Starting phenix.real_space_refine (version: dev) on Sat Feb 25 04:30:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xyi_6788/02_2023/5xyi_6788_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xyi_6788/02_2023/5xyi_6788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xyi_6788/02_2023/5xyi_6788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xyi_6788/02_2023/5xyi_6788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xyi_6788/02_2023/5xyi_6788_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xyi_6788/02_2023/5xyi_6788_neut.pdb" } resolution = 3.35 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= 0.000 sd= 0.005 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 Process input model Symmetric amino acids flipped Residue "A TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "D ARG 10": "NH1" <-> "NH2" Residue "D ARG 11": "NH1" <-> "NH2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D ASP 90": "OD1" <-> "OD2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ARG 11": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 241": "NH1" <-> "NH2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 68": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F GLU 83": "OE1" <-> "OE2" Residue "F ARG 116": "NH1" <-> "NH2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "H PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H ARG 86": "NH1" <-> "NH2" Residue "H PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Residue "H ARG 119": "NH1" <-> "NH2" Residue "H TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 135": "OD1" <-> "OD2" Residue "H ARG 155": "NH1" <-> "NH2" Residue "H PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 17": "NH1" <-> "NH2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "I ARG 31": "NH1" <-> "NH2" Residue "I ASP 177": "OD1" <-> "OD2" Residue "J ARG 8": "NH1" <-> "NH2" Residue "J PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 15": "NH1" <-> "NH2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 8": "NH1" <-> "NH2" Residue "K ARG 9": "NH1" <-> "NH2" Residue "K ARG 13": "NH1" <-> "NH2" Residue "K ASP 35": "OD1" <-> "OD2" Residue "K PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 76": "NH1" <-> "NH2" Residue "K TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 70": "NH1" <-> "NH2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 153": "NH1" <-> "NH2" Residue "N TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 57": "NH1" <-> "NH2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "N ARG 127": "NH1" <-> "NH2" Residue "N ARG 132": "NH1" <-> "NH2" Residue "O ASP 31": "OD1" <-> "OD2" Residue "O GLU 33": "OE1" <-> "OE2" Residue "O TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 125": "NH1" <-> "NH2" Residue "O ARG 149": "NH1" <-> "NH2" Residue "Q PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 111": "NH1" <-> "NH2" Residue "Q ARG 135": "NH1" <-> "NH2" Residue "Q ARG 140": "NH1" <-> "NH2" Residue "R ARG 5": "NH1" <-> "NH2" Residue "R ASP 27": "OD1" <-> "OD2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R ARG 59": "NH1" <-> "NH2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 104": "OE1" <-> "OE2" Residue "S PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 41": "NH1" <-> "NH2" Residue "S TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 48": "NH1" <-> "NH2" Residue "S ARG 56": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "S ARG 115": "NH1" <-> "NH2" Residue "S ARG 126": "NH1" <-> "NH2" Residue "T PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 39": "OE1" <-> "OE2" Residue "T PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 104": "NH1" <-> "NH2" Residue "U ARG 55": "NH1" <-> "NH2" Residue "U ARG 63": "NH1" <-> "NH2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "U TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 113": "OD1" <-> "OD2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "V ARG 59": "NH1" <-> "NH2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V ARG 83": "NH1" <-> "NH2" Residue "W ASP 9": "OD1" <-> "OD2" Residue "W PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 97": "NH1" <-> "NH2" Residue "W PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 114": "OE1" <-> "OE2" Residue "W ARG 117": "NH1" <-> "NH2" Residue "W PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 16": "NH1" <-> "NH2" Residue "X ARG 30": "NH1" <-> "NH2" Residue "X ARG 31": "NH1" <-> "NH2" Residue "X TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 9": "NH1" <-> "NH2" Residue "Y TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 19": "NH1" <-> "NH2" Residue "Y PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 6": "NH1" <-> "NH2" Residue "a ARG 10": "NH1" <-> "NH2" Residue "a PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 81": "NH1" <-> "NH2" Residue "a ARG 87": "NH1" <-> "NH2" Residue "a ARG 93": "NH1" <-> "NH2" Residue "b PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 71": "NH1" <-> "NH2" Residue "b ASP 76": "OD1" <-> "OD2" Residue "c ARG 23": "NH1" <-> "NH2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c ARG 50": "NH1" <-> "NH2" Residue "c GLU 51": "OE1" <-> "OE2" Residue "c ARG 62": "NH1" <-> "NH2" Residue "d ARG 23": "NH1" <-> "NH2" Residue "d ARG 28": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "d ARG 45": "NH1" <-> "NH2" Residue "e ARG 15": "NH1" <-> "NH2" Residue "e ARG 33": "NH1" <-> "NH2" Residue "e ARG 35": "NH1" <-> "NH2" Residue "e ARG 37": "NH1" <-> "NH2" Residue "e PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 26": "NH1" <-> "NH2" Residue "g PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 101": "OD1" <-> "OD2" Residue "g PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 212": "NH1" <-> "NH2" Residue "g TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 21": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 65924 Number of models: 1 Model: "" Number of chains: 34 Chain: "2" Number of atoms: 31820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1490, 31820 Classifications: {'RNA': 1490} Modifications used: {'rna2p_pur': 135, 'rna2p_pyr': 109, 'rna3p_pur': 665, 'rna3p_pyr': 581} Link IDs: {'rna2p': 243, 'rna3p': 1246} Chain breaks: 17 Chain: "A" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 194} Chain breaks: 3 Chain: "B" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1747 Classifications: {'peptide': 219} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1685 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain breaks: 1 Chain: "D" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1655 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain breaks: 1 Chain: "E" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1935 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 10, 'TRANS': 235} Chain breaks: 1 Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1476 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 179} Chain breaks: 1 Chain: "G" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 155 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "H" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1276 Classifications: {'peptide': 163} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 155} Chain breaks: 1 Chain: "I" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1300 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "J" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1321 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 731 Classifications: {'peptide': 90} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 84} Chain breaks: 1 Chain: "L" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1160 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 133} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 509 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 99} Chain breaks: 2 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 144 Chain: "N" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1190 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "O" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1005 Classifications: {'peptide': 135} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 127} Chain: "P" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 962 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 110} Chain breaks: 1 Chain: "Q" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1043 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 2 Chain: "R" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 961 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 112} Chain: "S" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1077 