Starting phenix.real_space_refine (version: dev) on Mon Feb 27 15:28:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxu_6780/02_2023/5xxu_6780_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxu_6780/02_2023/5xxu_6780.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/5xxu_6780/02_2023/5xxu_6780.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxu_6780/02_2023/5xxu_6780.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxu_6780/02_2023/5xxu_6780_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxu_6780/02_2023/5xxu_6780_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 ARG 81": "NH1" <-> "NH2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 94": "NH1" <-> "NH2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 99": "NH1" <-> "NH2" Residue "C ARG 103": "NH1" <-> "NH2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 215": "NH1" <-> "NH2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "D TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "E ARG 3": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 198": "NH1" <-> "NH2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 48": "NH1" <-> "NH2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F ARG 134": "NH1" <-> "NH2" Residue "F PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 186": "NH1" <-> "NH2" Residue "G ARG 194": "NH1" <-> "NH2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H ARG 120": "NH1" <-> "NH2" Residue "H ARG 143": "NH1" <-> "NH2" Residue "H PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 7": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I ARG 31": "NH1" <-> "NH2" Residue "I ARG 44": "NH1" <-> "NH2" Residue "I ARG 56": "NH1" <-> "NH2" Residue "I ARG 92": "NH1" <-> "NH2" Residue "I ARG 148": "NH1" <-> "NH2" Residue "I ARG 175": "NH1" <-> "NH2" Residue "I ARG 181": "NH1" <-> "NH2" Residue "I TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 17": "NH1" <-> "NH2" Residue "J ARG 40": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J ARG 79": "NH1" <-> "NH2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 107": "NH1" <-> "NH2" Residue "J ARG 149": "NH1" <-> "NH2" Residue "J TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 168": "NH1" <-> "NH2" Residue "J ARG 174": "NH1" <-> "NH2" Residue "K TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 103": "OE1" <-> "OE2" Residue "L ARG 139": "NH1" <-> "NH2" Residue "L PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 159": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N ARG 106": "NH1" <-> "NH2" Residue "N ARG 124": "NH1" <-> "NH2" Residue "O PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 109": "NH1" <-> "NH2" Residue "O ARG 130": "NH1" <-> "NH2" Residue "O ARG 152": "NH1" <-> "NH2" Residue "P TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 132": "NH1" <-> "NH2" Residue "Q PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "Q ARG 127": "NH1" <-> "NH2" Residue "Q ARG 148": "NH1" <-> "NH2" Residue "R TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 45": "NH1" <-> "NH2" Residue "R ARG 49": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "S ARG 16": "NH1" <-> "NH2" Residue "S ARG 41": "NH1" <-> "NH2" Residue "S ARG 57": "NH1" <-> "NH2" Residue "S PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 123": "NH1" <-> "NH2" Residue "T ARG 15": "NH1" <-> "NH2" Residue "T TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 101": "NH1" <-> "NH2" Residue "T ARG 150": "NH1" <-> "NH2" Residue "U ARG 133": "NH1" <-> "NH2" Residue "V ARG 44": "NH1" <-> "NH2" Residue "V ARG 61": "NH1" <-> "NH2" Residue "V PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 3": "NH1" <-> "NH2" 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 68": "NH1" <-> "NH2" Residue "W PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 117": "NH1" <-> "NH2" Residue "W TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 35": "NH1" <-> "NH2" Residue "X PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 34": "NH1" <-> "NH2" Residue "Y PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 96": "NH1" <-> "NH2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y ARG 117": "NH1" <-> "NH2" Residue "Z ARG 111": "NH1" <-> "NH2" Residue "Z ARG 134": "NH1" <-> "NH2" Residue "a ARG 22": "NH1" <-> "NH2" Residue "a ARG 51": "NH1" <-> "NH2" Residue "a ARG 54": "NH1" <-> "NH2" Residue "a TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 19": "NH1" <-> "NH2" Residue "c ARG 62": "NH1" <-> "NH2" Residue "d PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "m ARG 7": "NH1" <-> "NH2" Residue "m ARG 29": "NH1" <-> "NH2" Residue "m ARG 35": "NH1" <-> "NH2" Residue "m ARG 37": "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: 68955 Number of models: 1 Model: "" Number of chains: 34 Chain: "2" Number of atoms: 34513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1619, 34513 Classifications: {'RNA': 1619} Modifications used: {'rna2p_pur': 141, 'rna2p_pyr': 118, 'rna3p_pur': 717, 'rna3p_pyr': 643} Link IDs: {'rna2p': 258, 'rna3p': 1360} Chain breaks: 16 Chain: "A" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1565 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 12, 'TRANS': 185} Chain: "B" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1691 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 205} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1750 Classifications: {'peptide': 225} Link IDs: {'CIS': 2, 'PTRANS': 14, 'TRANS': 208} Chain: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1568 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 1 Chain: "E" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2085 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 15, 'TRANS': 243} Chain breaks: 1 Chain: "F" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1475 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "G" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1782 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1354 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 2, 'PTRANS': 6, 'TRANS': 168} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "I" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1496 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 2 Chain: "J" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1457 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "K" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 675 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 7, 'TRANS': 86} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "L" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1206 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 141} Chain breaks: 1 Chain: "M" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 508 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain breaks: 2 Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 330 Unresolved non-hydrogen dihedrals: 216 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 123 Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1204 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 139} Chain: "O" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 966 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain breaks: 1 Chain: "P" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 939 Classifications: {'peptide': 115} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 108} Chain breaks: 1 Chain: "Q" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1086 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 131} Chain breaks: 1 Chain: "R" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 111} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1091 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 2, 'TRANS': 132} Chain: "T" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1236 Classifications: {'peptide': 151} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 141} Chain: "U" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 823 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "V" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 618 Classifications: {'peptide': 80} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 76} Chain: "W" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1040 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "X" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1040 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Y" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1020 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "Z" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 576 