Starting phenix.real_space_refine on Tue Feb 20 09:42:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3g_6878/02_2024/5z3g_6878_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3g_6878/02_2024/5z3g_6878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3g_6878/02_2024/5z3g_6878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3g_6878/02_2024/5z3g_6878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3g_6878/02_2024/5z3g_6878_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z3g_6878/02_2024/5z3g_6878_neut.pdb" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1722 5.49 5 S 106 5.16 5 C 47742 2.51 5 N 15565 2.21 5 O 20764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 74": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 130": "NH1" <-> "NH2" Residue "D PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 205": "NH1" <-> "NH2" Residue "D ARG 211": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D ARG 299": "NH1" <-> "NH2" Residue "E TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "F TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 369": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 326": "NH1" <-> "NH2" Residue "H ARG 34": "NH1" <-> "NH2" Residue "H PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 170": "NH1" <-> "NH2" Residue "H ARG 240": "NH1" <-> "NH2" Residue "H ARG 277": "NH1" <-> "NH2" Residue "H ARG 285": "NH1" <-> "NH2" Residue "J ARG 30": "NH1" <-> "NH2" Residue "J ARG 100": "NH1" <-> "NH2" Residue "J ARG 110": "NH1" <-> "NH2" Residue "J TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "L ARG 23": "NH1" <-> "NH2" Residue "L ARG 91": "NH1" <-> "NH2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 166": "NH1" <-> "NH2" Residue "L ARG 168": "NH1" <-> "NH2" Residue "L ARG 173": "NH1" <-> "NH2" Residue "L TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 2": "NH1" <-> "NH2" Residue "M ARG 13": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 34": "NH1" <-> "NH2" Residue "M TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 92": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 104": "NH1" <-> "NH2" Residue "M ARG 109": "NH1" <-> "NH2" Residue "M TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 174": "NH1" <-> "NH2" Residue "M PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 369": "NH1" <-> "NH2" Residue "M PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 414": "NH1" <-> "NH2" Residue "M ARG 424": "NH1" <-> "NH2" Residue "N PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 85": "NH1" <-> "NH2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "N PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 142": "NH1" <-> "NH2" Residue "O PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 205": "NH1" <-> "NH2" Residue "O ARG 212": "NH1" <-> "NH2" Residue "O ARG 227": "NH1" <-> "NH2" Residue "O ARG 236": "NH1" <-> "NH2" Residue "O ARG 242": "NH1" <-> "NH2" Residue "O ARG 243": "NH1" <-> "NH2" Residue "O ARG 253": "NH1" <-> "NH2" Residue "O PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 269": "NH1" <-> "NH2" Residue "P ARG 42": "NH1" <-> "NH2" Residue "P ARG 49": "NH1" <-> "NH2" Residue "P ARG 73": "NH1" <-> "NH2" Residue "P PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 19": "NH1" <-> "NH2" Residue "Q ARG 108": "NH1" <-> "NH2" Residue "R ARG 20": "NH1" <-> "NH2" Residue "R TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 56": "NH1" <-> "NH2" Residue "T TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 92": "NH1" <-> "NH2" Residue "V ARG 54": "NH1" <-> "NH2" Residue "V PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 280": "NH1" <-> "NH2" Residue "V ARG 293": "NH1" <-> "NH2" Residue "V PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 117": "NH1" <-> "NH2" Residue "W TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 15": "NH1" <-> "NH2" Residue "Y ARG 71": "NH1" <-> "NH2" Residue "Y ARG 80": "NH1" <-> "NH2" Residue "Y PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 112": "NH1" <-> "NH2" Residue "Y ARG 135": "NH1" <-> "NH2" Residue "Y ARG 154": "NH1" <-> "NH2" Residue "Y ARG 211": "NH1" <-> "NH2" Residue "Y ARG 222": "NH1" <-> "NH2" Residue "Y ARG 240": "NH1" <-> "NH2" Residue "Y ARG 244": "NH1" <-> "NH2" Residue "Y ARG 276": "NH1" <-> "NH2" Residue "Y ARG 286": "NH1" <-> "NH2" Residue "Y TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 340": "NH1" <-> "NH2" Residue "Y ARG 371": "NH1" <-> "NH2" Residue "Y ARG 382": "NH1" <-> "NH2" Residue "Y PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 403": "NH1" <-> "NH2" Residue "Y ARG 448": "NH1" <-> "NH2" Residue "Z PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 40": "NH1" <-> "NH2" Residue "Z TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 143": "NH1" <-> "NH2" Residue "a PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 258": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 121": "NH1" <-> "NH2" Residue "i TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 48": "NH1" <-> "NH2" Residue "j ARG 60": "NH1" <-> "NH2" Residue "j TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 105": "NH1" <-> "NH2" Residue "m TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 63": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 85899 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 32146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1501, 32146 Classifications: {'RNA': 1501} Modifications used: {'rna2p_pur': 149, 'rna2p_pyr': 86, 'rna3p_pur': 691, 'rna3p_pyr': 575} Link IDs: {'rna2p': 235, 'rna3p': 1265} Chain breaks: 19 Chain: "B" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3313 Classifications: {'RNA': 156} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 14, 'rna3p_pur': 61, 'rna3p_pyr': 64} Link IDs: {'rna2p': 31, 'rna3p': 124} Chain: "C" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1370 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 17, 'rna3p_pur': 21, 'rna3p_pyr': 19} Link