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 128} Chain: "T" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1148 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "U" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 777 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain breaks: 2 Chain: "V" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 671 Classifications: {'peptide': 87} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 81} Chain: "W" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 124} Chain breaks: 1 Chain: "X" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1062 Classifications: {'peptide': 140} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 133} Chain: "Y" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "Z" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 560 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "a" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "b" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 632 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 8, 'TRANS': 73} Chain: "c" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 475 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "d" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "e" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 337 Classifications: {'peptide': 42} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 37} Chain: "g" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2380 Classifications: {'peptide': 305} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain breaks: 2 Chain: "n" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 225 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Time building chain proxies: 29.22, per 1000 atoms: 0.44 Number of scatterers: 65924 At special positions: 0 Unit cell: (216.48, 223.08, 198, 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 159 16.00 P 1490 15.00 O 16469 8.00 N 12093 7.00 C 35713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 26 " distance=2.36 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 77 " distance=2.66 Simple disulfide: pdb=" SG CYS a 26 " - pdb=" SG CYS a 77 " distance=1.53 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 43 " distance=2.86 Simple disulfide: pdb=" SG CYS d 25 " - pdb=" SG CYS d 43 " distance=2.95 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: 25.23 Conformation dependent library (CDL) restraints added in 4.3 seconds 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8152 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 57 sheets defined 35.0% alpha, 15.3% beta 367 base pairs and 759 stacking pairs defined. Time for finding SS restraints: 17.24 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 removed outlier: 4.570A pdb=" N VAL A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 63 removed outlier: 3.653A pdb=" N TYR A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 129 through 136 removed outlier: 4.052A pdb=" N ALA A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 185 removed outlier: 4.327A pdb=" N GLY A 170 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.960A pdb=" N LYS A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.946A pdb=" N VAL B 71 " --> pdb=" O HIS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 110 removed outlier: 3.942A pdb=" N MET B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 175 removed outlier: 3.841A pdb=" N VAL B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.023A pdb=" N VAL B 185 " --> pdb=" O CYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.627A pdb=" N ASN B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 230 through 237 removed outlier: 3.668A pdb=" N ALA B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 removed outlier: 3.560A pdb=" N ARG C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 74 removed outlier: 4.272A pdb=" N ILE C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 removed outlier: 4.240A pdb=" N VAL C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 150 removed outlier: 3.728A pdb=" N ALA C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 removed outlier: 3.852A pdb=" N LEU C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 239 removed outlier: 4.578A pdb=" N PHE C 237 " --> pdb=" O MET C 233 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.604A pdb=" N ASN C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.537A pdb=" N THR D 15 " --> pdb=" O ARG D 11 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 79 removed outlier: 3.676A pdb=" N VAL D 60 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N HIS D 63 " --> pdb=" O PHE D 59 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ARG D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU D 67 " --> pdb=" O HIS D 63 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN D 68 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 70 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET D 72 " --> pdb=" O GLN D 68 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 112 removed outlier: 3.553A pdb=" N GLU D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 132 removed outlier: 3.640A pdb=" N ILE D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG D 125 " --> pdb=" O TYR D 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D 132 " --> pdb=" O MET D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 169 removed outlier: 3.789A pdb=" N GLN D 167 " --> pdb=" O ASP D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 removed outlier: 3.983A pdb=" N LEU E 48 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG E 49 " --> pdb=" O ASN E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.556A pdb=" N ILE E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 65 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS E 66 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.895A pdb=" N SER E 120 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE E 121 " --> pdb=" O GLU E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 121' Processing helix chain 'F' and resid 7 through 9 No H-bonds generated for 'chain 'F' and resid 7 through 9' Processing helix chain 'F' and resid 16 through 21 removed outlier: 3.775A pdb=" N ASP F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 removed outlier: 4.172A pdb=" N LYS F 52 " --> pdb=" O ARG F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 65 Processing helix chain 'F' and resid 74 through 94 removed outlier: 4.269A pdb=" N ARG F 80 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE F 88 " --> pdb=" O HIS F 84 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA F 90 " --> pdb=" O PHE F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 4.132A pdb=" N THR F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 104 " --> pdb=" O THR F 100 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS F 108 " --> pdb=" O GLY F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 152 removed outlier: 3.513A pdb=" N ILE F 136 " --> pdb=" O PRO F 132 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 140 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU F 142 " --> pdb=" O GLN F 138 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY F 146 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.616A pdb=" N GLU F 165 " --> pdb=" O CYS F 161 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA F 168 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER F 170 " --> pdb=" O LEU F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 193 removed outlier: 4.160A pdb=" N ASP F 183 " --> pdb=" O CYS F 179 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG F 187 " --> pdb=" O ASP F 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 208 removed outlier: 3.934A pdb=" N TYR G 206 " --> pdb=" O LYS G 202 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA G 208 " --> pdb=" O GLU G 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 13 removed outlier: 3.633A pdb=" N GLU H 11 " --> pdb=" O ALA H 7 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE H 12 " --> pdb=" O ALA H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 52 Processing helix chain 'H' and resid 57 through 66 Processing helix chain 'H' and resid 97 through 110 removed outlier: 3.828A pdb=" N LEU H 106 " --> pdb=" O ASN H 102 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP H 107 " --> pdb=" O ASP H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 144 Processing helix chain 'H' and resid 145 through 157 removed outlier: 3.627A pdb=" N PHE H 149 