Starting phenix.real_space_refine (version: dev) on Sun May 15 18:42:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4g_20248/05_2022/6p4g_20248.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4g_20248/05_2022/6p4g_20248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4g_20248/05_2022/6p4g_20248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4g_20248/05_2022/6p4g_20248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4g_20248/05_2022/6p4g_20248.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p4g_20248/05_2022/6p4g_20248.pdb" } resolution = 3.1 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B ARG 63": "NH1" <-> "NH2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C ARG 107": "NH1" <-> "NH2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 165": "NH1" <-> "NH2" Residue "C TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "D ARG 68": "NH1" <-> "NH2" Residue "D ARG 117": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 227": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 11": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 68": "NH1" <-> "NH2" Residue "F ARG 77": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 198": "NH1" <-> "NH2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 252": "NH1" <-> "NH2" Residue "G TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 127": "NH1" <-> "NH2" Residue "G ARG 164": "NH1" <-> "NH2" Residue "G TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 198": "NH1" <-> "NH2" Residue "H ARG 72": "NH1" <-> "NH2" Residue "H ARG 131": "NH1" <-> "NH2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 178": "NH1" <-> "NH2" Residue "H ARG 198": "NH1" <-> "NH2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 81": "NH1" <-> "NH2" Residue "I ARG 143": "NH1" <-> "NH2" Residue "I PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 12": "NH1" <-> "NH2" Residue "J ARG 25": "NH1" <-> "NH2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 41": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J ARG 141": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 83": "NH1" <-> "NH2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 138": "NH1" <-> "NH2" Residue "K PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 65": "NH1" <-> "NH2" Residue "L TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "N ARG 45": "NH1" <-> "NH2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 104": "NH1" <-> "NH2" Residue "O ASP 110": "OD1" <-> "OD2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 121": "NH1" <-> "NH2" Residue "P PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 104": "NH1" <-> "NH2" Residue "P ARG 117": "NH1" <-> "NH2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P ASP 138": "OD1" <-> "OD2" Residue "P ARG 141": "NH1" <-> "NH2" Residue "P ARG 150": "NH1" <-> "NH2" Residue "Q PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q ARG 130": "NH1" <-> "NH2" Residue "R PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 140": "NH1" <-> "NH2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ARG 78": "NH1" <-> "NH2" Residue "T PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 14": "NH1" <-> "NH2" Residue "T ARG 39": "NH1" <-> "NH2" Residue "T ARG 55": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 121": "NH1" <-> "NH2" Residue "U ARG 16": "NH1" <-> "NH2" Residue "U PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 62": "NH1" <-> "NH2" Residue "U TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 84": "NH1" <-> "NH2" Residue "U ARG 102": "NH1" <-> "NH2" Residue "U ARG 121": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "V ARG 87": "NH1" <-> "NH2" Residue "W TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 38": "OE1" <-> "OE2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 54": "OD1" <-> "OD2" Residue "X PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 8": "NH1" <-> "NH2" Residue "Y ARG 17": "NH1" <-> "NH2" Residue "Y ARG 18": "NH1" <-> "NH2" Residue "Y ARG 67": "NH1" <-> "NH2" Residue "Y PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 107": "NH1" <-> "NH2" Residue "Z ARG 20": "NH1" <-> "NH2" Residue "Z PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 61": "NH1" <-> "NH2" Residue "Z ARG 110": "NH1" <-> "NH2" Residue "a ARG 80": "NH1" <-> "NH2" Residue "a ARG 85": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 85": "NH1" <-> "NH2" Residue "b ARG 87": "NH1" <-> "NH2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "c ARG 72": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ASP 37": "OD1" <-> "OD2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 44": "NH1" <-> "NH2" Residue "d ARG 66": "NH1" <-> "NH2" Residue "d ARG 67": "NH1" <-> "NH2" Residue "e PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 81": "NH1" <-> "NH2" Residue "f ARG 101": "NH1" <-> "NH2" Residue "f ARG 104": "NH1" <-> "NH2" Residue "g TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "h PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 47": "NH1" <-> "NH2" Residue "h ARG 60": "NH1" <-> "NH2" Residue "h ARG 100": "NH1" <-> "NH2" Residue "h TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 2": "NH1" <-> "NH2" Residue "n ARG 9": "NH1" <-> "NH2" Residue "n ARG 15": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 79374 Number of models: 1 Model: "" Number of chains: 36 Chain: "2" Number of atoms: 36229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1697, 36229 Classifications: {'RNA': 1697} Modifications used: {'5*END': 1, 'rna2p_pur': 145, 'rna3p_pur': 753, 'rna2p_pyr': 109, 'rna3p_pyr': 690} Link IDs: {'rna3p': 1443, 'rna2p': 253} Chain breaks: 11 Chain: "B" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1706 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "C" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1712 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1768 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "F" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2073 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1462 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "L" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1175 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Chain: "N" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 990 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "R" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135, 'PCIS': 1} Chain: "S" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'CIS': 1, 'TRANS': 124} Chain: "T" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1168 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 3, 'TRANS': 137} Chain: "U" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 136} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "X" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125, 'PCIS': 1} Chain: "Y" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 557 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "b" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 778 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain: "c" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 488 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "e" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 457 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "g" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "1" Number of atoms: 4323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 