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "a" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 794 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "b" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 605 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain: "c" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 448 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain breaks: 1 Chain: "d" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 429 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "e" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 391 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 4, 'TRANS': 45} Chain breaks: 1 Chain: "f" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 229 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 42} Chain breaks: 1 Unresolved non-hydrogen bonds: 145 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 86 Chain: "m" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 348 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Time building chain proxies: 29.15, per 1000 atoms: 0.42 Number of scatterers: 68955 At special positions: 0 Unit cell: (229.68, 217.8, 203.28, 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 171 16.00 P 1619 15.00 O 17304 8.00 N 12701 7.00 C 37160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS a 26 " - pdb=" SG CYS a 77 " distance=2.03 Simple disulfide: pdb=" SG CYS d 19 " - pdb=" SG CYS d 37 " distance=2.04 Simple disulfide: pdb=" SG CYS d 37 " - pdb=" SG CYS d 40 " distance=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 27181 O4' U 21430 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.42 Conformation dependent library (CDL) restraints added in 4.9 seconds 8562 Ramachandran restraints generated. 4281 Oldfield, 0 Emsley, 4281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8146 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 46 sheets defined 37.6% alpha, 14.3% beta 371 base pairs and 862 stacking pairs defined. Time for finding SS restraints: 19.75 Creating SS restraints... Processing helix chain 'A' and resid 13 through 23 removed outlier: 3.751A pdb=" N LEU A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS A 23 " --> pdb=" O MET A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 67 removed outlier: 3.536A pdb=" N TRP A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 82 through 95 removed outlier: 4.595A pdb=" N ARG A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.799A pdb=" N VAL A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 4.184A pdb=" N ALA A 173 " --> pdb=" O LYS A 169 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.596A pdb=" N LYS B 27 " --> pdb=" O PHE B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.686A pdb=" N GLY B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 106 through 114 removed outlier: 3.519A pdb=" N ILE B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 179 Processing helix chain 'B' and resid 180 through 189 removed outlier: 3.752A pdb=" N LYS B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.539A pdb=" N LYS B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.506A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU B 230 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 50 removed outlier: 3.508A pdb=" N ARG C 48 " --> pdb=" O GLY C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 62 removed outlier: 4.049A pdb=" N ILE C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 75 removed outlier: 3.737A pdb=" N PHE C 74 " --> pdb=" O ILE C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 removed outlier: 3.539A pdb=" N ALA C 132 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 198 removed outlier: 3.648A pdb=" N ILE C 195 " --> pdb=" O THR C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 232 removed outlier: 3.587A pdb=" N LYS C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TYR C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.717A pdb=" N TRP C 238 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 removed outlier: 3.528A pdb=" N TRP C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 257 removed outlier: 3.693A pdb=" N LEU C 255 " --> pdb=" O TRP C 251 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 31 removed outlier: 3.509A pdb=" N GLN D 20 " --> pdb=" O ASP D 16 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.549A pdb=" N LEU D 61 " --> pdb=" O THR D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 79 removed outlier: 3.622A pdb=" N ARG D 69 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL D 75 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN D 76 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.727A pdb=" N LEU D 98 " --> pdb=" O ASN D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 99 through 114 removed outlier: 3.860A pdb=" N GLN D 103 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 132 removed outlier: 3.503A pdb=" N CYS D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR D 122 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 128 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 132 " --> pdb=" O ILE D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 169 removed outlier: 4.242A pdb=" N LYS D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 19 removed outlier: 3.825A pdb=" N TRP E 18 " --> pdb=" O PRO E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 removed outlier: 3.574A pdb=" N LEU E 48 " --> pdb=" O LEU E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 66 removed outlier: 3.574A pdb=" N VAL E 61 " --> pdb=" O THR E 57 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET E 62 " --> pdb=" O TYR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 135 No H-bonds generated for 'chain 'E' and resid 133 through 135' Processing helix chain 'E' and resid 239 through 243 removed outlier: 4.512A pdb=" N GLY E 243 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 260 removed outlier: 3.508A pdb=" N LEU E 255 " --> pdb=" O ASN E 251 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN E 260 " --> pdb=" O LEU E 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 63 Processing helix chain 'F' and resid 73 through 91 removed outlier: 3.537A pdb=" N ARG F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU F 86 " --> pdb=" O ARG F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 108 removed outlier: 4.542A pdb=" N GLY F 108 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 150 Processing helix chain 'F' and resid 156 through 170 Processing helix chain 'F' and resid 175 through 191 removed outlier: 3.614A pdb=" N ILE F 184 " --> pdb=" O LYS F 180 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA F 190 " --> pdb=" O ARG F 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 25 Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.658A pdb=" N PHE G 145 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 221 removed outlier: 3.616A pdb=" N LYS G 185 " --> pdb=" O ARG G 181 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL G 196 " --> pdb=" O GLN G 192 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE G 197 " --> pdb=" O ARG G 193 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP G 208 " --> pdb=" O LYS G 204 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS G 219 " --> pdb=" O HIS G 215 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS G 220 " --> pdb=" O GLU G 216 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 32 removed outlier: 4.039A pdb=" N PHE H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP H 29 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR H 32 " --> pdb=" O PHE H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 43 removed outlier: 3.943A pdb=" N ARG H 43 " --> pdb=" O LYS H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 80 through 92 Processing helix chain 'H' and resid 105 through 110 removed outlier: 4.514A pdb=" N LYS H 109 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 135 removed outlier: 3.587A pdb=" N LEU H 130 " --> pdb=" O GLN H 126 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER H 135 " --> pdb=" O GLU H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 184 removed outlier: 4.128A pdb=" N GLU H 169 " --> pdb=" O LYS H 165 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLU H 173 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR H 174 " --> pdb=" O ASP H 170 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE H 175 " --> pdb=" O LYS H 171 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA H 176 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA H 177 " --> pdb=" O GLU H 