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN H 154 " --> pdb=" O ALA H 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 106 through 117 removed outlier: 3.883A pdb=" N GLU I 114 " --> pdb=" O LYS I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 158 removed outlier: 3.758A pdb=" N ALA I 155 " --> pdb=" O PRO I 151 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP I 158 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 174 Processing helix chain 'I' and resid 183 through 194 removed outlier: 3.616A pdb=" N ALA I 187 " --> pdb=" O GLY I 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 33 removed outlier: 4.252A pdb=" N GLN J 27 " --> pdb=" O HIS J 23 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU J 31 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 60 removed outlier: 3.501A pdb=" N TRP J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL J 43 " --> pdb=" O GLU J 39 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS J 49 " --> pdb=" O TYR J 45 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA J 53 " --> pdb=" O LYS J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 82 removed outlier: 3.590A pdb=" N PHE J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA J 72 " --> pdb=" O ILE J 68 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 81 " --> pdb=" O ARG J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 95 Processing helix chain 'J' and resid 98 through 105 removed outlier: 3.610A pdb=" N ASP J 104 " --> pdb=" O ASN J 100 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG J 105 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 115 Processing helix chain 'J' and resid 119 through 129 Processing helix chain 'J' and resid 158 through 163 Processing helix chain 'K' and resid 4 through 19 removed outlier: 3.540A pdb=" N CYS K 14 " --> pdb=" O ARG K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 52 removed outlier: 3.813A pdb=" N TYR K 42 " --> pdb=" O ASN K 38 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE K 44 " --> pdb=" O TYR K 40 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA K 47 " --> pdb=" O GLN K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 80 removed outlier: 3.598A pdb=" N ILE K 72 " --> pdb=" O THR K 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG K 76 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 48 removed outlier: 3.503A pdb=" N ALA L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU L 48 " --> pdb=" O THR L 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 13 removed outlier: 3.501A pdb=" N GLY M 8 " --> pdb=" O VAL M 4 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN M 11 " --> pdb=" O HIS M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 31 Processing helix chain 'M' and resid 46 through 60 removed outlier: 3.952A pdb=" N LYS M 58 " --> pdb=" O GLY M 54 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 76 removed outlier: 3.780A pdb=" N ALA M 75 " --> pdb=" O LEU M 71 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU M 76 " --> pdb=" O LEU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 113 Processing helix chain 'N' and resid 29 through 43 removed outlier: 3.641A pdb=" N VAL N 34 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN N 35 " --> pdb=" O GLU N 31 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR N 40 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS N 43 " --> pdb=" O ASP N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 57 removed outlier: 3.783A pdb=" N GLY N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 68 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 removed outlier: 3.544A pdb=" N LEU N 91 " --> pdb=" O GLU N 87 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN N 97 " --> pdb=" O LYS N 93 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 116 Processing helix chain 'N' and resid 118 through 132 removed outlier: 3.604A pdb=" N HIS N 123 " --> pdb=" O GLU N 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG N 127 " --> pdb=" O HIS N 123 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 removed outlier: 3.560A pdb=" N LEU N 149 " --> pdb=" O THR N 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 97 removed outlier: 3.874A pdb=" N ALA O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG O 92 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS O 94 " --> pdb=" O ALA O 90 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU O 95 " --> pdb=" O ALA O 91 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY O 97 " --> pdb=" O LEU O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 129 removed outlier: 4.532A pdb=" N GLN O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER O 122 " --> pdb=" O GLN O 118 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG O 125 " --> pdb=" O GLN O 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 25 removed outlier: 3.525A pdb=" N LEU P 22 " --> pdb=" O THR P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 31 removed outlier: 4.311A pdb=" N ASP P 29 " --> pdb=" O MET P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 34 No H-bonds generated for 'chain 'P' and resid 32 through 34' Processing helix chain 'P' and resid 38 through 44 removed outlier: 3.563A pdb=" N ILE P 42 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 64 removed outlier: 3.886A pdb=" N LEU P 53 " --> pdb=" O LYS P 49 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE P 54 " --> pdb=" O HIS P 50 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL P 64 " --> pdb=" O ALA P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 89 Processing helix chain 'P' and resid 107 through 111 Processing helix chain 'P' and resid 114 through 119 removed outlier: 3.682A pdb=" N PHE P 118 " --> pdb=" O LEU P 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 46 removed outlier: 3.514A pdb=" N LEU Q 46 " --> pdb=" O ARG Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 52 Processing helix chain 'Q' and resid 70 through 93 removed outlier: 3.661A pdb=" N VAL Q 75 " --> pdb=" O HIS Q 71 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE Q 78 " --> pdb=" O GLN Q 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN Q 80 " --> pdb=" O TYR Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 110 removed outlier: 3.638A pdb=" N GLU Q 101 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU Q 106 " --> pdb=" O ILE Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 114 removed outlier: 3.579A pdb=" N LEU Q 114 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 111 through 114' Processing helix chain 'R' and resid 6 through 20 removed outlier: 3.554A pdb=" N LEU R 15 " --> pdb=" O ARG R 11 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 38 removed outlier: 3.697A pdb=" N ASN R 31 " --> pdb=" O ASP R 27 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG R 33 " --> pdb=" O GLN R 29 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 62 removed outlier: 4.180A pdb=" N ARG R 47 " --> pdb=" O SER R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 84 removed outlier: 3.525A pdb=" N LYS R 80 " --> pdb=" O GLN R 76 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 109 Processing helix chain 'S' and resid 31 through 35 Processing helix chain 'S' and resid 39 through 49 removed outlier: 3.537A pdb=" N TYR S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 75 removed outlier: 3.596A pdb=" N GLU S 66 " --> pdb=" O THR S 62 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU S 68 " --> pdb=" O LYS S 64 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE S 69 " --> pdb=" O GLU S 65 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER S 71 " --> pdb=" O GLU S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 120 removed outlier: 3.796A pdb=" N ALA S 107 " --> pdb=" O THR S 103 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG S 110 " --> pdb=" O GLY S 106 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA S 111 " --> pdb=" O ALA S 107 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET S 116 " --> pdb=" O GLU S 112 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS S 117 " --> pdb=" O ILE S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 130 removed outlier: 3.599A pdb=" N ARG S 126 " --> pdb=" O LYS S 122 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY S 128 " --> pdb=" O GLY S 124 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 31 removed outlier: 4.051A pdb=" N ASN T 23 " --> pdb=" O ASP T 19 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE T 29 " --> pdb=" O LEU T 25 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN T 30 " --> pdb=" O ALA T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 74 removed outlier: 4.089A pdb=" N THR T 62 " --> pdb=" O ASN T 58 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE T 68 " --> pdb=" O ALA T 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS T 74 " --> pdb=" O GLN T 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 87 Processing helix chain 'T' and resid 104 through 114 removed outlier: 3.555A pdb=" N ILE T 110 " --> pdb=" O VAL T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 130 through 147 removed outlier: 3.507A pdb=" N ARG T 135 " --> pdb=" O PRO T 131 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP T 138 " --> pdb=" O GLN T 134 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR T 142 " --> pdb=" O ASP T 138 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS T 146 " --> pdb=" O THR T 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS T 147 " --> pdb=" O SER T 143 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 51 removed outlier: 3.999A pdb=" N VAL U 39 " --> pdb=" O ASN U 35 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU U 47 " --> pdb=" O LEU U 43 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS U 48 " --> pdb=" O MET U 44 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS U 49 " --> pdb=" O GLY U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 99 through 107 removed outlier: 3.606A pdb=" N LYS U 103 " --> pdb=" O ALA U 99 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN U 104 " --> pdb=" O GLU U 100 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL U 105 " --> pdb=" O ALA U 101 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN U 107 " --> pdb=" O LYS U 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 62 removed outlier: 3.528A pdb=" N ARG V 59 " --> pdb=" O SER V 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY V 62 " --> pdb=" O VAL V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 63 through 76 Processing helix chain 'W' and resid 6 through 21 removed outlier: 3.655A pdb=" N LEU W 11 " --> pdb=" O LEU W 7 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS W 12 " --> pdb=" O ALA W 8 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG W 20 " --> pdb=" O ASN W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 44 removed outlier: 3.576A pdb=" N MET W 41 " --> pdb=" O PHE W 37 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 94 removed outlier: 4.280A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA W 91 " --> pdb=" O GLU W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 120 removed outlier: 3.675A pdb=" N LYS W 118 " --> pdb=" O GLU W 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 24 removed outlier: 3.541A pdb=" N SER X 21 " --> pdb=" O LEU X 17 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TRP X 24 " --> pdb=" O LYS X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 35 removed outlier: 3.828A pdb=" N THR X 35 " --> pdb=" O ARG X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 96 removed outlier: 4.416A pdb=" N ASP X 96 " --> pdb=" O LEU X 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 137 Processing helix chain 'Y' and resid 35 through 47 Processing helix chain 'Y' and resid 78 through 84 removed outlier: 3.922A pdb=" N LYS Y 82 " --> pdb=" O LEU Y 78 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS Y 83 " --> pdb=" O ASP Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 94 removed outlier: 4.006A pdb=" N LEU Y 90 " --> pdb=" O PRO Y 86 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS Y 92 " --> pdb=" O HIS Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 116 removed outlier: 3.943A pdb=" N ARG Y 111 " --> pdb=" O LYS Y 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN Y 112 " --> pdb=" O ASN Y 108 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS Y 113 " --> pdb=" O ALA Y 109 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL Y 114 " --> pdb=" O ARG Y 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 27 through 38 removed outlier: 3.967A pdb=" N ALA Z 32 " --> pdb=" O PRO Z 28 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP Z 33 " --> pdb=" O GLU Z 29 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS Z 36 " --> pdb=" O ALA Z 32 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL Z 38 " --> pdb=" O MET Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 53 removed outlier: 3.552A pdb=" N ALA Z 50 " --> pdb=" O ALA Z 46 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU Z 51 " --> pdb=" O GLY Z 47 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG Z 52 " --> pdb=" O LYS Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 71 removed outlier: 3.612A pdb=" N LYS Z 62 " --> pdb=" O THR Z 58 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU Z 64 " --> pdb=" O ALA Z 60 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA Z 69 " --> pdb=" O GLU Z 65 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU Z 70 " --> pdb=" O ALA Z 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 49 through 54 Processing helix chain 'a' and resid 74 through 81 Processing helix chain 'b' and resid 12 through 19 removed outlier: 3.591A pdb=" N LEU b 17 " --> pdb=" O VAL b 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 33 through 37 removed outlier: 3.727A pdb=" N LEU d 37 " --> pdb=" O GLN d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 47 removed outlier: 3.558A pdb=" N GLU d 46 " --> pdb=" O ARG d 42 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG d 47 " --> pdb=" O CYS d 43 " (cutoff:3.500A) Processing helix chain 'e' and resid 12 through 17 removed outlier: 3.794A pdb=" N SER e 16 " --> pdb=" O GLY e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 44 removed outlier: 3.643A pdb=" N LEU e 36 " --> pdb=" O GLY e 32 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 23 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 4.273A pdb=" N VAL A 46 " --> pdb=" O PHE A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 73 removed outlier: 7.403A pdb=" N VAL A 72 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N CYS A 142 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 158 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA A 144 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 66 removed outlier: 5.394A pdb=" N ARG B 84 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE B 96 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE B 86 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR B 94 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 12.179A pdb=" N GLN B 95 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 11.553A pdb=" N LYS B 215 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ALA B 97 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 213 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 130 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.657A pdb=" N PHE B 138 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY B 205 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 103 removed outlier: 3.501A pdb=" N GLY C 129 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 173 through 177 Processing sheet with id=AA8, first strand: chain 'D' and resid 35 through 42 removed outlier: 4.212A pdb=" N GLY D 37 " --> pdb=" O LYS D 52 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR D 47 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE D 88 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE D 49 " --> pdb=" O PHE D 88 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP D 90 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE D 51 " --> pdb=" O ASP D 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 151 through 155 removed outlier: 3.527A pdb=" N SER D 151 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 134 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 210 through 211 removed outlier: 3.637A pdb=" N LYS D 210 " --> pdb=" O ASP R 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 70 through 72 Processing sheet with id=AB3, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.122A pdb=" N ILE E 102 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 147 through 148 removed outlier: 3.799A pdb=" N GLN E 128 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 191 through 193 removed outlier: 3.855A pdb=" N ARG E 191 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 197 through 199 removed outlier: 3.552A pdb=" N LYS E 197 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE E 218 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AB8, first strand: chain 'F' and