0.13), residues: 1905 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 742 time to evaluate : 4.103 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 outliers start: 126 outliers final: 66 residues processed: 808 average time/residue: 0.9654 time to fit residues: 1268.7072 Evaluate side-chains 776 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 710 time to evaluate : 4.038 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.6587 time to fit residues: 86.6056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 5.9990 chunk 426 optimal weight: 4.9990 chunk 294 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 270 optimal weight: 20.0000 chunk 381 optimal weight: 20.0000 chunk 569 optimal weight: 0.9980 chunk 603 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 chunk 539 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 288 ASN L 134 HIS L 170 GLN ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN R 202 ASN S 53 GLN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** T 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 137 GLN ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.128 98702 Z= 0.360 Angle : 0.792 14.897 147908 Z= 0.400 Chirality : 0.044 0.367 18873 Planarity : 0.006 0.090 7648 Dihedral : 16.926 179.929 39363 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.77 % Allowed : 10.41 % Favored : 88.82 % Rotamer Outliers : 4.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.13), residues: 3362 helix: -0.38 (0.16), residues: 921 sheet: -2.16 (0.21), residues: 552 loop : -2.61 (0.13), residues: 1889 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 753 time to evaluate : 4.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 69 residues processed: 802 average time/residue: 1.0215 time to fit residues: 1344.7466 Evaluate side-chains 800 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 731 time to evaluate : 3.973 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.7082 time to fit residues: 95.1902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 3.9990 chunk 342 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 449 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 514 optimal weight: 0.7980 chunk 416 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 1.9990 chunk 541 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 106 GLN O 12 GLN ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN ** 5 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 137 GLN ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.095 98702 Z= 0.328 Angle : 0.760 15.699 147908 Z= 0.386 Chirality : 0.043 0.391 18873 Planarity : 0.006 0.094 7648 Dihedral : 16.862 179.829 39363 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.04 % Favored : 88.28 % Rotamer Outliers : 4.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.67 (0.14), residues: 3362 helix: -0.30 (0.17), residues: 920 sheet: -2.11 (0.21), residues: 522 loop : -2.52 (0.13), residues: 1920 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 863 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 746 time to evaluate : 4.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 74 residues processed: 811 average time/residue: 0.9530 time to fit residues: 1252.8415 Evaluate side-chains 783 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 709 time to evaluate : 4.044 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.6728 time to fit residues: 97.6639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 5.9990 chunk 543 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 354 optimal weight: 0.9980 chunk 148 optimal weight: 10.0000 chunk 603 optimal weight: 6.9990 chunk 501 optimal weight: 0.7980 chunk 279 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 316 optimal weight: 3.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 61 GLN O 12 GLN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 85 GLN R 202 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN X 75 GLN ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.115 98702 Z= 0.347 Angle : 0.781 15.380 147908 Z= 0.394 Chirality : 0.044 0.406 18873 Planarity : 0.006 0.093 7648 Dihedral : 16.886 179.961 39363 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.12 % Favored : 88.22 % Rotamer Outliers : 3.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.71 (0.14), residues: 3362 helix: -0.36 (0.17), residues: 922 sheet: -1.99 (0.21), residues: 537 loop : -2.57 (0.13), residues: 1903 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 730 time to evaluate : 4.128 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 outliers start: 112 outliers final: 67 residues processed: 784 average time/residue: 0.9833 time to fit residues: 1259.4168 Evaluate side-chains 770 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 703 time to evaluate : 4.109 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.7294 time to fit residues: 93.7452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 343 optimal weight: 6.9990 chunk 440 optimal weight: 4.9990 chunk 341 optimal weight: 7.9990 chunk 508 optimal weight: 5.9990 chunk 337 optimal weight: 8.9990 chunk 601 optimal weight: 0.9980 chunk 376 optimal weight: 9.9990 chunk 366 optimal weight: 6.9990 chunk 277 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 ASN ** P 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 HIS Q 85 GLN R 202 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN X 75 GLN ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.145 98702 Z= 0.367 Angle : 0.797 15.273 147908 Z= 0.401 Chirality : 0.044 0.417 18873 Planarity : 0.006 0.090 7648 Dihedral : 16.936 179.926 39363 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.65 % Allowed : 12.28 % Favored : 87.06 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.14), residues: 3362 helix: -0.40 (0.17), residues: 924 sheet: -1.88 (0.22), residues: 475 loop : -2.61 (0.13), residues: 1963 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 722 time to evaluate : 4.