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 87 through 93 removed outlier: 4.012A pdb=" N VAL I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 117 Processing helix chain 'I' and resid 141 through 151 Processing helix chain 'I' and resid 156 through 165 removed outlier: 3.709A pdb=" N ASN I 164 " --> pdb=" O GLU I 160 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR I 165 " --> pdb=" O GLU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 180 Processing helix chain 'I' and resid 189 through 201 removed outlier: 3.721A pdb=" N ARG I 197 " --> pdb=" O MET I 193 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS I 198 " --> pdb=" O PHE I 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 35 removed outlier: 3.716A pdb=" N GLN J 26 " --> pdb=" O GLU J 22 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU J 30 " --> pdb=" O GLN J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 61 removed outlier: 4.106A pdb=" N VAL J 42 " --> pdb=" O ASN J 38 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL J 45 " --> pdb=" O GLU J 41 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE J 52 " --> pdb=" O ALA J 48 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 83 removed outlier: 3.509A pdb=" N PHE J 71 " --> pdb=" O PRO J 67 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR J 74 " --> pdb=" O VAL J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 98 removed outlier: 4.046A pdb=" N LEU J 97 " --> pdb=" O LEU J 93 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY J 98 " --> pdb=" O ASP J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 93 through 98' Processing helix chain 'J' and resid 100 through 106 removed outlier: 3.755A pdb=" N PHE J 104 " --> pdb=" O THR J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 117 Processing helix chain 'J' and resid 121 through 131 removed outlier: 3.534A pdb=" N ARG J 126 " --> pdb=" O ILE J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 180 Processing helix chain 'K' and resid 12 through 27 removed outlier: 3.661A pdb=" N LYS K 17 " --> pdb=" O LYS K 13 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR K 22 " --> pdb=" O ALA K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 59 removed outlier: 3.515A pdb=" N VAL K 50 " --> pdb=" O PRO K 46 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR K 59 " --> pdb=" O ARG K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 89 removed outlier: 3.628A pdb=" N GLU K 82 " --> pdb=" O ASN K 78 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE K 83 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG K 85 " --> pdb=" O ILE K 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 53 removed outlier: 3.960A pdb=" N LYS L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 39 removed outlier: 3.961A pdb=" N VAL M 31 " --> pdb=" O ALA M 27 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS M 33 " --> pdb=" O ARG M 29 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU M 36 " --> pdb=" O LEU M 32 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE M 37 " --> pdb=" O LYS M 33 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N HIS M 38 " --> pdb=" O ASN M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 53 Processing helix chain 'M' and resid 68 through 83 removed outlier: 3.759A pdb=" N HIS M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 99 removed outlier: 3.991A pdb=" N TRP M 98 " --> pdb=" O LEU M 95 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 139 removed outlier: 3.987A pdb=" N ASN M 136 " --> pdb=" O THR M 132 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS M 137 " --> pdb=" O PHE M 133 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS M 139 " --> pdb=" O GLN M 135 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 removed outlier: 3.860A pdb=" N VAL N 33 " --> pdb=" O LYS N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 58 removed outlier: 3.897A pdb=" N GLY N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 67 removed outlier: 3.597A pdb=" N VAL N 66 " --> pdb=" O GLN N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 103 Processing helix chain 'N' and resid 108 through 132 removed outlier: 3.618A pdb=" N ILE N 116 " --> pdb=" O LYS N 112 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG N 131 " --> pdb=" O ARG N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 removed outlier: 3.585A pdb=" N LEU N 149 " --> pdb=" O THR N 145 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL N 150 " --> pdb=" O ALA N 146 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA N 151 " --> pdb=" O SER N 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 145 through 151' Processing helix chain 'O' and resid 63 through 67 Processing helix chain 'O' and resid 75 through 94 removed outlier: 3.731A pdb=" N ASP O 85 " --> pdb=" O MET O 81 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS O 91 " --> pdb=" O ALA O 87 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU O 92 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY O 94 " --> pdb=" O CYS O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 128 removed outlier: 4.220A pdb=" N GLN O 118 " --> pdb=" O GLY O 114 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER O 119 " --> pdb=" O PRO O 115 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA O 125 " --> pdb=" O LEU O 121 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY O 128 " --> pdb=" O LEU O 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 4.541A pdb=" N LEU P 31 " --> pdb=" O LEU P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 39 Processing helix chain 'P' and resid 44 through 53 removed outlier: 3.643A pdb=" N ARG P 48 " --> pdb=" O ALA P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 68 removed outlier: 3.581A pdb=" N LEU P 61 " --> pdb=" O LYS P 57 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS P 63 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG P 66 " --> pdb=" O MET P 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 48 No H-bonds generated for 'chain 'Q' and resid 46 through 48' Processing helix chain 'Q' and resid 49 through 54 removed outlier: 3.573A pdb=" N PHE Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 61 Processing helix chain 'Q' and resid 61 through 66 removed outlier: 4.208A pdb=" N PHE Q 65 " --> pdb=" O GLY Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 101 removed outlier: 3.651A pdb=" N ILE Q 83 " --> pdb=" O TYR Q 79 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA Q 91 " --> pdb=" O ARG Q 87 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN Q 98 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN Q 99 " --> pdb=" O VAL Q 95 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR Q 101 " --> pdb=" O PHE Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 117 removed outlier: 4.207A pdb=" N LYS Q 108 " --> pdb=" O GLU Q 104 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP Q 112 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU Q 114 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 20 removed outlier: 3.643A pdb=" N ALA R 12 " --> pdb=" O THR R 8 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL R 17 " --> pdb=" O ALA R 13 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 39 removed outlier: 3.936A pdb=" N ASN R 31 " --> pdb=" O ASP R 27 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS R 33 " --> pdb=" O GLN R 29 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 64 removed outlier: 3.508A pdb=" N ARG R 47 " --> pdb=" O SER R 43 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN R 48 " --> pdb=" O LYS R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 84 removed outlier: 3.612A pdb=" N ARG R 80 " --> pdb=" O GLU R 76 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE R 84 " --> pdb=" O ARG R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 110 removed outlier: 3.747A pdb=" N ASP R 104 " --> pdb=" O GLN R 100 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU R 106 " --> pdb=" O THR R 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA R 108 " --> pdb=" O ASP R 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 32 Processing helix chain 'S' and resid 33 through 35 No H-bonds generated for 'chain 'S' and resid 33 through 35' Processing helix chain 'S' and resid 39 through 50 Processing helix chain 'S' and resid 62 through 75 Processing helix chain 'S' and resid 103 through 120 removed outlier: 3.551A pdb=" N LEU S 116 " --> pdb=" O ASP S 112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS S 118 " --> pdb=" O GLU