4323 Classifications: {'RNA': 203} Modifications used: {'rna3p_pyr': 86, 'rna2p_pur': 18, 'rna3p_pur': 87, 'rna2p_pyr': 12} Link IDs: {'rna3p': 172, 'rna2p': 30} Time building chain proxies: 36.90, per 1000 atoms: 0.46 Number of scatterers: 79374 At special positions: 0 Unit cell: (234.27, 261.396, 209.61, 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 184 16.00 P 1899 15.00 O 20064 8.00 N 14588 7.00 C 42639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 26 " distance=1.89 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 74 " distance=2.37 Simple disulfide: pdb=" SG CYS b 23 " - pdb=" SG CYS b 77 " distance=1.94 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 74 " distance=1.86 Simple disulfide: pdb=" SG CYS b 26 " - pdb=" SG CYS b 77 " distance=2.33 Simple disulfide: pdb=" SG CYS b 74 " - pdb=" SG CYS b 77 " distance=1.90 Simple disulfide: pdb=" SG CYS e 21 " - pdb=" SG CYS e 24 " distance=2.04 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 39 " distance=2.05 Simple disulfide: pdb=" SG CYS e 24 " - pdb=" SG CYS e 42 " distance=1.98 Simple disulfide: pdb=" SG CYS e 39 " - pdb=" SG CYS e 42 " distance=2.09 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.84 Conformation dependent library (CDL) restraints added in 5.2 seconds 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9018 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 58 sheets defined 34.9% alpha, 17.2% beta 512 base pairs and 1013 stacking pairs defined. Time for finding SS restraints: 23.34 Creating SS restraints... Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.513A pdb=" N VAL B 15 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.739A pdb=" N GLU B 35 " --> pdb=" O PHE B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 68 removed outlier: 3.689A pdb=" N ILE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 95 removed outlier: 4.604A pdb=" N ALA B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 removed outlier: 3.794A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 187 Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 206 through 214 removed outlier: 3.514A pdb=" N GLU B 213 " --> pdb=" O GLU B 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 26 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 106 through 114 removed outlier: 3.683A pdb=" N VAL C 114 " --> pdb=" O MET C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 175 Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 192 through 201 removed outlier: 3.519A pdb=" N GLU C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.576A pdb=" N LEU C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 72 Processing helix chain 'D' and resid 77 through 84 removed outlier: 3.642A pdb=" N ILE D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N PHE D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.517A pdb=" N ASP D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 98 " --> pdb=" O ILE D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 162 Processing helix chain 'D' and resid 207 through 217 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 247 through 250 removed outlier: 3.798A pdb=" N TYR D 250 " --> pdb=" O THR D 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 247 through 250' Processing helix chain 'D' and resid 252 through 257 removed outlier: 4.596A pdb=" N LYS D 257 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 269 Processing helix chain 'D' and resid 269 through 277 removed outlier: 3.612A pdb=" N MET D 274 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS D 275 " --> pdb=" O ASN D 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 29 Processing helix chain 'E' and resid 54 through 60 removed outlier: 3.561A pdb=" N VAL E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.689A pdb=" N ARG E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 96 removed outlier: 3.545A pdb=" N LEU E 96 " --> pdb=" O THR E 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 96' Processing helix chain 'E' and resid 97 through 110 Processing helix chain 'E' and resid 114 through 130 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'F' and resid 10 through 14 Processing helix chain 'F' and resid 15 through 19 Processing helix chain 'F' and resid 44 through 50 Processing helix chain 'F' and resid 57 through 66 removed outlier: 3.948A pdb=" N VAL F 61 " --> pdb=" O THR F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 Processing helix chain 'F' and resid 223 through 225 No H-bonds generated for 'chain 'F' and resid 223 through 225' Processing helix chain 'F' and resid 247 through 263 removed outlier: 3.762A pdb=" N GLY F 263 " --> pdb=" O LYS F 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 36 Processing helix chain 'G' and resid 61 through 66 Processing helix chain 'G' and resid 67 through 77 removed outlier: 3.816A pdb=" N MET G 77 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 105 removed outlier: 3.705A pdb=" N THR G 89 " --> pdb=" O LYS G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 120 removed outlier: 3.931A pdb=" N VAL G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 163 removed outlier: 3.515A pdb=" N ALA G 161 " --> pdb=" O GLY G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 187 through 203 removed outlier: 3.580A pdb=" N ASN G 203 " --> pdb=" O VAL G 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 137 through 145 Processing helix chain 'H' and resid 153 through 157 removed outlier: 3.834A pdb=" N VAL H 157 " --> pdb=" O ARG H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 237 removed outlier: 4.767A pdb=" N LYS H 195 " --> pdb=" O ARG H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 32 Processing helix chain 'I' and resid 36 through 40 Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 68 through 75 removed outlier: 3.700A pdb=" N LYS I 74 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 87 removed outlier: 4.175A pdb=" N GLU I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 120 Processing helix chain 'I' and resid 121 through 132 removed outlier: 3.708A pdb=" N LEU I 130 " --> pdb=" O HIS I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 167 Processing helix chain 'I' and resid 169 through 182 removed outlier: 3.544A pdb=" N GLY I 175 " --> pdb=" O GLU I 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 93 removed outlier: 3.680A pdb=" N ARG J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 115 Processing helix chain 'J' and resid 135 through 139 removed outlier: 3.586A pdb=" N ASN J 138 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS J 139 " --> pdb=" O ILE J 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 135 through 139' Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.833A pdb=" N GLN J 146 " --> pdb=" O SER J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 168 removed outlier: 3.603A pdb=" N GLN J 167 " --> pdb=" O GLU J 163 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN J 168 " --> pdb=" O GLU J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 183 Processing helix chain 'J' and resid 191 through 207 removed outlier: 3.642A pdb=" N LEU J 195 " --> pdb=" O GLU J 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 36 removed outlier: 3.660A pdb=" N LYS K 30 " --> pdb=" O ASP K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 63 removed outlier: 3.897A pdb=" N VAL K 46 " --> pdb=" O