IDs: {'rna2p': 24, 'rna3p': 40} Chain breaks: 1 Chain: "D" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1956 Classifications: {'peptide': 247} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 8, 'TRANS': 236} Chain breaks: 1 Chain: "E" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 127} Chain: "F" Number of atoms: 2670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2670 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 324} Chain breaks: 1 Chain: "G" Number of atoms: 2749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2749 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Chain: "H" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2063 Classifications: {'peptide': 256} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 244} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1198 Classifications: {'peptide': 150} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 142} Chain breaks: 1 Chain: "J" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1918 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain: "K" Number of atoms: 1247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1247 Classifications: {'peptide': 162} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 152} Chain breaks: 1 Chain: "L" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1518 Classifications: {'peptide': 191} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 184} Chain: "M" Number of atoms: 3030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3030 Classifications: {'peptide': 371} Link IDs: {'CIS': 4, 'PCIS': 2, 'PTRANS': 19, 'TRANS': 345} Chain breaks: 2 Chain: "N" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1709 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 7, 'TRANS': 218} Chain: "O" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1591 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 180} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 867 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "Q" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1059 Classifications: {'peptide': 137} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 131} Chain: "R" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1498 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain breaks: 1 Chain: "S" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "T" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1057 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 1 Chain: "U" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1035 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 7, 'TRANS': 126} Chain: "V" Number of atoms: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3096 Classifications: {'peptide': 392} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 378} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "W" Number of atoms: 1425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1425 Classifications: {'peptide': 170} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 161} Chain: "X" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1718 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain breaks: 5 Chain: "Y" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3486 Classifications: {'peptide': 438} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 414} Chain breaks: 1 Chain: "Z" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1410 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "a" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1747 Classifications: {'peptide': 212} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 10, 'TRANS': 197} Chain breaks: 2 Chain: "b" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 689 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "c" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "d" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 770 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 154} Link IDs: {'TRANS': 153} Chain breaks: 6 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 462 Unresolved non-hydrogen dihedrals: 154 Planarities with less than four sites: {'UNK:plan-1': 154} Unresolved non-hydrogen planarities: 154 Chain: "i" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1001 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "j" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "l" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 959 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "m" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 1, 'TRANS': 65} Chain: "n" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 575 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'TRANS': 70} Time building chain proxies: 32.18, per 1000 atoms: 0.37 Number of scatterers: 85899 At special positions: 0 Unit cell: (306.36, 220.8, 227.7, 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 106 16.00 P 1722 15.00 O 20764 8.00 N 15565 7.00 C 47742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS Z 28 " - pdb=" SG CYS Z 38 " distance=2.01 Simple disulfide: pdb=" SG CYS Z 38 " - pdb=" SG CYS Z 43 " distance=2.02 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: 35.28 Conformation dependent library (CDL) restraints added in 6.5 seconds 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11700 Finding SS restraints... Secondary structure from input PDB file: 214 helices and 64 sheets defined 40.3% alpha, 14.9% beta 523 base pairs and 769 stacking pairs defined. Time for finding SS restraints: 26.72 Creating SS restraints... Processing helix chain 'D' and resid 57 through 85 removed outlier: 3.693A pdb=" N ILE D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 167 removed outlier: 3.878A pdb=" N LEU D 166 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 4.165A pdb=" N ILE D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 210 removed outlier: 3.624A pdb=" N LYS D 210 " --> pdb=" O SER D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 239 Processing helix chain 