S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 130 removed outlier: 3.563A pdb=" N HIS S 127 " --> pdb=" O ARG S 123 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 22 removed outlier: 3.622A pdb=" N ASP T 21 " --> pdb=" O THR T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 23 through 39 removed outlier: 3.502A pdb=" N ILE T 28 " --> pdb=" O ALA T 24 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU T 30 " --> pdb=" O ALA T 26 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN T 33 " --> pdb=" O ALA T 29 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS T 36 " --> pdb=" O ALA T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 49 removed outlier: 4.479A pdb=" N ASP T 48 " --> pdb=" O LYS T 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 80 removed outlier: 3.528A pdb=" N ILE T 68 " --> pdb=" O ASP T 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU T 74 " --> pdb=" O ALA T 70 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR T 78 " --> pdb=" O LEU T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 92 removed outlier: 3.655A pdb=" N LYS T 90 " --> pdb=" O GLY T 86 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE T 92 " --> pdb=" O PHE T 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 124 removed outlier: 3.809A pdb=" N ILE T 113 " --> pdb=" O SER T 109 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE T 116 " --> pdb=" O ILE T 112 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU T 117 " --> pdb=" O ILE T 113 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET T 123 " --> pdb=" O GLN T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 138 through 154 removed outlier: 3.546A pdb=" N ARG T 143 " --> pdb=" O LYS T 139 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE T 148 " --> pdb=" O GLU T 144 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG T 150 " --> pdb=" O ASP T 146 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN T 151 " --> pdb=" O VAL T 147 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA T 153 " --> pdb=" O ALA T 149 " (cutoff:3.500A) Processing helix chain 'U' and resid 143 through 161 removed outlier: 3.521A pdb=" N ARG U 148 " --> pdb=" O LYS U 144 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL U 149 " --> pdb=" O SER U 145 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR U 151 " --> pdb=" O GLU U 147 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE U 154 " --> pdb=" O CYS U 150 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN U 155 " --> pdb=" O THR U 151 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS U 160 " --> pdb=" O GLY U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 208 through 218 removed outlier: 3.789A pdb=" N VAL U 212 " --> pdb=" O PRO U 208 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS U 213 " --> pdb=" O SER U 209 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLN U 214 " --> pdb=" O ASP U 210 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE U 215 " --> pdb=" O VAL U 211 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE U 218 " --> pdb=" O GLN U 214 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 62 removed outlier: 3.933A pdb=" N ARG V 61 " --> pdb=" O ALA V 57 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY V 62 " --> pdb=" O VAL V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 63 through 72 removed outlier: 3.581A pdb=" N CYS V 67 " --> pdb=" O GLU V 63 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG V 70 " --> pdb=" O ALA V 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 5 through 21 removed outlier: 3.713A pdb=" N ASP W 9 " --> pdb=" O ASN W 5 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS W 10 " --> pdb=" O VAL W 6 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS W 12 " --> pdb=" O ALA W 8 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA W 17 " --> pdb=" O THR W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 45 removed outlier: 4.214A pdb=" N ARG W 44 " --> pdb=" O CYS W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 93 removed outlier: 3.543A pdb=" N ASN W 92 " --> pdb=" O GLN W 88 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 removed outlier: 3.781A pdb=" N ARG W 118 " --> pdb=" O GLU W 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 21 removed outlier: 3.504A pdb=" N LEU X 13 " --> pdb=" O THR X 9 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG X 17 " --> pdb=" O LEU X 13 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG X 18 " --> pdb=" O ARG X 14 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 32 removed outlier: 3.712A pdb=" N LYS X 28 " --> pdb=" O ASP X 24 " (cutoff:3.500A) Processing helix chain 'X' and resid 33 through 38 removed outlier: 4.226A pdb=" N LYS X 37 " --> pdb=" O GLY X 33 " (cutoff:3.500A) Processing helix chain 'X' and resid 129 through 136 removed outlier: 3.967A pdb=" N LEU X 133 " --> pdb=" O SER X 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 51 removed outlier: 3.953A pdb=" N GLU Y 44 " --> pdb=" O LYS Y 40 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS Y 45 " --> pdb=" O GLU Y 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 81 through 89 removed outlier: 3.696A pdb=" N ALA Y 85 " --> pdb=" O ASN Y 81 " (cutoff:3.500A) Processing helix chain 'Y' and resid 90 through 98 removed outlier: 3.926A pdb=" N LEU Y 94 " --> pdb=" O ASN Y 90 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG Y 96 " --> pdb=" O PHE Y 92 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU Y 97 " --> pdb=" O ARG Y 93 " (cutoff:3.500A) Processing helix chain 'Y' and resid 107 through 121 removed outlier: 3.593A pdb=" N LYS Y 115 " --> pdb=" O TYR Y 111 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG Y 117 " --> pdb=" O GLU Y 113 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS Y 120 " --> pdb=" O ASN Y 116 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL Y 121 " --> pdb=" O ARG Y 117 " (cutoff:3.500A) Processing helix chain 'Y' and resid 126 through 132 removed outlier: 4.131A pdb=" N SER Y 130 " --> pdb=" O LYS Y 126 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 110 removed outlier: 4.091A pdb=" N LYS Z 102 " --> pdb=" O ALA Z 98 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU Z 104 " --> pdb=" O TYR Z 100 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA Z 105 " --> pdb=" O ASP Z 101 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE Z 107 " --> pdb=" O LEU Z 103 " (cutoff:3.500A) Proline residue: Z 108 - end of helix Processing helix chain 'Z' and resid 114 through 122 removed outlier: 3.977A pdb=" N VAL Z 118 " --> pdb=" O THR Z 114 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N CYS Z 119 " --> pdb=" O PRO Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 125 through 139 removed outlier: 4.004A pdb=" N ALA Z 129 " --> pdb=" O ASN Z 125 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN Z 131 " --> pdb=" O SER Z 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 50 through 57 Processing helix chain 'a' and resid 75 through 82 Processing helix chain 'a' and resid 90 through 94 removed outlier: 3.588A pdb=" N VAL a 94 " --> pdb=" O GLN a 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 16 removed outlier: 3.676A pdb=" N SER b 15 " --> pdb=" O LYS b 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 38 through 44 removed outlier: 4.309A pdb=" N GLU d 43 " --> pdb=" O GLN d 39 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG d 44 " --> pdb=" O CYS d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 49 Processing helix chain 'e' and resid 13 through 18 Processing helix chain 'e' and resid 32 through 45 removed outlier: 3.571A pdb=" N GLN e 38 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG e 43 " --> pdb=" O GLN e 39 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE e 44 " --> pdb=" O PHE e 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 9 removed outlier: 4.419A pdb=" N TYR m 8 " --> pdb=" O ALA m 5 " (cutoff:3.500A) Processing helix chain 'm' and resid 16 through 38 removed outlier: 3.654A pdb=" N LYS m 33 " --> pdb=" O ARG m 29 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N SER m 38 " --> pdb=" O MET m 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.752A pdb=" N LEU A 49 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 removed outlier: 6.384A pdb=" N VAL A 75 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE A 100 " --> pdb=" O VAL A 75 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 77 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 47 removed outlier: 6.971A pdb=" N CYS B 96 