GLU K 42 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 84 Processing helix chain 'K' and resid 101 through 107 removed outlier: 3.971A pdb=" N PHE K 105 " --> pdb=" O LYS K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 117 Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 171 through 186 Processing helix chain 'L' and resid 4 through 18 removed outlier: 3.509A pdb=" N LEU L 14 " --> pdb=" O ALA L 10 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 55 removed outlier: 3.626A pdb=" N VAL L 45 " --> pdb=" O PRO L 41 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU L 52 " --> pdb=" O ALA L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 83 Processing helix chain 'M' and resid 47 through 53 removed outlier: 3.753A pdb=" N ILE M 51 " --> pdb=" O PRO M 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 27 Processing helix chain 'N' and resid 34 through 44 Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 81 through 89 removed outlier: 3.525A pdb=" N LEU N 85 " --> pdb=" O ASP N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 119 through 128 removed outlier: 4.164A pdb=" N VAL N 123 " --> pdb=" O GLN N 119 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 44 Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 62 through 67 Processing helix chain 'O' and resid 70 through 79 removed outlier: 3.833A pdb=" N LYS O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 102 Processing helix chain 'O' and resid 108 through 132 Processing helix chain 'P' and resid 59 through 61 No H-bonds generated for 'chain 'P' and resid 59 through 61' Processing helix chain 'P' and resid 70 through 88 removed outlier: 3.747A pdb=" N GLU P 87 " --> pdb=" O GLN P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 122 removed outlier: 4.515A pdb=" N SER P 114 " --> pdb=" O PRO P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 21 through 27 Processing helix chain 'Q' and resid 29 through 34 Processing helix chain 'Q' and resid 38 through 47 Processing helix chain 'Q' and resid 52 through 54 No H-bonds generated for 'chain 'Q' and resid 52 through 54' Processing helix chain 'Q' and resid 55 through 65 removed outlier: 3.711A pdb=" N LYS Q 65 " --> pdb=" O ARG Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 112 removed outlier: 3.704A pdb=" N ILE Q 112 " --> pdb=" O PRO Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 120 removed outlier: 3.587A pdb=" N SER Q 120 " --> pdb=" O GLY Q 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 42 Processing helix chain 'R' and resid 44 through 48 removed outlier: 3.700A pdb=" N LEU R 47 " --> pdb=" O PRO R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 59 removed outlier: 3.503A pdb=" N LEU R 58 " --> pdb=" O PRO R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 99 removed outlier: 3.609A pdb=" N ILE R 88 " --> pdb=" O ILE R 84 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER R 89 " --> pdb=" O ARG R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 3.652A pdb=" N LYS R 105 " --> pdb=" O ASP R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 120 Processing helix chain 'S' and resid 6 through 20 removed outlier: 3.861A pdb=" N ALA S 12 " --> pdb=" O THR S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 38 removed outlier: 3.525A pdb=" N ARG S 33 " --> pdb=" O HIS S 29 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 63 Processing helix chain 'S' and resid 80 through 84 Processing helix chain 'S' and resid 99 through 107 Processing helix chain 'T' and resid 25 through 30 Processing helix chain 'T' and resid 31 through 33 No H-bonds generated for 'chain 'T' and resid 31 through 33' Processing helix chain 'T' and resid 37 through 48 removed outlier: 3.627A pdb=" N VAL T 43 " --> pdb=" O ARG T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 73 removed outlier: 3.521A pdb=" N THR T 69 " --> pdb=" O GLU T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 80 through 84 Processing helix chain 'T' and resid 99 through 117 removed outlier: 3.665A pdb=" N LEU T 114 " --> pdb=" O ASP T 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 119 through 127 Processing helix chain 'U' and resid 5 through 9 Processing helix chain 'U' and resid 10 through 26 removed outlier: 4.318A pdb=" N ARG U 16 " --> pdb=" O GLN U 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 31 through 35 removed outlier: 3.858A pdb=" N ASP U 35 " --> pdb=" O GLU U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 67 removed outlier: 3.972A pdb=" N THR U 55 " --> pdb=" O ASN U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 79 Processing helix chain 'U' and resid 96 through 110 removed outlier: 3.563A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU U 108 " --> pdb=" O LEU U 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 142 Processing helix chain 'V' and resid 28 through 46 removed outlier: 3.522A pdb=" N LEU V 32 " --> pdb=" O ASN V 28 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS V 46 " --> pdb=" O GLY V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 94 through 102 removed outlier: 3.646A pdb=" N VAL V 98 " --> pdb=" O PRO V 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 56 through 63 removed outlier: 3.568A pdb=" N ARG W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 75 Processing helix chain 'X' and resid 5 through 21 Processing helix chain 'X' and resid 31 through 44 removed outlier: 3.514A pdb=" N HIS X 44 " --> pdb=" O VAL X 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 94 removed outlier: 3.667A pdb=" N LEU X 94 " --> pdb=" O GLN X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 119 removed outlier: 3.606A pdb=" N ARG X 118 " --> pdb=" O GLU X 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 21 Processing helix chain 'Y' and resid 24 through 31 removed outlier: 3.697A pdb=" N ALA Y 30 " --> pdb=" O GLN Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 39 removed outlier: 4.156A pdb=" N LEU Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 130 through 135 Processing helix chain 'Z' and resid 36 through 49 removed outlier: 3.615A pdb=" N MET Z 47 " --> pdb=" O LYS Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 53 No H-bonds generated for 'chain 'Z' and resid 51 through 53' Processing helix chain 'Z' and resid 78 through 83 Processing helix chain 'Z' and resid 87 through 93 Processing helix chain 'Z' and resid 103 through 115 Processing helix chain 'Z' and resid 118 through 124 removed outlier: 4.049A pdb=" N ALA Z 121 " --> pdb=" O ARG Z 118 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 62 removed outlier: 3.598A pdb=" N TYR a 55 " --> pdb=" O ASP a 51 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP a 56 " --> pdb=" O LYS a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 65 No H-bonds generated for 'chain 'a' and resid 63 through 65' Processing helix chain 'a' and resid 69 through 77 removed outlier: 3.615A pdb=" N GLU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 94 removed outlier: 3.515A pdb=" N LEU a 92 " --> pdb=" O LEU a 88 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 56 removed outlier: 3.714A pdb=" N SER b 54 " --> pdb=" O VAL b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 81 Processing helix chain 'c' and resid 11 through 18 removed outlier: 3.512A pdb=" N ARG c 17 " --> pdb=" O GLU c 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 3 through 7 