'D' and resid 247 through 255 removed outlier: 3.685A pdb=" N HIS D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 3.637A pdb=" N ASN D 265 " --> pdb=" O PHE D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 299 removed outlier: 3.764A pdb=" N LEU D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 287 " --> pdb=" O LEU D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 322 removed outlier: 4.649A pdb=" N LEU D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'E' and resid 141 through 153 Processing helix chain 'E' and resid 192 through 214 removed outlier: 3.915A pdb=" N LEU E 196 " --> pdb=" O PRO E 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 117 Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 144 through 154 Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 188 through 199 Processing helix chain 'F' and resid 372 through 381 Processing helix chain 'G' and resid 31 through 44 Processing helix chain 'G' and resid 114 through 132 removed outlier: 3.688A pdb=" N ALA G 130 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL G 131 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA G 132 " --> pdb=" O ALA G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 139 removed outlier: 3.913A pdb=" N GLY G 139 " --> pdb=" O VAL G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 159 Processing helix chain 'G' and resid 161 through 173 Processing helix chain 'G' and resid 174 through 181 Processing helix chain 'G' and resid 215 through 222 removed outlier: 4.577A pdb=" N ASN G 221 " --> pdb=" O LYS G 217 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL G 222 " --> pdb=" O ALA G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 239 Processing helix chain 'G' and resid 252 through 262 removed outlier: 4.358A pdb=" N ASP G 259 " --> pdb=" O PHE G 255 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN G 260 " --> pdb=" O THR G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 291 Processing helix chain 'G' and resid 320 through 327 removed outlier: 3.624A pdb=" N LEU G 324 " --> pdb=" O ASN G 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 335 Processing helix chain 'G' and resid 352 through 361 removed outlier: 3.562A pdb=" N THR G 356 " --> pdb=" O ALA G 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.868A pdb=" N VAL H 37 " --> pdb=" O PRO H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 77 Processing helix chain 'H' and resid 106 through 115 Processing helix chain 'H' and resid 136 through 145 removed outlier: 3.721A pdb=" N LEU H 140 " --> pdb=" O SER H 136 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP H 142 " --> pdb=" O ASP H 138 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN H 143 " --> pdb=" O ASP H 139 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 156 through 162 Processing helix chain 'H' and resid 166 through 175 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'H' and resid 189 through 199 removed outlier: 4.032A pdb=" N LEU H 193 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY H 196 " --> pdb=" O LYS H 192 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LYS H 197 " --> pdb=" O LEU H 193 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA H 198 " --> pdb=" O MET H 194 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR H 199 " --> pdb=" O GLY H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 231 removed outlier: 3.680A pdb=" N LYS H 227 " --> pdb=" O THR H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 275 removed outlier: 4.013A pdb=" N PHE H 259 " --> pdb=" O ARG H 255 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP H 261 " --> pdb=" O GLU H 257 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS H 272 " --> pdb=" O GLU H 268 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA H 273 " --> pdb=" O GLN H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 298 No H-bonds generated for 'chain 'H' and resid 296 through 298' Processing helix chain 'H' and resid 299 through 305 removed outlier: 3.740A pdb=" N LYS H 304 " --> pdb=" O GLU H 300 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 107 Processing helix chain 'I' and resid 131 through 150 removed outlier: 3.510A pdb=" N VAL I 135 " --> pdb=" O LYS I 131 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 160 Processing helix chain 'J' and resid 10 through 72 removed outlier: 4.248A pdb=" N LYS J 14 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS J 15 " --> pdb=" O SER J 11 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU J 29 " --> pdb=" O GLN J 25 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA J 42 " --> pdb=" O LYS J 38 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE J 43 " --> pdb=" O GLU J 39 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU J 45 " --> pdb=" O ARG J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 106 Processing helix chain 'J' and resid 120 through 131 removed outlier: 3.733A pdb=" N LEU J 124 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU J 125 " --> pdb=" O LYS J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 150 Processing helix chain 'J' and resid 165 through 174 removed outlier: 4.131A pdb=" N ILE J 169 " --> pdb=" O ASP J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'J' and resid 180 through 189 Processing helix chain 'J' and resid 194 through 201 Processing helix chain 'J' and resid 222 through 226 removed outlier: 3.594A pdb=" N GLY J 226 " --> pdb=" O PHE J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 235 through 244 removed outlier: 3.728A pdb=" N SER J 242 " --> pdb=" O LYS J 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 95 Processing helix chain 'K' and resid 101 through 119 Processing helix chain 'K' and resid 135 through 143 Processing helix chain 'K' and resid 159 through 164 removed outlier: 3.730A pdb=" N VAL K 163 " --> pdb=" O ILE K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 165 through 174 Processing helix chain 