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE B 91 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N THR B 98 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU B 89 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N PHE B 100 " --> pdb=" O CYS B 87 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N CYS B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 102 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 44 through 47 Processing sheet with id=AA5, first strand: chain 'B' and resid 120 through 128 removed outlier: 6.213A pdb=" N ILE B 140 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 210 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 85 through 97 removed outlier: 5.314A pdb=" N ASP C 86 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLY C 113 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL C 88 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA C 111 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS C 118 " --> pdb=" O ASP C 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 166 through 169 removed outlier: 7.084A pdb=" N VAL C 187 " --> pdb=" O SER C 206 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N SER C 208 " --> pdb=" O VAL C 187 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 36 through 42 removed outlier: 4.170A pdb=" N GLY D 38 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE D 50 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 152 through 156 removed outlier: 3.792A pdb=" N GLY D 135 " --> pdb=" O MET D 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 10 removed outlier: 4.651A pdb=" N LEU E 9 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AB3, first strand: chain 'E' and resid 70 through 72 removed outlier: 3.626A pdb=" N GLU E 97 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN E 98 " --> pdb=" O ILE E 114 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 137 through 141 removed outlier: 3.663A pdb=" N LYS E 128 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP E 171 " --> pdb=" O ARG E 161 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 217 through 221 removed outlier: 3.540A pdb=" N ILE E 207 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ARG E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ILE E 195 " --> pdb=" O ARG E 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 195 " --> pdb=" O ASN E 179 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASN E 179 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 111 through 115 Processing sheet with id=AB7, first strand: chain 'G' and resid 12 through 17 removed outlier: 3.573A pdb=" N LEU G 5 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU G 109 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL G 108 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY G 55 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN G 110 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 73 through 77 removed outlier: 3.728A pdb=" N LYS G 93 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 50 through 53 removed outlier: 3.558A pdb=" N VAL H 53 " --> pdb=" O ALA H 62 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE H 63 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL H 98 " --> pdb=" O PHE H 63 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL H 65 " --> pdb=" O VAL H 98 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLN H 100 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL H 67 " --> pdb=" O GLN H 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 187 through 188 removed outlier: 6.458A pdb=" N LEU H 154 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASP W 49 " --> pdb=" O GLU W 64 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS W 60 " --> pdb=" O VAL W 53 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 3 through 4 removed outlier: 4.141A pdb=" N ILE I 3 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 43 through 47 Processing sheet with id=AC4, first strand: chain 'I' and resid 62 through 67 removed outlier: 4.268A pdb=" N GLY I 80 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE I 101 " --> pdb=" O VAL I 82 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 135 through 136 removed outlier: 3.735A pdb=" N HIS J 139 " --> pdb=" O VAL J 136 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 28 through 30 removed outlier: 4.255A pdb=" N ILE K 29 " --> pdb=" O TYR K 74 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR K 74 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 72 through 79 removed outlier: 17.551A pdb=" N VAL L 72 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 14.888A pdb=" N LEU L 93 " --> pdb=" O VAL L 72 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N LYS L 74 " --> pdb=" O ASN L 91 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN L 91 " --> pdb=" O LYS L 74 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL L 87 " --> pdb=" O ILE L 78 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE L 140 " --> pdb=" O THR L 110 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR L 127 " --> pdb=" O LEU L 143 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VAL L 145 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE L 125 " --> pdb=" O VAL L 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 41 through 42 removed outlier: 3.637A pdb=" N VAL M 119 " --> pdb=" O PHE M 61 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL M 59 " --> pdb=" O VAL M 121 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 38 through 40 removed outlier: 3.617A pdb=" N VAL O 59 " --> pdb=" O VAL O 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 97 through 102 removed outlier: 3.770A pdb=" N VAL O 100 " --> pdb=" O GLY O 132 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE O 134 " --> pdb=" O VAL O 100 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL O 102 " --> pdb=" O ILE O 134 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP O 136 " --> pdb=" O VAL O 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 81 through 83 removed outlier: 6.499A pdb=" N VAL P 81 " --> pdb=" O GLY P 100 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR P 102 " --> pdb=" O VAL P 81 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N THR P 83 " --> pdb=" O TYR P 102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 11 through 16 removed outlier: 3.721A pdb=" N GLY Q 16 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA Q 23 " --> pdb=" O GLY Q 16 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG Q 35 " --> pdb=" O VAL Q 72 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL Q 74 " --> pdb=" O ARG Q 35 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 94 through 96 removed outlier: 3.512A pdb=" N CYS T 94 " --> pdb=" O SER T 106 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS T 104 " --> pdb=" O GLN T 96 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 126 through 127 removed outlier: 3.613A pdb=" N ARG T 136 " --> pdb=" O GLU T 127 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'U' and resid 165 through 169 removed outlier: 5.796A pdb=" N GLY U 166 " --> pdb=" O ASP U 204 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP U 204 " --> pdb=" O GLY U 166 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU U 227 " --> pdb=" O THR U 137 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 173 through 177 Processing sheet with id=AD8, first strand: chain 'V' and resid 32 through 37 Processing sheet with id=AD9, first strand: chain 'W' and resid 71 through 74 removed outlier: 5.327A pdb=" N ILE W 125 " --> pdb=" O THR W 105 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR W 105 " --> pdb=" O ILE W 125 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET W 111 " --> pdb=" O LEU W 104 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 46 through 47 removed outlier: 6.398A pdb=" N LEU X 101 " --> pdb=" O VAL X 123 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE X 120 " --> pdb=" O THR X 82 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU X 53 " --> pdb=" O ARG X 71 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN X 73 " --> pdb=" O VAL X 51 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL X 51 " --> pdb=" O GLN X 73 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Y' and resid 8 through 17 removed outlier: 4.300A pdb=" N LEU Y 14 " --> pdb=" O GLN Y 24 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN Y 24 " --> pdb=" O LEU Y 14 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR Y 16 " --> pdb=" O ARG Y 22 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ARG