resid 113 through 115 Processing sheet with id=AB9, first strand: chain 'H' and resid 26 through 31 removed outlier: 3.998A pdb=" N SER H 26 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL H 39 " --> pdb=" O LYS H 28 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL H 37 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN H 68 " --> pdb=" O THR H 36 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 115 through 117 removed outlier: 3.547A pdb=" N GLY H 117 " --> pdb=" O ILE H 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 120 through 122 Processing sheet with id=AC3, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'I' and resid 47 through 48 removed outlier: 3.816A pdb=" N GLY I 51 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 62 through 67 removed outlier: 4.222A pdb=" N ASN I 80 " --> pdb=" O SER I 103 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL I 101 " --> pdb=" O THR I 82 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER I 100 " --> pdb=" O ILE I 166 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 132 through 133 Processing sheet with id=AC7, first strand: chain 'K' and resid 20 through 24 removed outlier: 3.791A pdb=" N LEU K 21 " --> pdb=" O TYR K 65 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 68 through 73 removed outlier: 16.692A pdb=" N VAL L 68 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 14.284A pdb=" N LEU L 89 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N ARG L 70 " --> pdb=" O ASP L 87 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP L 87 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL L 72 " --> pdb=" O ARG L 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG L 97 " --> pdb=" O ILE L 92 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE L 135 " --> pdb=" O PRO L 106 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL L 137 " --> pdb=" O ALA L 124 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA L 124 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS L 139 " --> pdb=" O THR L 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 34 through 39 Processing sheet with id=AD1, first strand: chain 'O' and resid 35 through 38 removed outlier: 6.456A pdb=" N VAL O 35 " --> pdb=" O GLY O 100 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS O 102 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY O 37 " --> pdb=" O HIS O 102 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS O 104 " --> pdb=" O GLY O 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 35 through 38 removed outlier: 6.456A pdb=" N VAL O 35 " --> pdb=" O GLY O 100 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS O 102 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY O 37 " --> pdb=" O HIS O 102 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS O 104 " --> pdb=" O GLY O 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 75 through 77 removed outlier: 3.563A pdb=" N TYR P 96 " --> pdb=" O THR P 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 4 through 8 removed outlier: 3.529A pdb=" N VAL Q 4 " --> pdb=" O CYS Q 19 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU Q 25 " --> pdb=" O ILE Q 62 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL Q 64 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS Q 27 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL Q 66 " --> pdb=" O LYS Q 27 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 16 through 17 removed outlier: 3.610A pdb=" N THR S 20 " --> pdb=" O MET S 17 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 76 through 77 removed outlier: 3.526A pdb=" N LYS T 121 " --> pdb=" O GLN T 128 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 88 through 89 Processing sheet with id=AD8, first strand: chain 'U' and resid 60 through 67 removed outlier: 5.788A pdb=" N LYS U 90 " --> pdb=" O PRO U 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU U 86 " --> pdb=" O LEU U 65 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 94 through 95 removed outlier: 3.510A pdb=" N LYS d 54 " --> pdb=" O GLU U 85 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 32 through 33 Processing sheet with id=AE2, first strand: chain 'V' and resid 36 through 40 removed outlier: 7.192A pdb=" N ILE V 36 " --> pdb=" O GLU V 48 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU V 48 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LYS V 38 " --> pdb=" O THR V 46 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR V 46 " --> pdb=" O LYS V 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 24 through 27 removed outlier: 3.501A pdb=" N VAL W 25 " --> pdb=" O ILE W 63 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 71 through 73 removed outlier: 3.748A pdb=" N VAL W 73 " --> pdb=" O MET W 128 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET W 128 " --> pdb=" O VAL W 73 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 80 through 81 removed outlier: 3.574A pdb=" N LYS W 124 " --> pdb=" O SER W 105 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 47 through 56 removed outlier: 7.137A pdb=" N ARG X 72 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS X 55 " --> pdb=" O ALA X 70 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA X 70 " --> pdb=" O LYS X 55 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N PHE X 121 " --> pdb=" O THR X 83 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU X 102 " --> pdb=" O ILE X 124 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL X 126 " --> pdb=" O ARG X 100 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ARG X 100 " --> pdb=" O VAL X 126 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 7 through 14 removed outlier: 5.874A pdb=" N ILE Y 8 " --> pdb=" O ASP Y 25 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP Y 25 " --> pdb=" O ILE Y 8 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS Y 10 " --> pdb=" O VAL Y 23 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL Y 23 " --> pdb=" O LYS Y 10 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE Y 71 " --> pdb=" O GLY Y 58 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY Y 58 " --> pdb=" O PHE Y 71 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE Y 73 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE Y 56 " --> pdb=" O PHE Y 73 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N TYR Y 75 " --> pdb=" O VAL Y 54 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL Y 54 " --> pdb=" O TYR Y 75 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 44 through 45 removed outlier: 7.055A pdb=" N CYS Z 84 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AF1, first strand: chain 'a' and resid 37 through 43 Processing sheet with id=AF2, first strand: chain 'b' and resid 33 through 36 Processing sheet with id=AF3, first strand: chain 'b' and resid 65 through 66 Processing sheet with id=AF4, first strand: chain 'c' and resid 40 through 45 removed outlier: 3.863A pdb=" N GLY c 18 " --> pdb=" O GLN c 28 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG c 30 " --> pdb=" O VAL c 16 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL c 16 " --> pdb=" O ARG c 30 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLU c 32 " --> pdb=" O LYS c 14 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS c 14 " --> pdb=" O GLU c 32 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'd' and resid 31 through 32 removed outlier: 3.602A pdb=" N ILE d 39 " --> pdb=" O ILE d 32 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 24 through 29 removed outlier: 7.246A pdb=" N GLU g 331 " --> pdb=" O PRO g 25 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA g 27 " --> pdb=" O ALA g 329 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS g 308 " --> pdb=" O GLY g 321 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'g' and resid 36 through 41 removed outlier: 3.850A pdb=" N SER g 38 " --> pdb=" O ALA g 51 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU g 48 " --> pdb=" O TRP g 60 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER g 50 " --> pdb=" O LEU g 58 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU g 58 " --> pdb=" O SER g 50 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA g 57 " --> pdb=" O ARG g 75 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG g 75 " --> pdb=" O ALA g 57 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL g 59 " --> pdb=" O PHE g 73 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TRP g 69 " --> pdb=" O ASN g 63 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 83 through 87 removed outlier: 