'K' and resid 182 through 190 removed outlier: 3.699A pdb=" N LEU K 186 " --> pdb=" O GLY K 182 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL K 190 " --> pdb=" O LEU K 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 207 through 221 Processing helix chain 'K' and resid 221 through 226 removed outlier: 4.401A pdb=" N LYS K 225 " --> pdb=" O ASN K 221 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR K 226 " --> pdb=" O PHE K 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 221 through 226' Processing helix chain 'K' and resid 227 through 231 Processing helix chain 'L' and resid 61 through 83 removed outlier: 3.586A pdb=" N THR L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR L 83 " --> pdb=" O ILE L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 163 Processing helix chain 'M' and resid 10 through 15 Processing helix chain 'M' and resid 17 through 26 Processing helix chain 'M' and resid 28 through 40 removed outlier: 4.377A pdb=" N GLY M 40 " --> pdb=" O CYS M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 54 removed outlier: 4.357A pdb=" N ASN M 53 " --> pdb=" O LYS M 49 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS M 54 " --> pdb=" O LYS M 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 49 through 54' Processing helix chain 'M' and resid 64 through 69 removed outlier: 3.916A pdb=" N ILE M 68 " --> pdb=" O TYR M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 97 Processing helix chain 'M' and resid 98 through 109 Processing helix chain 'M' and resid 114 through 122 removed outlier: 3.895A pdb=" N ILE M 118 " --> pdb=" O LEU M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 125 through 132 removed outlier: 4.641A pdb=" N ASP M 131 " --> pdb=" O ASP M 127 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE M 132 " --> pdb=" O ALA M 128 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 145 removed outlier: 3.642A pdb=" N MET M 138 " --> pdb=" O ASP M 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 174 Processing helix chain 'M' and resid 215 through 238 Processing helix chain 'M' and resid 249 through 256 removed outlier: 3.693A pdb=" N ASP M 253 " --> pdb=" O ASP M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 383 Processing helix chain 'M' and resid 391 through 395 Processing helix chain 'M' and resid 428 through 439 removed outlier: 4.232A pdb=" N ILE M 432 " --> pdb=" O GLN M 428 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE M 433 " --> pdb=" O PRO M 429 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP M 434 " --> pdb=" O GLN M 430 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N CYS M 435 " --> pdb=" O TRP M 431 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE M 436 " --> pdb=" O ILE M 432 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN M 437 " --> pdb=" O PHE M 433 " (cutoff:3.500A) Processing helix chain 'M' and resid 443 through 447 removed outlier: 4.059A pdb=" N LYS M 446 " --> pdb=" O PRO M 443 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 37 Processing helix chain 'N' and resid 77 through 87 removed outlier: 3.575A pdb=" N LEU N 81 " --> pdb=" O THR N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 132 removed outlier: 4.186A pdb=" N GLU N 126 " --> pdb=" O ASP N 122 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER N 130 " --> pdb=" O GLU N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 178 Processing helix chain 'N' and resid 192 through 197 removed outlier: 4.319A pdb=" N GLY N 196 " --> pdb=" O VAL N 192 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET N 197 " --> pdb=" O VAL N 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 192 through 197' Processing helix chain 'N' and resid 211 through 223 Processing helix chain 'O' and resid 104 through 118 removed outlier: 3.795A pdb=" N TYR O 108 " --> pdb=" O LYS O 104 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU O 116 " --> pdb=" O ASN O 112 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE O 117 " --> pdb=" O ILE O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 142 removed outlier: 3.763A pdb=" N ILE O 135 " --> pdb=" O LYS O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 218 removed outlier: 3.566A pdb=" N VAL O 210 " --> pdb=" O LEU O 206 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU O 218 " --> pdb=" O PHE O 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 284 through 288 removed outlier: 3.835A pdb=" N ASP O 287 " --> pdb=" O PRO O 284 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 43 removed outlier: 3.623A pdb=" N VAL P 33 " --> pdb=" O ALA P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 83 Processing helix chain 'P' and resid 86 through 91 Processing helix chain 'P' and resid 105 through 123 Processing helix chain 'Q' and resid 77 through 89 Processing helix chain 'Q' and resid 89 through 97 Processing helix chain 'Q' and resid 97 through 111 removed outlier: 3.627A pdb=" N ALA Q 111 " --> pdb=" O GLU Q 107 " (cutoff:3.500A) Processing helix chain 'Q' and resid 113 through 135 Processing helix chain 'R' and resid 3 through 12 Processing helix chain 'R' and resid 16 through 32 removed outlier: 3.534A pdb=" N TRP R 28 " --> pdb=" O ARG R 24 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN R 32 " --> pdb=" O TRP R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 51 Processing helix chain 'R' and resid 98 through 110 removed outlier: 3.500A pdb=" N VAL R 106 " --> pdb=" O ALA R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 157 removed outlier: 3.750A pdb=" N ILE R 151 " --> pdb=" O TYR R 148 " (cutoff:3.500A) Proline residue: R 154 - end of helix Processing helix chain 'R' and resid 167 through 172 removed outlier: 3.701A pdb=" N ARG R 172 " --> pdb=" O GLY R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 195 Processing helix chain 'S' and resid 16 through 29 Processing helix chain 'S' and resid 37 through 40 Processing helix chain 'S' and resid 46 through 59 