Y 22 " --> pdb=" O THR Y 16 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ARG Y 71 " --> pdb=" O THR Y 65 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR Y 65 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER Y 73 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU Y 63 " --> pdb=" O SER Y 73 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 112 through 113 removed outlier: 3.836A pdb=" N LYS Z 143 " --> pdb=" O THR Z 156 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AE5, first strand: chain 'a' and resid 37 through 42 removed outlier: 3.545A pdb=" N ILE a 69 " --> pdb=" O ASN a 40 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'b' and resid 42 through 45 Processing sheet with id=AE7, first strand: chain 'b' and resid 62 through 63 Processing sheet with id=AE8, first strand: chain 'c' and resid 41 through 45 removed outlier: 7.590A pdb=" N GLN c 24 " --> pdb=" O VAL c 12 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL c 12 " --> pdb=" O GLN c 24 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ARG c 26 " --> pdb=" O GLU c 10 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'd' and resid 28 through 29 Processing sheet with id=AF1, first strand: chain 'f' and resid 132 through 133 removed outlier: 3.634A pdb=" N TYR f 140 " --> pdb=" O ALA f 133 " (cutoff:3.500A) 1166 hydrogen bonds defined for protein. 3345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 867 hydrogen bonds 1422 hydrogen bond angles 0 basepair planarities 371 basepair parallelities 862 stacking parallelities Total time for adding SS restraints: 49.00 Time building geometry restraints manager: 31.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.56: 70095 1.56 - 1.91: 3495 1.91 - 2.26: 0 2.26 - 2.60: 0 2.60 - 2.95: 1 Bond restraints: 73591 Sorted by residual: bond pdb=" C SER H 135 " pdb=" N THR H 137 " ideal model delta sigma weight residual 1.329 2.950 -1.621 1.40e-02 5.10e+03 1.34e+04 bond pdb=" C ILE B 189 " pdb=" N PRO B 190 " ideal model delta sigma weight residual 1.332 1.387 -0.055 8.90e-03 1.26e+04 3.80e+01 bond pdb=" C LEU K 90 " pdb=" N PRO K 91 " ideal model delta sigma weight residual 1.329 1.391 -0.062 1.18e-02 7.18e+03 2.74e+01 bond pdb=" C VAL H 55 " pdb=" N PRO H 56 " ideal model delta sigma weight residual 1.331 1.392 -0.061 1.20e-02 6.94e+03 2.55e+01 bond pdb=" C MET C 92 " pdb=" N PRO C 93 " ideal model delta sigma weight residual 1.334 1.388 -0.054 1.11e-02 8.12e+03 2.39e+01 ... (remaining 73586 not shown) Histogram of bond angle deviations from ideal: 41.02 - 65.05: 1 65.05 - 89.07: 0 89.07 - 113.10: 49408 113.10 - 137.13: 57613 137.13 - 161.15: 30 Bond angle restraints: 107052 Sorted by residual: angle pdb=" O SER H 135 " pdb=" C SER H 135 " pdb=" N THR H 137 " ideal model delta sigma weight residual 122.59 41.02 81.57 1.33e+00 5.65e-01 3.76e+03 angle pdb=" CA SER H 135 " pdb=" C SER H 135 " pdb=" N THR H 137 " ideal model delta sigma weight residual 116.84 161.15 -44.31 1.71e+00 3.42e-01 6.71e+02 angle pdb=" N ILE X 94 " pdb=" CA ILE X 94 " pdb=" C ILE X 94 " ideal model delta sigma weight residual 110.42 120.02 -9.60 9.60e-01 1.09e+00 1.00e+02 angle pdb=" N ALA a 35 " pdb=" CA ALA a 35 " pdb=" C ALA a 35 " ideal model delta sigma weight residual 111.28 120.91 -9.63 1.09e+00 8.42e-01 7.80e+01 angle pdb=" N THR H 75 " pdb=" CA THR H 75 " pdb=" C THR H 75 " ideal model delta sigma weight residual 111.28 120.89 -9.61 1.09e+00 8.42e-01 7.78e+01 ... (remaining 107047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 39364 35.95 - 71.91: 1527 71.91 - 107.86: 125 107.86 - 143.81: 17 143.81 - 179.77: 56 Dihedral angle restraints: 41089 sinusoidal: 28500 harmonic: 12589 Sorted by residual: dihedral pdb=" O4' U 2 827 " pdb=" C1' U 2 827 " pdb=" N1 U 2 827 " pdb=" C2 U 2 827 " ideal model delta sinusoidal sigma weight residual -160.00 18.34 -178.34 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 764 " pdb=" C1' U 2 764 " pdb=" N1 U 2 764 " pdb=" C2 U 2 764 " ideal model delta sinusoidal sigma weight residual -160.00 18.18 -178.18 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 21151 " pdb=" C1' C 21151 " pdb=" N1 C 21151 " pdb=" C2 C 21151 " ideal model delta sinusoidal sigma weight residual 200.00 24.27 175.73 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 41086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 10767 0.117 - 0.234: 2464 0.234 - 0.351: 65 0.351 - 0.468: 7 0.468 - 0.585: 9 Chirality restraints: 13312 Sorted by residual: chirality pdb=" C3' A 2 541 " pdb=" C4' A 2 541 " pdb=" O3' A 2 541 " pdb=" C2' A 2 541 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.59 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" C3' A 2 135 " pdb=" C4' A 2 135 " pdb=" O3' A 2 135 " pdb=" C2' A 2 135 " both_signs ideal model delta sigma weight residual False -2.74 -2.16 -0.58 2.00e-01 2.50e+01 8.53e+00 chirality pdb=" C3' U 2 154 " pdb=" C4' U 2 154 " pdb=" O3' U 2 154 " pdb=" C2' U 2 154 " both_signs ideal model delta sigma weight residual False -2.74 -2.17 -0.58 2.00e-01 2.50e+01 8.36e+00 ... (remaining 13309 not shown) Planarity restraints: 7623 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER H 135 " -0.061 2.00e-02 2.50e+03 5.26e-02 2.76e+01 pdb=" C SER H 135 " 0.067 2.00e-02 2.50e+03 pdb=" O SER H 135 " 0.035 2.00e-02 2.50e+03 pdb=" N THR H 137 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY E 34 " -0.083 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO E 35 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO E 35 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO E 35 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 116 " -0.081 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO H 117 " 0.215 5.00e-02 4.00e+02 pdb=" CA PRO H 117 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO H 117 " -0.065 5.00e-02 4.00e+02 ... (remaining 7620 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 62 2.03 - 2.75: 6789 2.75 - 3.47: 88075 3.47 - 4.18: 194333 4.18 - 4.90: 285456 Nonbonded interactions: 574715 Sorted by model distance: nonbonded pdb=" O2' G 2 80 " pdb=" O5' C 2 81 " model vdw 1.315 2.440 nonbonded pdb=" O ILE X 94 " pdb=" OD2 ASP X 98 " model vdw 1.415 3.040 nonbonded pdb=" NZ LYS B 27 " pdb=" OE2 GLU O 56 " model vdw 1.464 2.520 nonbonded pdb=" O2' C 2 693 " pdb=" CE LYS H 111 " model vdw 1.465 3.440 nonbonded pdb=" O HIS J 155 " pdb=" OD1 ASP J 157 " model vdw 1.530 3.040 ... (remaining 574710 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 1619 5.49 5 S 171 5.16 5 C 37160 2.51 5 N 12701 2.21 5 O 17304 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: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 11.330 Check model and map are aligned: 0.780 Process input model: 181.180 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.480 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:2.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 199.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 : 0.009 1.621 73591 Z= 0.648 Angle : 1.107 81.567 107052 Z= 0.744 Chirality : 0.091 0.585 13312 Planarity : 0.004 0.127 7623 Dihedral : 17.753 179.765 32934 Min Nonbonded Distance : 1.315 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 2.62 % Allowed : 6.96 % Favored : 90.42 % Rotamer Outliers : 3.58 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -3.13 (0.11), residues: 4281 helix: -1.87 (0.12), residues: 1328 sheet: -2.26 (0.18), residues: 629 loop : -2.15 (0.11), residues: 2324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8562 Ramachandran restraints generated. 4281 Oldfield, 0 Emsley, 4281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8562 Ramachandran restraints generated. 