3.601A pdb=" N ASP g 85 " --> pdb=" O SER g 98 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU g 95 " --> pdb=" O TRP g 107 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU g 104 " --> pdb=" O LEU g 117 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU g 117 " --> pdb=" O LEU g 104 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU g 106 " --> pdb=" O LYS g 115 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP g 108 " --> pdb=" O THR g 113 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N THR g 113 " --> pdb=" O ASP g 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 125 through 127 removed outlier: 4.248A pdb=" N GLY g 141 " --> pdb=" O GLN g 145 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN g 145 " --> pdb=" O GLY g 141 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL g 146 " --> pdb=" O GLU g 158 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU g 158 " --> pdb=" O VAL g 146 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE g 148 " --> pdb=" O LYS g 156 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 165 through 170 removed outlier: 3.711A pdb=" N SER g 167 " --> pdb=" O GLY g 185 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS g 204 " --> pdb=" O ILE g 193 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 215 through 218 removed outlier: 3.650A pdb=" N SER g 215 " --> pdb=" O GLY g 228 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY g 228 " --> pdb=" O SER g 215 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE g 246 " --> pdb=" O MET g 236 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU g 238 " --> pdb=" O LYS g 244 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS g 244 " --> pdb=" O LEU g 238 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 257 through 259 removed outlier: 3.613A pdb=" N CYS g 267 " --> pdb=" O ALA g 258 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA g 268 " --> pdb=" O ALA g 275 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL g 276 " --> pdb=" O ILE g 285 " (cutoff:3.500A) 1130 hydrogen bonds defined for protein. 3183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 858 hydrogen bonds 1420 hydrogen bond angles 0 basepair planarities 367 basepair parallelities 759 stacking parallelities Total time for adding SS restraints: 37.76 Time building geometry restraints manager: 27.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13413 1.33 - 1.46: 23740 1.46 - 1.58: 29896 1.58 - 1.71: 2962 1.71 - 1.83: 243 Bond restraints: 70254 Sorted by residual: bond pdb=" C ASP Q 117 " pdb=" N PRO Q 118 " ideal model delta sigma weight residual 1.332 1.386 -0.054 8.90e-03 1.26e+04 3.66e+01 bond pdb=" CA VAL R 93 " pdb=" CB VAL R 93 " ideal model delta sigma weight residual 1.534 1.570 -0.036 6.80e-03 2.16e+04 2.75e+01 bond pdb=" C THR H 81 " pdb=" N PRO H 82 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.20e-02 6.94e+03 2.41e+01 bond pdb=" C LEU K 81 " pdb=" N PRO K 82 " ideal model delta sigma weight residual 1.330 1.388 -0.058 1.22e-02 6.72e+03 2.30e+01 bond pdb=" C ALA g 171 " pdb=" N PRO g 172 " ideal model delta sigma weight residual 1.330 1.388 -0.058 1.22e-02 6.72e+03 2.22e+01 ... (remaining 70249 not shown) Histogram of bond angle deviations from ideal: 98.87 - 106.85: 9855 106.85 - 114.83: 43684 114.83 - 122.80: 35483 122.80 - 130.78: 12497 130.78 - 138.76: 572 Bond angle restraints: 102091 Sorted by residual: angle pdb=" N VAL Q 115 " pdb=" CA VAL Q 115 " pdb=" C VAL Q 115 " ideal model delta sigma weight residual 110.72 122.23 -11.51 1.01e+00 9.80e-01 1.30e+02 angle pdb=" C4' A 2 92 " pdb=" C3' A 2 92 " pdb=" O3' A 2 92 " ideal model delta sigma weight residual 109.40 122.64 -13.24 1.50e+00 4.44e-01 7.79e+01 angle pdb=" N VAL M 18 " pdb=" CA VAL M 18 " pdb=" C VAL M 18 " ideal model delta sigma weight residual 108.35 119.56 -11.21 1.32e+00 5.74e-01 7.22e+01 angle pdb=" C4' G 21374 " pdb=" C3' G 21374 " pdb=" O3' G 21374 " ideal model delta sigma weight residual 109.40 121.92 -12.52 1.50e+00 4.44e-01 6.97e+01 angle pdb=" N HIS F 31 " pdb=" CA HIS F 31 " pdb=" C HIS F 31 " ideal model delta sigma weight residual 109.62 121.71 -12.09 1.50e+00 4.44e-01 6.50e+01 ... (remaining 102086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 37353 35.82 - 71.63: 1514 71.63 - 107.45: 135 107.45 - 143.27: 9 143.27 - 179.08: 44 Dihedral angle restraints: 39055 sinusoidal: 26480 harmonic: 12575 Sorted by residual: dihedral pdb=" O4' U 2 684 " pdb=" C1' U 2 684 " pdb=" N1 U 2 684 " pdb=" C2 U 2 684 " ideal model delta sinusoidal sigma weight residual -160.00 14.37 -174.37 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U 2 615 " pdb=" C1' U 2 615 " pdb=" N1 U 2 615 " pdb=" C2 U 2 615 " ideal model delta sinusoidal sigma weight residual 200.00 29.10 170.90 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U 21174 " pdb=" C1' U 21174 " pdb=" N1 U 21174 " pdb=" C2 U 21174 " ideal model delta sinusoidal sigma weight residual 200.00 34.39 165.61 1 1.50e+01 4.44e-03 8.40e+01 ... (remaining 39052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 10486 0.128 - 0.256: 2177 0.256 - 0.383: 44 0.383 - 0.511: 7 0.511 - 0.639: 6 Chirality restraints: 12720 Sorted by residual: chirality pdb=" C3' G 21374 " pdb=" C4' G 21374 " pdb=" O3' G 21374 " pdb=" C2' G 21374 " both_signs ideal model delta sigma weight residual False -2.74 -2.11 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C3' A 21150 " pdb=" C4' A 21150 " pdb=" O3' A 21150 " pdb=" C2' A 21150 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.57 2.00e-01 2.50e+01 8.02e+00 chirality pdb=" C3' G 2 24 " pdb=" C4' G 2 24 " pdb=" O3' G 2 24 " pdb=" C2' G 2 24 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.56 2.00e-01 2.50e+01 7.94e+00 ... (remaining 12717 not shown) Planarity restraints: 7439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 16 " -0.062 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO H 17 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO H 17 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO H 17 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU Q 114 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C LEU Q 114 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU Q 114 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL Q 115 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 26 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C ASP F 26 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP F 26 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR F 27 " -0.016 2.00e-02 2.50e+03 ... (remaining 7436 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 18 1.87 - 2.63: 1121 2.63 - 3.39: 78394 3.39 - 4.14: 185475 4.14 - 4.90: 285375 Nonbonded interactions: 550383 Sorted by model distance: nonbonded pdb=" NH1 ARG O 129 " pdb=" NH2 ARG c 39 " model vdw 1.113 3.200 nonbonded pdb=" CE1 PHE S 11 " pdb=" CD1 ILE Z 25 " model vdw 1.205 3.760 nonbonded pdb=" O TYR P 14 " pdb=" O ARG S 92 " model vdw 1.235 3.040 nonbonded pdb=" CE1 HIS g 32 " pdb=" OG SER g 52 " model vdw 1.388 3.260 nonbonded pdb=" OP1 A 21154 " pdb=" O ARG U 55 " model vdw 1.460 3.040 ... (remaining 550378 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 1490 5.49 5 S 159 5.16 5 C 35713 2.51 5 N 12093 2.21 5 O 16469 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 11.980 Check model and map are aligned: 0.880 Process input model: 162.100 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.460 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 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 : 0.007 0.070 70254 Z= 0.427 Angle : 1.113 16.884 102091 Z= 0.745 Chirality : 0.091 0.639 12720 Planarity : 0.004 0.095 7439 Dihedral : 18.001 179.084 30888 Min Nonbonded Distance : 1.113 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 2.71 % Allowed : 8.28 % Favored : 89.01 % Rotamer Outliers : 5.14 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % 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: -3.65 (0.11), residues: 4250 helix: -2.23 (0.12), residues: 1268 sheet: -2.55 (0.18), residues: 651 loop : -2.52 (0.11), residues: 2331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1674 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1491 time to evaluate : 3.