removed outlier: 3.521A pdb=" N ASN S 50 " --> pdb=" O GLU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 92 through 99 removed outlier: 3.554A pdb=" N LYS S 96 " --> pdb=" O THR S 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 124 through 129 Processing helix chain 'S' and resid 138 through 145 Processing helix chain 'S' and resid 149 through 186 removed outlier: 4.172A pdb=" N VAL S 162 " --> pdb=" O ALA S 158 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS S 177 " --> pdb=" O ALA S 173 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL S 178 " --> pdb=" O PHE S 174 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA S 183 " --> pdb=" O ALA S 179 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR S 184 " --> pdb=" O SER S 180 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA S 185 " --> pdb=" O ALA S 181 " (cutoff:3.500A) Processing helix chain 'S' and resid 188 through 197 Processing helix chain 'T' and resid 25 through 35 Processing helix chain 'T' and resid 40 through 53 Processing helix chain 'T' and resid 70 through 76 removed outlier: 3.689A pdb=" N GLY T 73 " --> pdb=" O THR T 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 106 removed outlier: 4.519A pdb=" N VAL T 88 " --> pdb=" O PRO T 84 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS T 89 " --> pdb=" O ALA T 85 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 23 through 41 removed outlier: 4.092A pdb=" N PHE U 35 " --> pdb=" O LYS U 31 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP U 41 " --> pdb=" O ALA U 37 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 51 removed outlier: 4.009A pdb=" N LYS U 46 " --> pdb=" O ALA U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 64 through 71 Processing helix chain 'U' and resid 107 through 118 Processing helix chain 'U' and resid 123 through 131 Processing helix chain 'V' and resid 47 through 50 Processing helix chain 'V' and resid 125 through 132 removed outlier: 3.773A pdb=" N LEU V 131 " --> pdb=" O LYS V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 290 through 292 No H-bonds generated for 'chain 'V' and resid 290 through 292' Processing helix chain 'V' and resid 332 through 335 Processing helix chain 'W' and resid 33 through 49 removed outlier: 3.790A pdb=" N LYS W 47 " --> pdb=" O TYR W 43 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N HIS W 49 " --> pdb=" O LEU W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 98 through 113 removed outlier: 3.879A pdb=" N ALA W 102 " --> pdb=" O SER W 98 " (cutoff:3.500A) Processing helix chain 'W' and resid 137 through 142 Processing helix chain 'W' and resid 143 through 145 No H-bonds generated for 'chain 'W' and resid 143 through 145' Processing helix chain 'X' and resid 4 through 12 Processing helix chain 'X' and resid 15 through 30 removed outlier: 4.191A pdb=" N THR X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 39 through 55 removed outlier: 3.996A pdb=" N PHE X 55 " --> pdb=" O TYR X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 72 removed outlier: 3.784A pdb=" N ALA X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 90 through 109 removed outlier: 3.635A pdb=" N PHE X 102 " --> pdb=" O PHE X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 117 through 137 Processing helix chain 'X' and resid 145 through 157 removed outlier: 4.465A pdb=" N ARG X 155 " --> pdb=" O LYS X 151 " (cutoff:3.500A) Processing helix chain 'X' and resid 167 through 186 removed outlier: 3.600A pdb=" N ILE X 171 " --> pdb=" O THR X 167 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS X 172 " --> pdb=" O GLY X 168 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP X 175 " --> pdb=" O ILE X 171 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU X 185 " --> pdb=" O TRP X 181 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS X 186 " --> pdb=" O GLU X 182 " (cutoff:3.500A) Processing helix chain 'X' and resid 199 through 211 removed outlier: 3.950A pdb=" N LYS X 211 " --> pdb=" O GLU X 207 " (cutoff:3.500A) Processing helix chain 'X' and resid 211 through 227 removed outlier: 3.518A pdb=" N ASP X 227 " --> pdb=" O ASP X 223 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 242 Processing helix chain 'Y' and resid 50 through 58 Processing helix chain 'Y' and resid 59 through 61 No H-bonds generated for 'chain 'Y' and resid 59 through 61' Processing helix chain 'Y' and resid 66 through 71 Processing helix chain 'Y' and resid 72 through 77 removed outlier: 3.690A pdb=" N LEU Y 77 " --> pdb=" O ILE Y 73 " (cutoff:3.500A) Processing helix chain 'Y' and resid 91 through 107 removed outlier: 3.947A pdb=" N ALA Y 95 " --> pdb=" O GLY Y 91 " (cutoff:3.500A) Proline residue: Y 99 - end of helix Processing helix chain 'Y' and resid 123 through 133 Processing helix chain 'Y' and resid 153 through 162 Processing helix chain 'Y' and resid 171 through 182 Processing helix chain 'Y' and resid 182 through 187 Processing helix chain 'Y' and resid 188 through 190 No H-bonds generated for 'chain 'Y' and resid 188 through 190' Processing helix chain 'Y' and resid 197 through 203 removed outlier: 4.469A pdb=" N ILE Y 201 " --> pdb=" O GLU Y 197 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU Y 203 " --> pdb=" O ASP Y 199 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 217 Processing helix chain 'Y' and resid 233 through 240 removed outlier: 3.957A pdb=" N ASP Y 237 " --> pdb=" O THR Y 233 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 312 Processing helix chain 'Y' and resid 324 through 337 Processing helix chain 'Y' and resid 369 through 376 Processing helix chain 'Y' and resid 377 through 380 removed outlier: 3.632A pdb=" N THR Y 380 " --> pdb=" O VAL Y 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 377 through 380' Processing helix chain 'Y' and resid 395 through 397 No H-bonds generated for 'chain 'Y' and resid 395 through 397' Processing helix chain 'Y' and resid 398 through 408 removed