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 57 residues processed: 767 average time/residue: 0.9983 time to fit residues: 1245.5947 Evaluate side-chains 760 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 703 time to evaluate : 4.079 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 0 residues processed: 57 average time/residue: 0.6562 time to fit residues: 76.5434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 0.1980 chunk 240 optimal weight: 4.9990 chunk 359 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 382 optimal weight: 8.9990 chunk 409 optimal weight: 0.9990 chunk 297 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 472 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 GLN ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 HIS Q 85 GLN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 118 GLN ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 141 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 98702 Z= 0.253 Angle : 0.699 16.560 147908 Z= 0.356 Chirality : 0.040 0.406 18873 Planarity : 0.006 0.087 7648 Dihedral : 16.697 179.730 39363 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.32 % Favored : 89.08 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.54 (0.14), residues: 3362 helix: -0.24 (0.17), residues: 933 sheet: -1.77 (0.22), residues: 483 loop : -2.50 (0.13), residues: 1946 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 726 time to evaluate : 4.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 41 residues processed: 747 average time/residue: 0.9562 time to fit residues: 1158.4906 Evaluate side-chains 742 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 701 time to evaluate : 4.003 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.7337 time to fit residues: 58.3260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 3.9990 chunk 576 optimal weight: 7.9990 chunk 525 optimal weight: 2.9990 chunk 560 optimal weight: 1.9990 chunk 337 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 440 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 506 optimal weight: 8.9990 chunk 530 optimal weight: 9.9990 chunk 558 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 98702 Z= 0.243 Angle : 0.694 16.644 147908 Z= 0.352 Chirality : 0.039 0.413 18873 Planarity : 0.006 0.089 7648 Dihedral : 16.632 179.858 39363 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.89 % Favored : 88.55 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.41 (0.14), residues: 3362 helix: -0.17 (0.17), residues: 931 sheet: -1.72 (0.22), residues: 481 loop : -2.40 (0.13), residues: 1950 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 699 time to evaluate : 4.249 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 outliers start: 37 outliers final: 22 residues processed: 712 average time/residue: 0.9543 time to fit residues: 1107.0870 Evaluate side-chains 709 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 687 time to evaluate : 4.144 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.7105 time to fit residues: 32.8434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 0.5980 chunk 592 optimal weight: 0.9990 chunk 361 optimal weight: 7.9990 chunk 281 optimal weight: 20.0000 chunk 411 optimal weight: 0.7980 chunk 621 optimal weight: 6.9990 chunk 572 optimal weight: 0.9980 chunk 495 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 382 optimal weight: 7.9990 chunk 303 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 HIS ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 241 ASN G 52 ASN ** L 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN R 202 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN ** W 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 146 ASN Y 93 HIS ** 5 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 216 ASN ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 98702 Z= 0.145 Angle : 0.614 16.812 147908 Z= 0.314 Chirality : 0.035 0.378 18873 Planarity : 0.005 0.091 7648 Dihedral : 16.347 179.819 39363 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.15 % Favored : 91.34 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.07 (0.14), residues: 3362 helix: 0.23 (0.17), residues: 919 sheet: -1.74 (0.22), residues: 521 loop : -2.15 (0.14), residues: 1922 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 722 time to evaluate : 4.082 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 outliers start: 25 outliers final: 13 residues processed: 732 average time/residue: 0.9900 time to fit residues: 1171.8621 Evaluate side-chains 703 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 690 time to evaluate : 4.009 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.7319 time to fit residues: 21.6206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 2.9990 chunk 527 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 456 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 495 optimal weight: 5.9990 chunk 207 optimal weight: 40.0000 chunk 509 optimal weight: 0.5980 chunk 62 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 HIS F 241 ASN L 234 GLN Q 85 GLN R 202 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN ** 5 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 137 GLN 9 216 ASN ** 7 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121616 restraints weight = 151631.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124820 restraints weight = 51371.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125162 restraints weight = 27306.490| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.115 98702 Z= 0.358 Angle : 0.776 14.856 147908 Z= 0.387 Chirality : 0.043 0.476 18873 Planarity : 0.006 0.090 7648 Dihedral : 16.620 179.637 39363 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.54 % Allowed : 11.48 % Favored : 87.98 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.14), residues: 3362 helix: -0.10 (0.17), residues: 927 sheet: -1.58 (0.23), residues: 482 loop : -2.34 (0.13), residues: 1953 =============================================================================== Job complete usr+sys time: 18452.52 seconds wall clock time: 327 minutes 10.03 seconds (19630.03 seconds total)