4281 Oldfield, 0 Emsley, 4281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1662 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1533 time to evaluate : 5.187 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 outliers start: 129 outliers final: 41 residues processed: 1608 average time/residue: 0.8507 time to fit residues: 2175.7097 Evaluate side-chains 1089 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1048 time to evaluate : 4.084 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.6000 time to fit residues: 49.3640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 491 optimal weight: 0.3980 chunk 441 optimal weight: 5.9990 chunk 244 optimal weight: 0.8980 chunk 150 optimal weight: 7.9990 chunk 297 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 456 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 339 optimal weight: 0.9980 chunk 528 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN ** C 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS D 127 HIS E 50 ASN E 165 ASN E 216 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN F 17 ASN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN F 71 ASN G 13 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 215 HIS ** H 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN I 139 HIS J 131 GLN J 133 HIS J 155 HIS K 68 ASN L 148 ASN N 105 ASN N 134 GLN N 142 GLN O 48 HIS ** O 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 71 ASN R 31 ASN V 69 ASN W 56 HIS X 61 GLN ** Y 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 116 ASN Z 116 HIS b 47 HIS b 49 GLN b 63 GLN d 6 ASN e 39 GLN m 3 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 73591 Z= 0.197 Angle : 0.696 19.589 107052 Z= 0.360 Chirality : 0.040 0.285 13312 Planarity : 0.005 0.063 7623 Dihedral : 16.675 179.541 24241 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 1.24 % Allowed : 5.63 % Favored : 93.14 % Rotamer Outliers : 3.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -2.23 (0.12), residues: 4283 helix: -0.50 (0.13), residues: 1421 sheet: -1.73 (0.18), residues: 704 loop : -2.07 (0.12), residues: 2158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1300 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1156 time to evaluate : 4.151 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: 144 outliers final: 77 residues processed: 1226 average time/residue: 0.7513 time to fit residues: 1498.0612 Evaluate side-chains 1089 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1012 time to evaluate : 4.087 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 0 residues processed: 77 average time/residue: 0.5189 time to fit residues: 79.5546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 293 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 439 optimal weight: 0.9990 chunk 359 optimal weight: 0.0980 chunk 145 optimal weight: 7.9990 chunk 529 optimal weight: 0.9990 chunk 571 optimal weight: 0.8980 chunk 471 optimal weight: 6.9990 chunk 525 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 424 optimal weight: 10.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 HIS C 95 GLN C 102 GLN D 127 HIS ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN ** F 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 HIS ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 ASN H 85 GLN H 100 GLN H 126 GLN Q 82 GLN R 115 ASN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 137 HIS ** T 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 96 GLN T 103 ASN V 69 ASN X 61 GLN X 63 ASN ** Z 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 ASN b 63 GLN e 39 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 73591 Z= 0.192 Angle : 0.625 19.884 107052 Z= 0.321 Chirality : 0.038 0.271 13312 Planarity : 0.005 0.062 7623 Dihedral : 16.360 179.497 24241 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 1.12 % Allowed : 6.12 % Favored : 92.76 % Rotamer Outliers : 3.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.71 (0.12), residues: 4283 helix: 0.03 (0.13), residues: 1424 sheet: -1.29 (0.18), residues: 682 loop : -1.90 (0.13), residues: 2177 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1150 time to evaluate : 4.106 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 outliers start: 115 outliers final: 58 residues processed: 1206 average time/residue: 0.7516 time to fit residues: 1479.8330 Evaluate side-chains 1075 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1017 time to evaluate : 4.063 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 58 outliers final: 1 residues processed: 58 average time/residue: 0.5902 time to fit residues: 67.5447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 523 optimal weight: 4.9990 chunk 398 optimal weight: 0.9980 chunk 274 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 252 optimal weight: 0.2980 chunk 355 optimal weight: 0.9980 chunk 531 optimal weight: 6.9990 chunk 562 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 chunk 503 optimal weight: 0.8980 chunk 151 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 HIS C 95 GLN E 17 HIS ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 ASN F 71 ASN ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 59 GLN G 146 ASN H 85 GLN H 100 GLN I 21 HIS L 148 ASN R 31 ASN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 119 GLN W 82 GLN W 92 ASN X 5 ASN X 77 ASN ** Z 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 ASN b 63 GLN e 39 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 73591 Z= 0.158 Angle : 0.593 16.567 107052 Z= 0.302 Chirality : 0.036 0.266 13312 Planarity : 0.004 0.052 7623 Dihedral : 16.187 179.989 24241 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 1.10 % Allowed : 5.77 % Favored : 93.14 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.41 (0.12), residues: 4283 helix: 0.25 (0.13), residues: 1446 sheet: -0.95 (0.18), residues: 683 loop : -1.79 (0.13), residues: 2154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1087 time to evaluate : 4.054 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: 102 outliers final: 56 residues processed: 1138 average time/residue: 0.7435 time to fit residues: 1379.7645 Evaluate side-chains 1080 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1024 time to evaluate : 4.057 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 56 outliers final: 1 residues processed: 56 average time/residue: 0.5497 time to fit residues: 61.3938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 468 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 418 optimal weight: 0.9990 chunk 232 optimal weight: 4.9990 chunk 480 optimal weight: 0.4980 chunk 388 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 504 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 ASN C 95 GLN C 97 GLN E 142 HIS E 165 ASN E 188 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN ** F 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN G 146 ASN G 151 GLN H 80 GLN H 184 ASN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS ** T 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 142 GLN V 38 GLN V 73 HIS Y 83 ASN ** Z 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 148 HIS Z 158 ASN b 47 HIS b 63 GLN e 39 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 73591 Z= 0.347 Angle : 0.711 19.176 107052 Z= 0.359 Chirality : 0.041 0.333 13312 Planarity : 0.006 0.065 7623 Dihedral : 16.390 179.777 24241 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 1.03 % Allowed : 6.89 % Favored : 92.08 % Rotamer Outliers : 4.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.54 (0.12), residues: 4283 helix: 0.12 (0.13), residues: 1425 sheet: -0.95 (0.18), residues: 703 loop : -1.86 (0.13), residues: 2155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1076 time to evaluate : 4.157 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 outliers start: 155 outliers final: 97 residues processed: 1144 average time/residue: 0.7613 time to fit residues: 1415.3027 Evaluate side-chains 1108 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1011 time to evaluate : 4.467 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 0 residues processed: 97 average time/residue: 0.5534 time to fit residues: 105.2175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 189 optimal weight: 0.9990 chunk 506 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 330 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 563 optimal weight: 1.9990 chunk 467 optimal weight: 0.8980 chunk 260 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN C 102 GLN E 165 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN G 146 ASN J 91 GLN ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 GLN ** S 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 HIS ** T 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 206 HIS V 60 GLN W 24 GLN W 92 ASN ** Z 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 152 GLN Z 158 ASN b 58 ASN m 3 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 73591 Z= 0.235 Angle : 0.633 17.484 107052 Z= 0.320 Chirality : 0.038 0.310 13312 Planarity : 0.005 0.061 7623 Dihedral : 16.243 179.636 24241 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.98 % Allowed : 6.61 % Favored : 92.41 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.42 (0.12), residues: 4283 helix: 0.24 (0.14), residues: 1431 sheet: -0.76 (0.19), residues: 689 loop : -1.86 (0.13), residues: 2163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1079 time to evaluate : 4.