Processing helix chain 'e' and resid 32 through 36 Processing helix chain 'e' and resid 41 through 51 removed outlier: 5.737A pdb=" N LYS e 48 " --> pdb=" O ARG e 44 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP e 49 " --> pdb=" O GLN e 45 " (cutoff:3.500A) Processing helix chain 'f' and resid 78 through 82 removed outlier: 3.575A pdb=" N ARG f 81 " --> pdb=" O SER f 78 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL f 82 " --> pdb=" O LEU f 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 78 through 82' Processing helix chain 'f' and resid 83 through 88 Processing helix chain 'f' and resid 103 through 115 Processing helix chain 'g' and resid 101 through 106 Processing helix chain 'n' and resid 2 through 16 Processing helix chain 'n' and resid 16 through 21 removed outlier: 4.043A pdb=" N MET n 20 " --> pdb=" O LYS n 16 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 100 removed outlier: 6.123A pdb=" N LEU B 122 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LEU B 147 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL B 124 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR B 144 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE B 161 " --> pdb=" O THR B 144 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 146 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 43 through 50 removed outlier: 4.195A pdb=" N GLY C 45 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N CYS C 96 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 91 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR C 98 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLU C 89 " --> pdb=" O THR C 98 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE C 100 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE C 87 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 102 " --> pdb=" O LYS C 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 120 through 128 removed outlier: 6.617A pdb=" N VAL C 140 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL C 212 " --> pdb=" O VAL C 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 120 through 128 removed outlier: 3.827A pdb=" N LYS C 219 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG C 136 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N MET C 217 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 103 through 114 removed outlier: 5.885A pdb=" N ASP D 104 " --> pdb=" O GLY D 131 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N GLY D 131 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N VAL D 106 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA D 129 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS D 108 " --> pdb=" O PHE D 127 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HIS D 136 " --> pdb=" O ASP D 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 184 through 188 Processing sheet with id=AA7, first strand: chain 'E' and resid 34 through 39 removed outlier: 3.910A pdb=" N GLY E 36 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 150 through 155 Processing sheet with id=AA9, first strand: chain 'E' and resid 209 through 210 Processing sheet with id=AB1, first strand: chain 'F' and resid 42 through 43 removed outlier: 3.563A pdb=" N ALA F 84 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 75 through 76 removed outlier: 4.226A pdb=" N HIS F 112 " --> pdb=" O ARG F 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 147 through 148 removed outlier: 3.785A pdb=" N ASP F 171 " --> pdb=" O GLN F 161 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASP F 163 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE F 169 " --> pdb=" O ASP F 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 180 through 182 removed outlier: 5.243A pdb=" N ILE F 195 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LYS F 211 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN F 197 " --> pdb=" O HIS F 209 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AB6, first strand: chain 'G' and resid 123 through 126 removed outlier: 8.471A pdb=" N ALA G 138 " --> pdb=" O ASN d 45 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LYS d 47 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP G 140 " --> pdb=" O LYS d 47 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE d 42 " --> pdb=" O VAL d 32 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLN d 29 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL d 17 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG d 31 " --> pdb=" O THR d 15 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 12 through 16 removed outlier: 6.817A pdb=" N VAL H 49 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 12 through 16 removed outlier: 6.825A pdb=" N ASN H 56 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 72 through 76 Processing sheet with id=AC1, first strand: chain 'H' and resid 160 through 162 removed outlier: 3.514A pdb=" N LYS H 172 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG H 170 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 49 through 53 removed outlier: 4.396A pdb=" N ARG I 57 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 185 through 188 removed outlier: 3.694A pdb=" N GLY I 141 " --> pdb=" O HIS I 157 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS I 142 " --> pdb=" O ASP X 54 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL I 146 " --> pdb=" O PHE X 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE X 50 " --> pdb=" O VAL I 146 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 36 through 37 removed outlier: 4.363A pdb=" N THR J 36 " --> pdb=" O LEU J 96 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 42 through 48 removed outlier: 6.474A pdb=" N ARG J 42 " --> pdb=" O LEU J 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 62 through 66 removed outlier: 8.045A pdb=" N ILE J 79 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N ASP J 105 " --> pdb=" O ILE J 79 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL J 81 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU J 103 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N CYS J 100 " --> pdb=" O ILE J 175 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLY J 187 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN J 64 " --> pdb=" O GLY J 187 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL J 189 " --> pdb=" O ASN J 64 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER J 66 " --> pdb=" O VAL J 189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 135 through 137 removed outlier: 3.502A pdb=" N ASP K 158 " --> pdb=" O ARG K 136 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AC9, first strand: chain 'M' and resid 101 through 107 removed outlier: 4.855A pdb=" N PHE M 140 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR M 127 " --> pdb=" O LEU M 143 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL M 145 " --> pdb=" O ILE M 125 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N ILE M 125 " --> pdb=" O VAL M 145 " (cutoff:3.500A) removed outlier: 18.363A pdb=" N ILE M 72 " --> pdb=" O LEU M 93 " (cutoff:3.500A) removed outlier: 15.156A pdb=" N LEU M 93 " --> pdb=" O ILE M 72 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N SER M 74 " --> pdb=" O ASP M 91 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP M 91 " --> pdb=" O SER M 74 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL M 87 " --> pdb=" O THR M 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 32 through 33 removed outlier: 4.162A pdb=" N VAL N 110 " --> pdb=" O ALA N 32 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 51 through 52 Processing sheet with id=AD3, first strand: chain 'P' and resid 34 through 36 removed outlier: 3.850A pdb=" N ASP P 39 " --> pdb=" O SER P 36 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 34 through 36 removed outlier: 3.850A pdb=" N ASP P 39 " --> pdb=" O SER P 36 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU P 93 " --> pdb=" O GLY P 127 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE P 129 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE P 95 " --> pdb=" O ILE P 129 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASP P 131 " --> pdb=" O ILE P 95 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU P 97 " --> pdb=" O ASP P 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 76 through 78 Processing sheet with id=AD6, first strand: chain 'R' and resid 9 through 15 Processing sheet with id=AD7, first strand: chain 'S' and resid 96 through 98 removed outlier: 6.148A pdb=" N ILE S 96 " --> pdb=" O GLN S 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'T' and resid 12 through 15 Processing sheet with id=AD9, first strand: chain 'U' and resid 81 through 83 Processing sheet with id=AE1, first strand: chain 'U' and resid 113 through 115 Processing sheet with id=AE2, first strand: chain 'V' and resid 50 through 63 removed outlier: 3.642A pdb=" N ASP V 90 " --> pdb=" O LYS V 51 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU V 88 " --> pdb=" O PRO V 53 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG V 55 " --> pdb=" O LYS V 86 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LYS V 86 " --> pdb=" O ARG V 55 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE V 84 " --> pdb=" O PRO V 57 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS V 59 " --> pdb=" O MET V 82 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N MET V 82 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU V 61 " --> pdb=" O PHE V 80 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE V 80 " --> pdb=" O LEU V 61 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 32 through 39 removed outlier: 3.549A pdb=" N VAL W 36 " --> pdb=" O LYS W 51 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN W 49 " --> pdb=" O GLU W 38 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 71 through 74 Processing sheet with id=AE5, first strand: chain 'X' and resid 80 through 81 removed outlier: 3.587A pdb=" N MET X 111 " --> pdb=" O LEU X 104 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 128 through 129 removed outlier: 6.630A pdb=" N LEU Y 101 " --> pdb=" O VAL Y 123 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL Y 125 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU Y 99 " --> pdb=" O VAL Y 125 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL Y 51 " --> pdb=" O GLN Y 73 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN Y 73 " --> pdb=" O VAL Y 51 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU Y 53 " --> pdb=" O ARG Y 71 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N PHE Y 120 " --> pdb=" O THR Y 82 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Z' and resid 6 through 15 removed outlier: 5.459A pdb=" N ILE Z 7 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU Z 28 " --> pdb=" O ILE Z 7 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N THR Z 9 " --> pdb=" O ASP Z 26 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP Z 26 " --> pdb=" O THR Z 9 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS Z 11 " --> pdb=" O VAL Z 24 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL Z 24 " --> pdb=" O LYS Z 11 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR Z 70 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N PHE Z 60 " --> pdb=" O THR Z 70 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'a' and resid 98 through 102 removed outlier: 6.905A pdb=" N ILE a 108 " --> pdb=" O VAL a 100 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'b' and resid 20 through 22 Processing sheet with id=AF1, first strand: chain 'b' and resid 38 through 43 Processing sheet with id=AF2, first strand: chain 'c' and resid 44 through 47 removed outlier: 4.466A pdb=" N PHE c 32 " --> pdb=" O LYS c 82 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG c 80 " --> pdb=" O ASP c 34 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'c' and resid 64 through 65 Processing sheet with id=AF4, first strand: chain 'e' and resid 30 through 31 removed outlier: 3.542A pdb=" N MET e 38 " --> pdb=" O ILE e 31 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 133 through 134 removed outlier: 3.612A pdb=" N TYR g 140 " --> pdb=" O ALA g 133 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h' and resid 5 through 6 removed outlier: 3.715A pdb=" N VAL h 307 " --> pdb=" O LEU h 11 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 5 through 6 Processing sheet with id=AF8, first strand: chain 'h' and resid 21 through 22 removed outlier: 3.503A pdb=" N LEU h 32 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS h 44 " --> pdb=" O PRO h 55 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 66 through 71 removed outlier: 3.603A pdb=" N THR h 96 " --> pdb=" O ASP h 91 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'h' and resid 120 through 123 removed outlier: 3.804A pdb=" N ILE h 120 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE h 129 " --> pdb=" O VAL h 142 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 153 through 156 removed outlier: 3.975A pdb=" N CYS h 153 " --> pdb=" O CYS h 168 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASN h 178 " --> pdb=" O LEU h 184 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LEU h 184 " --> pdb=" O ASN h 178 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 195 through 200 removed outlier: 5.495A pdb=" N GLY h 211 " --> pdb=" O GLN h 215 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLN h 215 " --> pdb=" O GLY h 211 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU h 218 " --> pdb=" O TYR h 228 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR h 228 " --> pdb=" O LEU h 218 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP h 220 " --> pdb=" O HIS h 226 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N HIS h 226 " --> pdb=" O ASP h 220 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'h' and resid 236 through 241 removed outlier: 3.730A pdb=" N ALA h 238 " --> pdb=" O ALA h 251 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP h 268 " --> pdb=" O ILE h 258 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP h 260 " --> pdb=" O ILE h 266 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE h 266 " --> pdb=" O ASP h 260 " (cutoff:3.500A) 1472 hydrogen bonds defined for protein. 4140 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1276 hydrogen bonds 2082 hydrogen bond angles 0 basepair planarities 512 basepair parallelities 1013 stacking parallelities Total time for adding SS restraints: 67.96 Time building geometry restraints manager: 31.