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 183 outliers final: 64 residues processed: 1595 average time/residue: 0.7300 time to fit residues: 1871.7012 Evaluate side-chains 1052 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 988 time to evaluate : 3.913 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.5066 time to fit residues: 64.9651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 483 optimal weight: 0.7980 chunk 433 optimal weight: 0.8980 chunk 240 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 292 optimal weight: 0.2980 chunk 231 optimal weight: 0.0980 chunk 448 optimal weight: 0.9990 chunk 173 optimal weight: 0.7980 chunk 272 optimal weight: 0.9990 chunk 333 optimal weight: 0.8980 chunk 519 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN A 139 ASN B 38 HIS B 59 ASN ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS C 73 HIS C 102 GLN C 167 HIS C 218 HIS C 224 ASN F 31 HIS F 63 ASN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN H 84 HIS I 11 HIS I 18 GLN I 52 ASN J 100 ASN J 112 HIS J 131 HIS ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 GLN K 62 HIS K 84 ASN L 13 GLN N 5 HIS O 40 HIS O 73 GLN O 87 GLN P 105 GLN R 83 ASN S 99 HIS T 134 GLN U 42 ASN U 115 HIS Y 7 HIS Y 88 HIS Z 80 HIS a 17 HIS b 20 ASN b 50 HIS b 52 ASN ** c 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 32 HIS g 46 ASN g 94 HIS g 150 ASN g 155 ASN g 289 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 70254 Z= 0.186 Angle : 0.700 17.886 102091 Z= 0.362 Chirality : 0.041 0.362 12720 Planarity : 0.005 0.056 7439 Dihedral : 15.902 179.568 22621 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 1.39 % Allowed : 6.33 % Favored : 92.28 % Rotamer Outliers : 5.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.52 (0.11), residues: 4250 helix: -0.85 (0.13), residues: 1350 sheet: -1.75 (0.18), residues: 721 loop : -2.19 (0.12), residues: 2179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1329 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1138 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 191 outliers final: 93 residues processed: 1232 average time/residue: 0.6845 time to fit residues: 1395.4661 Evaluate side-chains 1064 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 971 time to evaluate : 3.948 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 0 residues processed: 93 average time/residue: 0.5040 time to fit residues: 92.7514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 288 optimal weight: 0.0470 chunk 161 optimal weight: 0.0570 chunk 432 optimal weight: 6.9990 chunk 353 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 520 optimal weight: 7.9990 chunk 562 optimal weight: 7.9990 chunk 463 optimal weight: 5.9990 chunk 516 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 417 optimal weight: 3.9990 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN D 75 GLN D 101 ASN E 112 HIS E 127 ASN E 128 GLN H 10 ASN ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 HIS J 100 ASN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 134 HIS N 101 HIS O 87 GLN ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 85 HIS T 99 HIS T 134 GLN V 2 GLN W 70 ASN ** W 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS X 78 ASN X 98 ASN c 28 GLN ** g 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 94 HIS g 155 ASN g 263 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.090 70254 Z= 0.334 Angle : 0.737 19.347 102091 Z= 0.377 Chirality : 0.043 0.305 12720 Planarity : 0.006 0.058 7439 Dihedral : 15.770 179.454 22621 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 1.18 % Allowed : 7.84 % Favored : 90.99 % Rotamer Outliers : 5.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.12), residues: 4250 helix: -0.46 (0.13), residues: 1370 sheet: -1.50 (0.17), residues: 745 loop : -2.15 (0.12), residues: 2135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1051 time to evaluate : 3.999 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: 180 outliers final: 102 residues processed: 1152 average time/residue: 0.6822 time to fit residues: 1305.0262 Evaluate side-chains 1044 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 942 time to evaluate : 3.957 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 0 residues processed: 102 average time/residue: 0.4866 time to fit residues: 99.2550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 514 optimal weight: 0.0980 chunk 391 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 349 optimal weight: 6.9990 chunk 522 optimal weight: 0.9990 chunk 552 optimal weight: 0.9990 chunk 272 optimal weight: 6.9990 chunk 494 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN B 72 ASN B 155 HIS C 109 GLN F 106 GLN H 51 GLN H 121 HIS I 11 HIS I 94 ASN J 100 ASN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN K 84 ASN N 78 ASN ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 67 HIS S 34 ASN ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 99 HIS V 87 HIS W 56 HIS a 7 ASN a 14 ASN c 15 GLN ** e 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 70254 Z= 0.193 Angle : 0.634 18.424 102091 Z= 0.325 Chirality : 0.038 0.287 12720 Planarity : 0.005 0.094 7439 Dihedral : 15.509 179.855 22621 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 1.11 % Allowed : 6.99 % Favored : 91.91 % Rotamer Outliers : 3.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.12), residues: 4250 helix: -0.12 (0.14), residues: 1384 sheet: -1.13 (0.17), residues: 782 loop : -1.99 (0.12), residues: 2084 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1046 time to evaluate : 4.006 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: 130 outliers final: 63 residues processed: 1114 average time/residue: 0.6738 time to fit residues: 1253.0808 Evaluate side-chains 1023 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 960 time to evaluate : 3.945 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.4912 time to fit residues: 64.1745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 460 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 411 optimal weight: 2.9990 chunk 228 optimal weight: 0.0870 chunk 471 optimal weight: 5.9990 chunk 382 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 496 optimal weight: 9.9990 chunk 139 optimal weight: 9.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 GLN C 263 HIS E 201 GLN F 63 ASN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 HIS I 94 ASN J 100 ASN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN K 43 GLN L 139 HIS N 78 ASN P 113 HIS S 34 ASN ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 GLN T 99 HIS T 134 GLN a 7 ASN c 15 GLN ** e 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 HIS ** g 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 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 0.098 70254 Z= 0.389 Angle : 0.758 18.883 102091 Z= 0.384 Chirality : 0.043 0.305 12720 Planarity : 0.006 0.056 7439 Dihedral : 15.728 179.921 22621 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 1.11 % Allowed : 8.66 % Favored : 90.24 % Rotamer Outliers : 5.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.12), residues: 4250 helix: -0.29 (0.14), residues: 1384 sheet: -1.10 (0.18), residues: 785 loop : -2.09 (0.12), residues: 2081 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1196 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1007 time to evaluate : 3.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 189 outliers final: 112 residues processed: 1112 average time/residue: 0.6793 time to fit residues: 1257.5606 Evaluate side-chains 1069 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 957 time to evaluate : 3.961 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 0 residues processed: 112 average time/residue: 0.5321 time to fit residues: 115.1242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 186 optimal weight: 0.0870 chunk 497 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 324 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 553 optimal weight: 5.9990 chunk 459 optimal weight: 0.9990 chunk 256 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 183 optimal weight: 0.8980 chunk 290 optimal weight: 0.8980 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS B 223 GLN C 125 HIS F 64 HIS I 11 HIS J 27 GLN J 89 GLN J 100 ASN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 ASN ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 HIS S 97 ASN T 70 GLN T 74 HIS T 99 HIS V 35 GLN a 7 ASN a 14 ASN c 28 GLN ** e 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 70254 Z= 0.160 Angle : 0.616 18.173 102091 Z= 0.313 Chirality : 0.036 0.262 12720 Planarity : 0.004 0.055 7439 Dihedral : 15.389 179.940 22621 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 1.08 % Allowed : 6.94 % Favored : 91.98 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.12), residues: 4250 helix: 0.08 (0.14), residues: 1386 sheet: -0.85 (0.18), residues: 772 loop : -1.98 (0.12), residues: 2092 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1118 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1040 time to evaluate : 3.947 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: 78 outliers final: 43 residues processed: 1076 average time/residue: 0.6778 time to fit residues: 1217.9955 Evaluate side-chains 1004 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 961 time to evaluate : 4.072 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4959 time to fit residues: 45.2758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 533 optimal weight: 0.0970 chunk 62 optimal weight: 5.9990 chunk 315 optimal weight: 0.9980 chunk 404 optimal weight: 4.9990 chunk 313 optimal weight: 0.8980 chunk 465 optimal weight: 0.8980 chunk 309 optimal weight: 0.0470 chunk 551 optimal weight: 3.9990 chunk 345 optimal weight: 4.9990 chunk 336 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN E 201 GLN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN I 11 HIS I 52 ASN J 100 ASN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 78 ASN ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 HIS Q 91 GLN S 97 ASN a 7 ASN a 14 ASN c 28 GLN ** g 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.051 70254 Z= 0.146 Angle : 0.587 18.086 102091 Z= 0.297 Chirality : 0.035 0.255 12720 Planarity : 0.004 0.052 7439 Dihedral : 15.187 179.725 22621 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 1.06 % Allowed : 7.41 % Favored : 91.53 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.12), residues: 4250 helix: 0.28 (0.14), residues: 1387 sheet: -0.59 (0.19), residues: 753 loop : -1.88 (0.12), residues: 2110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1026 time to evaluate : 4.026 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: 69 outliers final: 40 residues processed: 1057 average time/residue: 0.6778 time to fit residues: 1196.3689 Evaluate side-chains 1011 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 971 time to evaluate : 4.982 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.5589 time to fit residues: 45.0956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 341 optimal weight: 0.9990 chunk 220 optimal weight: 1.9990 chunk 329 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 350 optimal weight: 40.0000 chunk 375 optimal weight: 0.2980 chunk 272 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 433 optimal weight: 4.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN E 188 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN I 11 HIS ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN J 100 ASN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 HIS Q 91 GLN ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 23 ASN T 28 HIS T 99 HIS X 27 ASN a 7 ASN ** a 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 GLN c 28 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 70254 Z= 0.266 Angle : 0.663 18.461 102091 Z= 0.334 Chirality : 0.038 0.275 12720 Planarity : 0.005 0.053 7439 Dihedral : 15.310 179.713 22621 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 1.08 % Allowed : 8.00 % Favored : 90.92 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.12), residues: 4250 helix: 0.20 (0.14), residues: 1393 sheet: -0.68 (0.19), residues: 774 loop : -1.90 (0.13), residues: 2083 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 969 time to evaluate : 4.021 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: 83 outliers final: 59 residues processed: 1004 average time/residue: 0.7206 time to fit residues: 1211.3364 Evaluate side-chains 995 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 936 time to evaluate : 3.901 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.4860 time to fit residues: 59.7992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 501 optimal weight: 0.8980 chunk 528 optimal weight: 1.9990 chunk 481 optimal weight: 9.9990 chunk 513 optimal weight: 0.9990 chunk 309 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 chunk 403 optimal weight: 0.6980 chunk 157 optimal weight: 4.9990 chunk 464 optimal weight: 2.9990 chunk 485 optimal weight: 0.0980 chunk 511 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS D 42 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN I 11 HIS J 100 ASN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 113 HIS T 99 HIS X 27 ASN Z 41 ASN a 7 ASN c 28 GLN e 41 ASN ** g 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 284 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.070 70254 Z= 0.155 Angle : 0.605 18.363 102091 Z= 0.304 Chirality : 0.035 0.259 12720 Planarity : 0.004 0.053 7439 Dihedral : 15.188 179.928 22621 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.99 % Allowed : 7.34 % Favored : 91.67 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 4250 helix: 0.39 (0.14), residues: 1382 sheet: -0.55 (0.19), residues: 752 loop : -1.82 (0.12), residues: 2116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1010 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 979 time to evaluate : 4.027 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: 31 outliers final: 18 residues processed: 991 average time/residue: 0.6777 time to fit residues: 1124.2967 Evaluate side-chains 963 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 945 time to evaluate : 3.922 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.5161 time to fit residues: 22.1684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 337 optimal weight: 0.3980 chunk 543 optimal weight: 0.5980 chunk 331 optimal weight: 3.9990 chunk 257 optimal weight: 0.0970 chunk 377 optimal weight: 0.7980 chunk 569 optimal weight: 0.9980 chunk 524 optimal weight: 4.9990 chunk 453 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 350 optimal weight: 40.0000 chunk 278 optimal weight: 0.0270 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN B 38 HIS D 42 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN J 100 ASN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 ASN a 7 ASN e 41 ASN g 145 GLN g 160 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 70254 Z= 0.140 Angle : 0.586 18.116 102091 Z= 0.293 Chirality : 0.034 0.260 12720 Planarity : 0.004 0.062 7439 Dihedral : 15.059 179.802 22621 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.96 % Allowed : 7.29 % Favored : 91.74 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 4250 helix: 0.54 (0.14), residues: 1375 sheet: -0.44 (0.19), residues: 740 loop : -1.76 (0.13), residues: 2135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 988 time to evaluate : 4.035 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: 9 outliers final: 6 residues processed: 992 average time/residue: 0.6844 time to fit residues: 1129.8596 Evaluate side-chains 954 residues out of total 3698 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 948 time to evaluate : 3.963 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.5056 time to fit residues: 10.4319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 360 optimal weight: 0.9990 chunk 483 optimal weight: 0.6980 chunk 139 optimal weight: 9.9990 chunk 418 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 454 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 466 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN B 38 HIS D 42 GLN D 75 GLN ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 ASN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN H 75 HIS I 11 HIS J 100 ASN ** J 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 91 ASN P 113 HIS ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 99 HIS Y 28 HIS Z 41 ASN a 7 ASN c 15 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.140570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112173 restraints weight = 110569.524| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.41 r_work: 0.3162 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.082 70254 Z= 0.477 Angle : 0.848 18.781 102091 Z= 0.424 Chirality : 0.046 0.328 12720 Planarity : 0.006 0.103 7439 Dihedral : 15.697 179.925 22621 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.94 % Allowed : 9.11 % Favored : 89.95 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.12), residues: 4250 helix: -0.15 (0.14), residues: 1379 sheet: -0.62 (0.19), residues: 773 loop : -1.96 (0.13), residues: 2098 =============================================================================== Job complete usr+sys time: 18812.82 seconds wall clock time: 328 minutes 59.19 seconds (19739.19 seconds total)