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 55 residues processed: 1116 average time/residue: 0.7640 time to fit residues: 1385.1686 Evaluate side-chains 1091 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1036 time to evaluate : 4.106 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.5413 time to fit residues: 60.3230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 542 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 320 optimal weight: 5.9990 chunk 411 optimal weight: 0.9980 chunk 318 optimal weight: 0.9980 chunk 474 optimal weight: 0.9980 chunk 314 optimal weight: 10.0000 chunk 560 optimal weight: 2.9990 chunk 351 optimal weight: 0.5980 chunk 341 optimal weight: 3.9990 chunk 258 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 ASN E 165 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 GLN ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 151 GLN H 80 GLN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN S 89 GLN S 99 HIS ** T 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 83 ASN ** Z 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 152 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 73591 Z= 0.161 Angle : 0.596 16.701 107052 Z= 0.300 Chirality : 0.035 0.306 13312 Planarity : 0.004 0.053 7623 Dihedral : 16.060 179.760 24241 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.96 % Allowed : 6.72 % Favored : 92.32 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.15 (0.13), residues: 4283 helix: 0.47 (0.14), residues: 1434 sheet: -0.55 (0.19), residues: 685 loop : -1.72 (0.13), residues: 2164 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1133 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1077 time to evaluate : 4.122 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 outliers start: 56 outliers final: 37 residues processed: 1097 average time/residue: 0.7691 time to fit residues: 1371.5279 Evaluate side-chains 1056 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1019 time to evaluate : 4.059 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.5558 time to fit residues: 42.7661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 347 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 335 optimal weight: 0.6980 chunk 168 optimal weight: 0.9990 chunk 110 optimal weight: 10.0000 chunk 108 optimal weight: 20.0000 chunk 356 optimal weight: 0.9990 chunk 382 optimal weight: 4.9990 chunk 277 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 440 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN E 188 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 HIS F 89 HIS ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN N 36 HIS S 99 HIS ** T 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 ASN ** Z 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 152 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 73591 Z= 0.158 Angle : 0.591 15.269 107052 Z= 0.297 Chirality : 0.035 0.334 13312 Planarity : 0.004 0.050 7623 Dihedral : 15.961 179.942 24241 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.96 % Allowed : 6.61 % Favored : 92.44 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.08 (0.13), residues: 4283 helix: 0.56 (0.14), residues: 1430 sheet: -0.46 (0.19), residues: 694 loop : -1.71 (0.13), residues: 2159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1048 time to evaluate : 4.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 21 residues processed: 1063 average time/residue: 0.7675 time to fit residues: 1324.8860 Evaluate side-chains 1031 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1010 time to evaluate : 4.091 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 21 outliers final: 1 residues processed: 21 average time/residue: 0.5955 time to fit residues: 27.3653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 510 optimal weight: 5.9990 chunk 537 optimal weight: 7.9990 chunk 490 optimal weight: 0.9980 chunk 522 optimal weight: 2.9990 chunk 314 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 410 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 472 optimal weight: 9.9990 chunk 494 optimal weight: 6.9990 chunk 520 optimal weight: 3.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 86 GLN G 146 ASN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 99 HIS ** T 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 118 GLN ** W 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 77 ASN ** Z 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 73591 Z= 0.240 Angle : 0.637 15.359 107052 Z= 0.319 Chirality : 0.037 0.348 13312 Planarity : 0.005 0.087 7623 Dihedral : 16.017 179.558 24241 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.98 % Allowed : 7.10 % Favored : 91.92 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.20 (0.13), residues: 4283 helix: 0.44 (0.14), residues: 1439 sheet: -0.54 (0.19), residues: 696 loop : -1.79 (0.13), residues: 2148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 1037 time to evaluate : 5.746 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 outliers start: 58 outliers final: 48 residues processed: 1058 average time/residue: 0.7657 time to fit residues: 1322.8704 Evaluate side-chains 1059 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1011 time to evaluate : 4.123 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 48 outliers final: 1 residues processed: 48 average time/residue: 0.5620 time to fit residues: 54.5915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 343 optimal weight: 0.0470 chunk 552 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 384 optimal weight: 5.9990 chunk 579 optimal weight: 2.9990 chunk 533 optimal weight: 4.9990 chunk 461 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 356 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN B 75 ASN ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 ASN ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 GLN S 99 HIS ** T 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 73591 Z= 0.239 Angle : 0.640 15.108 107052 Z= 0.320 Chirality : 0.037 0.412 13312 Planarity : 0.005 0.064 7623 Dihedral : 16.022 179.556 24241 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.10 % Favored : 91.99 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.25 (0.13), residues: 4283 helix: 0.42 (0.14), residues: 1436 sheet: -0.56 (0.19), residues: 701 loop : -1.83 (0.13), residues: 2146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8566 Ramachandran restraints generated. 4283 Oldfield, 0 Emsley, 4283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1038 time to evaluate : 4.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 16 residues processed: 1042 average time/residue: 0.7523 time to fit residues: 1279.7803 Evaluate side-chains 1028 residues out of total 3779 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1012 time to evaluate : 4.114 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 16 outliers final: 1 residues processed: 16 average time/residue: 0.5365 time to fit residues: 21.0028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 582 random chunks: chunk 366 optimal weight: 3.9990 chunk 491 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 425 optimal weight: 6.9990 chunk 68 optimal weight: 20.0000 chunk 128 optimal weight: 10.0000 chunk 462 optimal weight: 10.0000 chunk 193 optimal weight: 0.7980 chunk 474 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN ** B 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 ASN H 80 GLN J 133 HIS ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 GLN S 99 HIS ** T 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 60 GLN ** W 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.134484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.101690 restraints weight = 121567.559| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.42 r_work: 0.3068 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 73591 Z= 0.400 Angle : 0.749 15.257 107052 Z= 0.374 Chirality : 0.043 0.423 13312 Planarity : 0.006 0.057 7623 Dihedral : 16.341 179.949 24241 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.06 % Favored : 91.06 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.22 % 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: -1.59 (0.12), residues: 4283 helix: 0.11 (0.14), residues: 1430 sheet: -0.68 (0.19), residues: 688 loop : -2.03 (0.13), residues: 2165 =============================================================================== Job complete usr+sys time: 20869.56 seconds wall clock time: 366 minutes 18.17 seconds (21978.17 seconds total)