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11868 1.33 - 1.46: 33012 1.46 - 1.59: 35955 1.59 - 1.71: 3708 1.71 - 1.84: 280 Bond restraints: 84823 Sorted by residual: bond pdb=" N ILE H 121 " pdb=" CA ILE H 121 " ideal model delta sigma weight residual 1.454 1.494 -0.039 7.70e-03 1.69e+04 2.57e+01 bond pdb=" N VAL L 40 " pdb=" CA VAL L 40 " ideal model delta sigma weight residual 1.460 1.497 -0.038 7.50e-03 1.78e+04 2.54e+01 bond pdb=" N VAL U 30 " pdb=" CA VAL U 30 " ideal model delta sigma weight residual 1.460 1.496 -0.037 7.50e-03 1.78e+04 2.38e+01 bond pdb=" N GLU V 107 " pdb=" CA GLU V 107 " ideal model delta sigma weight residual 1.453 1.490 -0.037 8.30e-03 1.45e+04 2.03e+01 bond pdb=" N ILE K 144 " pdb=" CA ILE K 144 " ideal model delta sigma weight residual 1.456 1.495 -0.038 8.70e-03 1.32e+04 1.96e+01 ... (remaining 84818 not shown) Histogram of bond angle deviations from ideal: 97.31 - 104.81: 8792 104.81 - 112.31: 43865 112.31 - 119.81: 38086 119.81 - 127.31: 28705 127.31 - 134.81: 4171 Bond angle restraints: 123619 Sorted by residual: angle pdb=" C ASP P 138 " pdb=" CA ASP P 138 " pdb=" CB ASP P 138 " ideal model delta sigma weight residual 109.71 129.02 -19.31 1.83e+00 2.99e-01 1.11e+02 angle pdb=" O3' U 2 688 " pdb=" C3' U 2 688 " pdb=" C2' U 2 688 " ideal model delta sigma weight residual 109.50 123.97 -14.47 1.50e+00 4.44e-01 9.30e+01 angle pdb=" O3' A 21489 " pdb=" C3' A 21489 " pdb=" C2' A 21489 " ideal model delta sigma weight residual 109.50 123.28 -13.78 1.50e+00 4.44e-01 8.45e+01 angle pdb=" C4' A 21476 " pdb=" C3' A 21476 " pdb=" O3' A 21476 " ideal model delta sigma weight residual 109.40 122.79 -13.39 1.50e+00 4.44e-01 7.97e+01 angle pdb=" C4' A 21664 " pdb=" C3' A 21664 " pdb=" O3' A 21664 " ideal model delta sigma weight residual 109.40 122.60 -13.20 1.50e+00 4.44e-01 7.75e+01 ... (remaining 123614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 45205 35.99 - 71.97: 1823 71.97 - 107.96: 146 107.96 - 143.94: 29 143.94 - 179.93: 53 Dihedral angle restraints: 47256 sinusoidal: 33279 harmonic: 13977 Sorted by residual: dihedral pdb=" C ASP P 138 " pdb=" N ASP P 138 " pdb=" CA ASP P 138 " pdb=" CB ASP P 138 " ideal model delta harmonic sigma weight residual -122.60 -160.78 38.18 0 2.50e+00 1.60e-01 2.33e+02 dihedral pdb=" N ASP P 138 " pdb=" C ASP P 138 " pdb=" CA ASP P 138 " pdb=" CB ASP P 138 " ideal model delta harmonic sigma weight residual 122.80 157.55 -34.75 0 2.50e+00 1.60e-01 1.93e+02 dihedral pdb=" C5' A 16541 " pdb=" C4' A 16541 " pdb=" C3' A 16541 " pdb=" O3' A 16541 " ideal model delta sinusoidal sigma weight residual 147.00 62.12 84.88 1 8.00e+00 1.56e-02 1.37e+02 ... (remaining 47253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.313: 15338 0.313 - 0.626: 20 0.626 - 0.938: 4 0.938 - 1.251: 0 1.251 - 1.564: 1 Chirality restraints: 15363 Sorted by residual: chirality pdb=" CA ASP P 138 " pdb=" N ASP P 138 " pdb=" C ASP P 138 " pdb=" CB ASP P 138 " both_signs ideal model delta sigma weight residual False 2.51 0.95 1.56 2.00e-01 2.50e+01 6.12e+01 chirality pdb=" C3' U 2 688 " pdb=" C4' U 2 688 " pdb=" O3' U 2 688 " pdb=" C2' U 2 688 " both_signs ideal model delta sigma weight residual False -2.74 -1.98 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C3' U 21377 " pdb=" C4' U 21377 " pdb=" O3' U 21377 " pdb=" C2' U 21377 " both_signs ideal model delta sigma weight residual False -2.48 -1.80 -0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 15360 not shown) Planarity restraints: 8630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Y 59 " -0.022 2.00e-02 2.50e+03 4.52e-02 2.04e+01 pdb=" C ALA Y 59 " 0.078 2.00e-02 2.50e+03 pdb=" O ALA Y 59 " -0.029 2.00e-02 2.50e+03 pdb=" N LYS Y 60 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU Q 118 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C GLU Q 118 " 0.057 2.00e-02 2.50e+03 pdb=" O GLU Q 118 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE Q 119 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO P 136 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.58e+00 pdb=" C PRO P 136 " -0.053 2.00e-02 2.50e+03 pdb=" O PRO P 136 " 0.021 2.00e-02 2.50e+03 pdb=" N SER P 137 " 0.018 2.00e-02 2.50e+03 ... (remaining 8627 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 10409 2.77 - 3.30: 70725 3.30 - 3.83: 151350 3.83 - 4.37: 194231 4.37 - 4.90: 268763 Nonbonded interactions: 695478 Sorted by model distance: nonbonded pdb=" OH TYR W 53 " pdb=" O LEU W 72 " model vdw 2.232 2.440 nonbonded pdb=" O2' A 16541 " pdb=" OP1 U 16542 " model vdw 2.235 2.440 nonbonded pdb=" O4' C 2 369 " pdb=" O2 C 2 369 " model vdw 2.247 3.040 nonbonded pdb=" O4' C 2 853 " pdb=" O2 C 2 853 " model vdw 2.254 3.040 nonbonded pdb=" O4' C 21117 " pdb=" O2 C 21117 " model vdw 2.254 3.040 ... (remaining 695473 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 1899 5.49 5 S 184 5.16 5 C 42639 2.51 5 N 14588 2.21 5 O 20064 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 12.210 Check model and map are aligned: 0.900 Convert atoms to be neutral: 0.540 Process input model: 217.510 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Set scattering table: 0.050 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 237.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.054 84823 Z= 0.646 Angle : 1.453 19.313 123619 Z= 1.029 Chirality : 0.101 1.564 15363 Planarity : 0.004 0.045 8630 Dihedral : 17.347 179.925 38208 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.90 % Favored : 90.23 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.06 (0.10), residues: 4788 helix: -2.98 (0.09), residues: 1486 sheet: -2.76 (0.15), residues: 811 loop : -2.45 (0.11), residues: 2491 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1564 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1423 time to evaluate : 4.645 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: 141 outliers final: 44 residues processed: 1510 average time/residue: 0.8380 time to fit residues: 2028.0384 Evaluate side-chains 927 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 883 time to evaluate : 4.656 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 44 outliers final: 1 residues processed: 44 average time/residue: 0.5893 time to fit residues: 53.3378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 557 optimal weight: 0.9980 chunk 500 optimal weight: 0.8980 chunk 277 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 337 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 517 optimal weight: 0.6980 chunk 200 optimal weight: 5.9990 chunk 314 optimal weight: 3.9990 chunk 385 optimal weight: 1.9990 chunk 599 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 ASN B 193 HIS C 92 GLN C 99 ASN C 186 ASN C 232 HIS D 272 HIS E 165 ASN E 174 HIS F 112 HIS G 149 GLN ** H 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN I 168 HIS J 22 HIS J 84 ASN J 99 ASN J 165 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 HIS L 42 ASN ** L 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN O 13 GLN O 36 GLN O 58 HIS P 94 HIS ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 HIS S 62 GLN T 87 GLN T 134 GLN V 81 GLN X 24 GLN X 113 HIS Y 46 HIS Z 63 HIS Z 94 HIS a 112 ASN b 17 HIS b 43 ASN ** b 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 HIS c 65 GLN h 15 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 84823 Z= 0.184 Angle : 0.664 16.158 123619 Z= 0.344 Chirality : 0.040 0.452 15363 Planarity : 0.005 0.085 8630 Dihedral : 16.947 179.794 28161 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.37 % Favored : 95.51 % Rotamer Outliers : 3.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.11), residues: 4788 helix: -0.71 (0.12), residues: 1549 sheet: -2.15 (0.15), residues: 880 loop : -1.84 (0.12), residues: 2359 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1013 time to evaluate : 5.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 158 outliers final: 74 residues processed: 1107 average time/residue: 0.8393 time to fit residues: 1532.3074 Evaluate side-chains 914 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 840 time to evaluate : 4.640 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 74 outliers final: 1 residues processed: 74 average time/residue: 0.6157 time to fit residues: 91.1448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 333 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 498 optimal weight: 0.6980 chunk 408 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 600 optimal weight: 0.2980 chunk 648 optimal weight: 10.0000 chunk 534 optimal weight: 4.9990 chunk 595 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 481 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 HIS C 92 GLN C 202 GLN D 178 HIS ** D 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 HIS F 36 HIS ** G 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 GLN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 GLN J 84 ASN J 99 ASN J 116 HIS J 138 ASN K 75 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN L 73 ASN M 100 ASN N 55 ASN ** O 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 32 HIS ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN S 118 GLN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 134 GLN U 85 ASN V 81 GLN W 49 GLN Z 63 HIS c 49 HIS d 26 GLN ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 139 HIS h 143 GLN h 222 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 84823 Z= 0.264 Angle : 0.677 16.390 123619 Z= 0.347 Chirality : 0.041 0.317 15363 Planarity : 0.005 0.080 8630 Dihedral : 16.877 179.874 28161 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.87 % Favored : 94.05 % Rotamer Outliers : 3.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.81 (0.11), residues: 4788 helix: -0.12 (0.13), residues: 1553 sheet: -1.81 (0.16), residues: 857 loop : -1.67 (0.12), residues: 2378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1062 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 897 time to evaluate : 4.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 96 residues processed: 1008 average time/residue: 0.7758 time to fit residues: 1315.5870 Evaluate side-chains 897 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 801 time to evaluate : 4.571 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 96 outliers final: 1 residues processed: 96 average time/residue: 0.5730 time to fit residues: 110.4763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 593 optimal weight: 0.9990 chunk 451 optimal weight: 5.9990 chunk 311 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 286 optimal weight: 0.6980 chunk 403 optimal weight: 0.7980 chunk 602 optimal weight: 9.9990 chunk 637 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 571 optimal weight: 0.7980 chunk 171 optimal weight: 0.0170 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN C 202 GLN D 277 HIS G 31 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN ** K 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 ASN M 108 ASN O 58 HIS O 62 GLN ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN T 17 ASN X 15 ASN d 29 GLN h 51 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.156 84823 Z= 0.155 Angle : 0.593 17.707 123619 Z= 0.303 Chirality : 0.036 0.311 15363 Planarity : 0.005 0.122 8630 Dihedral : 16.599 179.785 28161 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -1.34 (0.12), residues: 4788 helix: 0.38 (0.13), residues: 1551 sheet: -1.55 (0.17), residues: 862 loop : -1.47 (0.12), residues: 2375 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 918 time to evaluate : 4.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 39 residues processed: 974 average time/residue: 0.7861 time to fit residues: 1276.9572 Evaluate side-chains 849 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 810 time to evaluate : 4.646 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 39 outliers final: 1 residues processed: 39 average time/residue: 0.5618 time to fit residues: 47.5280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 531 optimal weight: 0.8980 chunk 362 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 475 optimal weight: 5.9990 chunk 263 optimal weight: 0.0170 chunk 544 optimal weight: 6.9990 chunk 440 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 325 optimal weight: 0.3980 chunk 572 optimal weight: 0.9990 chunk 160 optimal weight: 20.0000 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 ASN C 202 GLN D 277 HIS F 188 ASN ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN M 11 GLN M 100 ASN O 58 HIS O 62 GLN Q 24 GLN ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN S 93 GLN T 19 ASN X 15 ASN d 29 GLN h 143 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.120 84823 Z= 0.156 Angle : 0.584 17.227 123619 Z= 0.297 Chirality : 0.036 0.303 15363 Planarity : 0.005 0.123 8630 Dihedral : 16.463 179.949 28161 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -1.09 (0.12), residues: 4788 helix: 0.59 (0.13), residues: 1557 sheet: -1.37 (0.17), residues: 872 loop : -1.33 (0.12), residues: 2359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 849 time to evaluate : 4.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 45 residues processed: 906 average time/residue: 0.7842 time to fit residues: 1182.7057 Evaluate side-chains 834 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 789 time to evaluate : 4.752 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 45 outliers final: 1 residues processed: 45 average time/residue: 0.5573 time to fit residues: 53.4530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 214 optimal weight: 0.9980 chunk 574 optimal weight: 0.0770 chunk 126 optimal weight: 10.0000 chunk 374 optimal weight: 0.1980 chunk 157 optimal weight: 9.9990 chunk 638 optimal weight: 3.9990 chunk 530 optimal weight: 7.9990 chunk 295 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 335 optimal weight: 8.9990 overall best weight: 2.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS C 95 ASN D 277 HIS E 159 HIS ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN ** M 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 128 HIS S 118 GLN ** T 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN X 24 GLN d 29 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.173 84823 Z= 0.251 Angle : 0.643 20.699 123619 Z= 0.327 Chirality : 0.039 0.315 15363 Planarity : 0.005 0.133 8630 Dihedral : 16.546 179.511 28161 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.22 % Favored : 94.67 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -1.14 (0.12), residues: 4788 helix: 0.44 (0.13), residues: 1563 sheet: -1.26 (0.17), residues: 836 loop : -1.35 (0.12), residues: 2389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 816 time to evaluate : 4.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 61 residues processed: 885 average time/residue: 0.7847 time to fit residues: 1160.4846 Evaluate side-chains 819 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 758 time to evaluate : 5.747 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 61 outliers final: 1 residues processed: 61 average time/residue: 0.5764 time to fit residues: 71.9018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 615 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 363 optimal weight: 0.8980 chunk 466 optimal weight: 0.7980 chunk 361 optimal weight: 0.6980 chunk 537 optimal weight: 0.1980 chunk 356 optimal weight: 6.9990 chunk 636 optimal weight: 7.9990 chunk 398 optimal weight: 8.9990 chunk 387 optimal weight: 0.9980 chunk 293 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN X 15 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.593 84823 Z= 0.216 Angle : 0.659 73.857 123619 Z= 0.328 Chirality : 0.037 0.312 15363 Planarity : 0.005 0.124 8630 Dihedral : 16.512 179.716 28161 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.95 % Favored : 94.99 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -1.02 (0.12), residues: 4788 helix: 0.58 (0.13), residues: 1559 sheet: -1.24 (0.17), residues: 846 loop : -1.29 (0.12), residues: 2383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 807 time to evaluate : 4.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 32 residues processed: 842 average time/residue: 0.7871 time to fit residues: 1111.1258 Evaluate side-chains 796 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 764 time to evaluate : 4.695 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.6220 time to fit residues: 42.0184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 393 optimal weight: 7.9990 chunk 254 optimal weight: 0.9980 chunk 379 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 404 optimal weight: 2.9990 chunk 433 optimal weight: 0.6980 chunk 314 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 500 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN M 108 ASN ** M 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN X 24 GLN Y 127 ASN h 143 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.735 84823 Z= 0.398 Angle : 0.735 106.098 123619 Z= 0.354 Chirality : 0.037 0.557 15363 Planarity : 0.005 0.169 8630 Dihedral : 16.510 179.725 28161 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.92 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -1.03 (0.12), residues: 4788 helix: 0.58 (0.13), residues: 1559 sheet: -1.23 (0.17), residues: 846 loop : -1.30 (0.12), residues: 2383 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 767 time to evaluate : 4.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 786 average time/residue: 0.7825 time to fit residues: 1026.8214 Evaluate side-chains 775 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 755 time to evaluate : 4.630 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 20 outliers final: 1 residues processed: 20 average time/residue: 0.6169 time to fit residues: 28.0836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 578 optimal weight: 3.9990 chunk 609 optimal weight: 3.9990 chunk 556 optimal weight: 6.9990 chunk 592 optimal weight: 7.9990 chunk 356 optimal weight: 7.9990 chunk 258 optimal weight: 0.9990 chunk 465 optimal weight: 0.4980 chunk 181 optimal weight: 1.9990 chunk 535 optimal weight: 5.9990 chunk 560 optimal weight: 2.9990 chunk 590 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN ** M 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN Y 127 ASN h 117 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.735 84823 Z= 0.428 Angle : 0.751 106.100 123619 Z= 0.368 Chirality : 0.037 0.557 15363 Planarity : 0.005 0.169 8630 Dihedral : 16.510 179.725 28161 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.92 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -1.03 (0.12), residues: 4788 helix: 0.58 (0.13), residues: 1559 sheet: -1.23 (0.17), residues: 846 loop : -1.30 (0.12), residues: 2383 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 761 time to evaluate : 4.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 762 average time/residue: 0.8202 time to fit residues: 1045.3079 Evaluate side-chains 755 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 753 time to evaluate : 4.690 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.5545 time to fit residues: 7.6834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 389 optimal weight: 7.9990 chunk 626 optimal weight: 5.9990 chunk 382 optimal weight: 2.9990 chunk 297 optimal weight: 7.9990 chunk 435 optimal weight: 7.9990 chunk 657 optimal weight: 20.0000 chunk 605 optimal weight: 0.0980 chunk 523 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 chunk 404 optimal weight: 0.4980 chunk 321 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN ** M 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN X 24 GLN Y 127 ASN h 187 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.735 84823 Z= 0.428 Angle : 0.751 106.100 123619 Z= 0.368 Chirality : 0.037 0.557 15363 Planarity : 0.005 0.169 8630 Dihedral : 16.510 179.725 28161 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.92 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -1.03 (0.12), residues: 4788 helix: 0.58 (0.13), residues: 1559 sheet: -1.23 (0.17), residues: 846 loop : -1.30 (0.12), residues: 2383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9576 Ramachandran restraints generated. 4788 Oldfield, 0 Emsley, 4788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 754 time to evaluate : 5.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 756 average time/residue: 0.8069 time to fit residues: 1018.7951 Evaluate side-chains 757 residues out of total 4195 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 754 time to evaluate : 4.671 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.5927 time to fit residues: 8.8951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 660 random chunks: chunk 415 optimal weight: 0.9990 chunk 557 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 chunk 482 optimal weight: 0.0370 chunk 77 optimal weight: 8.9990 chunk 145 optimal weight: 10.0000 chunk 524 optimal weight: 1.9990 chunk 219 optimal weight: 0.8980 chunk 538 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 ASN ** M 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN Y 127 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.177091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147573 restraints weight = 124594.452| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.05 r_work: 0.3700 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 1.18 restraints_weight: 0.2500 r_work: 0.3668 rms_B_bonded: 1.48 restraints_weight: 0.1250 r_work: 0.3644 rms_B_bonded: 1.94 restraints_weight: 0.0625 r_work: 0.3611 rms_B_bonded: 2.67 restraints_weight: 0.0312 r_work: 0.3560 rms_B_bonded: 3.88 restraints_weight: 0.0156 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.735 84823 Z= 0.428 Angle : 0.751 106.100 123619 Z= 0.368 Chirality : 0.037 0.557 15363 Planarity : 0.005 0.169 8630 Dihedral : 16.510 179.725 28161 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.92 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.02 % 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: -1.03 (0.12), residues: 4788 helix: 0.58 (0.13), residues: 1559 sheet: -1.23 (0.17), residues: 846 loop : -1.30 (0.12), residues: 2383 =============================================================================== Job complete usr+sys time: 17941.63 seconds wall clock time: 317 minutes 0.24 seconds (19020.24 seconds total)