outlier: 3.831A pdb=" N LEU Y 402 " --> pdb=" O GLU Y 398 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 431 removed outlier: 3.655A pdb=" N GLU Y 430 " --> pdb=" O GLN Y 426 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS Y 431 " --> pdb=" O SER Y 427 " (cutoff:3.500A) Processing helix chain 'Y' and resid 442 through 457 removed outlier: 3.905A pdb=" N HIS Y 457 " --> pdb=" O ALA Y 453 " (cutoff:3.500A) Processing helix chain 'Y' and resid 471 through 477 Processing helix chain 'Z' and resid 3 through 13 Processing helix chain 'Z' and resid 72 through 76 Processing helix chain 'Z' and resid 85 through 97 Processing helix chain 'Z' and resid 101 through 127 removed outlier: 3.892A pdb=" N ARG Z 105 " --> pdb=" O SER Z 101 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN Z 110 " --> pdb=" O HIS Z 106 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU Z 127 " --> pdb=" O ARG Z 123 " (cutoff:3.500A) Processing helix chain 'Z' and resid 138 through 156 Processing helix chain 'Z' and resid 158 through 170 removed outlier: 3.590A pdb=" N ILE Z 162 " --> pdb=" O ILE Z 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 56 Processing helix chain 'a' and resid 73 through 81 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 160 Processing helix chain 'a' and resid 244 through 253 Processing helix chain 'b' and resid 198 through 209 removed outlier: 3.599A pdb=" N GLN b 209 " --> pdb=" O LEU b 205 " (cutoff:3.500A) Processing helix chain 'b' and resid 238 through 264 removed outlier: 4.519A pdb=" N ARG b 242 " --> pdb=" O ASP b 238 " (cutoff:3.500A) Processing helix chain 'c' and resid 11 through 21 Processing helix chain 'c' and resid 25 through 30 removed outlier: 3.798A pdb=" N VAL c 29 " --> pdb=" O SER c 25 " (cutoff:3.500A) Processing helix chain 'c' and resid 36 through 43 Processing helix chain 'c' and resid 100 through 102 No H-bonds generated for 'chain 'c' and resid 100 through 102' Processing helix chain 'c' and resid 112 through 122 removed outlier: 3.590A pdb=" N LYS c 122 " --> pdb=" O LEU c 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 118 removed outlier: 3.704A pdb=" N UNK d 95 " --> pdb=" O UNK d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 172 Processing helix chain 'd' and resid 181 through 188 Processing helix chain 'd' and resid 201 through 212 removed outlier: 4.316A pdb=" N UNK d 209 " --> pdb=" O UNK d 205 " (cutoff:3.500A) Processing helix chain 'd' and resid 221 through 230 Processing helix chain 'd' and resid 241 through 248 Processing helix chain 'd' and resid 261 through 266 removed outlier: 3.629A pdb=" N UNK d 266 " --> pdb=" O UNK d 262 " (cutoff:3.500A) Processing helix chain 'i' and resid 40 through 45 removed outlier: 3.580A pdb=" N ARG i 44 " --> pdb=" O SER i 40 " (cutoff:3.500A) Processing helix chain 'i' and resid 54 through 58 Processing helix chain 'i' and resid 78 through 83 Processing helix chain 'i' and resid 84 through 86 No H-bonds generated for 'chain 'i' and resid 84 through 86' Processing helix chain 'i' and resid 101 through 115 removed outlier: 4.281A pdb=" N VAL i 106 " --> pdb=" O ALA i 102 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL i 107 " --> pdb=" O LYS i 103 " (cutoff:3.500A) Processing helix chain 'j' and resid 37 through 45 removed outlier: 4.473A pdb=" N PHE j 43 " --> pdb=" O GLN j 39 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR j 44 " --> pdb=" O ASP j 40 " (cutoff:3.500A) Processing helix chain 'l' and resid 13 through 34 Processing helix chain 'l' and resid 35 through 37 No H-bonds generated for 'chain 'l' and resid 35 through 37' Processing helix chain 'l' and resid 42 through 71 removed outlier: 3.705A pdb=" N THR l 46 " --> pdb=" O PRO l 42 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG l 48 " --> pdb=" O ILE l 44 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA l 65 " --> pdb=" O GLN l 61 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 81 Processing helix chain 'l' and resid 93 through 99 Processing helix chain 'l' and resid 101 through 111 removed outlier: 3.649A pdb=" N ARG l 105 " --> pdb=" O THR l 101 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 49 removed outlier: 3.582A pdb=" N LYS m 38 " --> pdb=" O SER m 34 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY m 49 " --> pdb=" O ARG m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 51 through 62 Processing helix chain 'm' and resid 65 through 77 Processing helix chain 'm' and resid 81 through 97 removed outlier: 4.132A pdb=" N ALA m 85 " --> pdb=" O THR m 81 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS m 86 " --> pdb=" O ARG m 82 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 58 removed outlier: 4.248A pdb=" N HIS n 57 " --> pdb=" O ALA n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 66 through 68 No H-bonds generated for 'chain 'n' and resid 66 through 68' Processing helix chain 'n' and resid 69 through 76 removed outlier: 3.502A pdb=" N PHE n 74 " --> pdb=" O VAL n 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN n 76 " --> pdb=" O ARG n 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 129 through 133 Processing sheet with id=AA2, first strand: chain 'D' and resid 194 through 197 removed outlier: 3.733A pdb=" N ARG D 146 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR D 173 " --> pdb=" O ARG D 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 213 through 215 Processing sheet with id=AA4, first strand: chain 'E' and resid 119 through 124 removed outlier: 6.884A pdb=" N GLU E 119 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N PHE E 136 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ARG E 121 " --> pdb=" O TYR E 134 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR E 134 " --> pdb=" O ARG E 121 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA E 123 " --> pdb=" O ARG E 132 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LEU E 167 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE E 92 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ARG E 165 " --> pdb=" O ILE E 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 156 through 157 Processing sheet with id=AA6, first strand: chain 'F' and resid 354 through 359 removed outlier: 6.885A pdb=" N VAL F 57 " --> pdb=" O LYS F 357 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N ILE F 359 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR F 55 " --> pdb=" O ILE F 359 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE F 282 " --> pdb=" O LYS F 325 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS F 325 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG F 284 " --> pdb=" O MET F 323 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL F 72 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL F 57 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU F 74 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR F 55 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL F 76 " --> pdb=" O MET F 53 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N MET F 53 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL F 78 " --> pdb=" O ALA F 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 99 through 101 removed outlier: 4.868A pdb=" N VAL F 86 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N HIS F 163 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY F 88 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 99 through 101 removed outlier: 3.615A pdb=" N VAL F 84 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS F 201 " --> pdb=" O VAL F 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'G' and resid 150 through 152 Processing sheet with id=AB2, first strand: chain 'G' and resid 186 through 187 Processing sheet with id=AB3, first strand: chain 'G' and resid 206 through 209 removed outlier: 3.574A pdb=" N ALA G 228 " --> pdb=" O VAL G 207 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR G 209 " --> pdb=" O ALA G 228 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 243 through 250 removed outlier: 6.817A pdb=" N GLN H 79 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER H 278 " --> pdb=" O ASN H 84 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE H 279 " --> pdb=" O LEU H 291 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU H 291 " --> pdb=" O ILE H 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 97 through 101 Processing sheet with id=AB6, first strand: chain 'H' and resid 124 through 126 removed outlier: 6.690A pdb=" N LEU H 125 " --> pdb=" O ILE H 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'I' and resid 77 through 80 removed outlier: 6.694A pdb=" N THR I 62 " --> pdb=" O HIS I 57 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N HIS I 57 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU I 64 " --> pdb=" O LEU I 55 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 114 through 118 removed outlier: 6.498A pdb=" N VAL J 134 " --> pdb=" O GLY J 230 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AC1, first strand: chain 'K' and resid 177 through 179 removed outlier: 5.831A pdb=" N VAL K 151 " --> pdb=" O ALA K 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 5 through 11 Processing sheet with id=AC3, first strand: chain 'L' and resid 17 through 20 Processing sheet with id=AC4, first strand: chain 'L' and resid 132 through 136 removed outlier: 7.050A pdb=" N LYS L 87 " --> pdb=" O LYS L 184 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS L 184 " --> pdb=" O LYS L 87 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LYS L 89 " --> pdb=" O SER L 182 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 100 through 104 Processing sheet with id=AC6, first strand: chain 'M' and resid 178 through 181 Processing sheet with id=AC7, first strand: chain 'M' and resid 410 through 411 removed outlier: 5.059A pdb=" N GLN M 410 " --> pdb=" O ILE M 427 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'N' and resid 3 through 4 removed outlier: 6.395A pdb=" N THR N 3 " --> pdb=" O THR N 206 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL N 198 " --> pdb=" O VAL N 205 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 17 through 20 removed outlier: 3.982A pdb=" N THR N 20 " --> pdb=" O TYR N 23 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 64 through 66 Processing sheet with id=AD2, first strand: chain 'N' and resid 159 through 161 removed outlier: 6.322A pdb=" N GLY N 159 " --> pdb=" O VAL N 182 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'O' and resid 122 through 123 removed outlier: 4.336A pdb=" N THR O 122 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE O 96 " --> pdb=" O VAL O 148 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE O 150 " --> pdb=" O PHE O 96 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE O 147 " --> pdb=" O PHE O 162 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE O 162 " --> pdb=" O ILE O 147 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE O 149 " --> pdb=" O LEU O 160 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU O 160 " --> pdb=" O ILE O 149 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN O 151 " --> pdb=" O THR O 158 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR O 158 " --> pdb=" O LEU O 175 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU O 175 " --> pdb=" O THR O 158 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS O 174 " --> pdb=" O LEU O 267 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU O 267 " --> pdb=" O LYS O 174 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER O 176 " --> pdb=" O LEU O 265 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU O 265 " --> pdb=" O SER O 176 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLN O 257 " --> pdb=" O VAL O 247 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL O 247 " --> pdb=" O GLN O 257 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LEU O 259 " --> pdb=" O ARG O 245 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ARG O 245 " --> pdb=" O LEU O 259 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG O 243 " --> pdb=" O PRO O 261 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE O 263 " --> pdb=" O PHE O 241 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE O 241 " --> pdb=" O PHE O 263 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N GLU O 196 " --> pdb=" O ILE O 230 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N LEU O 232 " --> pdb=" O GLU O 196 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE O 198 " --> pdb=" O LEU O 232 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N ASN O 234 " --> pdb=" O ILE O 198 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 122 through 123 removed outlier: 4.336A pdb=" N THR O 122 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE O 96 " --> pdb=" O VAL O 148 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ILE O 150 " --> pdb=" O PHE O 96 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE O 147 " --> pdb=" O PHE O 162 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE O 162 " --> pdb=" O ILE O 147 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE O 149 " --> pdb=" O LEU O 160 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU O 160 " --> pdb=" O ILE O 149 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN O 151 " --> pdb=" O THR O 158 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR O 158 " --> pdb=" O LEU O 175 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU O 175 " --> pdb=" O THR O 158 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS O 174 " --> pdb=" O LEU O 267 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LEU O 267 " --> pdb=" O LYS O 174 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER O 176 " --> pdb=" O LEU O 265 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU O 265 " --> pdb=" O SER O 176 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU O 270 " --> pdb=" O GLU O 279 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 23 through 24 removed outlier: 6.724A pdb=" N LYS P 23 " --> pdb=" O LEU R 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'P' and resid 57 through 59 Processing sheet with id=AD7, first strand: chain 'Q' and resid 14 through 15 removed outlier: 3.590A pdb=" N PHE W 150 " --> pdb=" O VAL Q 15 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 56 through 59 removed outlier: 8.076A pdb=" N LYS Q 43 " --> pdb=" O ILE Q 38 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE Q 38 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU Q 45 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS Q 31 " --> pdb=" O ILE Q 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 36 through 39 removed outlier: 4.099A pdb=" N ILE R 61 " --> pdb=" O ALA R 39 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU R 131 " --> pdb=" O TRP R 120 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TRP R 120 " --> pdb=" O GLU R 131 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE R 133 " --> pdb=" O SER R 118 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N SER R 118 " --> pdb=" O ILE R 133 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N VAL R 135 " --> pdb=" O LEU R 116 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU R 116 " --> pdb=" O VAL R 135 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 6 through 10 removed outlier: 6.700A pdb=" N VAL S 7 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL S 36 " --> pdb=" O VAL S 7 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE S 9 " --> pdb=" O VAL S 36 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE S 33 " --> pdb=" O LYS S 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'S' and resid 42 through 44 Processing sheet with id=AE3, first strand: chain 'T' and resid 15 through 22 removed outlier: 5.746A pdb=" N SER T 144 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS T 145 " --> pdb=" O VAL T 119 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL T 119 " --> pdb=" O HIS T 145 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU T 147 " --> pdb=" O ILE T 117 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE T 117 " --> pdb=" O GLU T 147 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL T 149 " --> pdb=" O SER T 115 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 58 through 59 Processing sheet with id=AE5, first strand: chain 'U' and resid 62 through 63 removed outlier: 4.574A pdb=" N VAL U 101 " --> pdb=" O VAL U 81 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL U 83 " --> pdb=" O VAL U 101 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA U 103 " --> pdb=" O VAL U 83 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLY U 85 " --> pdb=" O ALA U 103 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG U 105 " --> pdb=" O GLY U 85 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 62 through 63 Processing sheet with id=AE7, first strand: chain 'V' and resid 39 through 41 removed outlier: 4.351A pdb=" N PHE V 411 " --> pdb=" O SER V 11 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 52 through 57 removed outlier: 6.626A pdb=" N VAL V 72 " --> pdb=" O SER V 118 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER V 118 " --> pdb=" O VAL V 72 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU V 74 " --> pdb=" O THR V 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS V 76 " --> pdb=" O GLU V 114 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU V 114 " --> pdb=" O LYS V 76 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER V 78 " --> pdb=" O GLU V 112 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU V 112 " --> pdb=" O SER V 78 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE V 110 " --> pdb=" O HIS V 80 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'V' and resid 147 through 151 removed outlier: 4.107A pdb=" N THR V 147 " --> pdb=" O ALA V 163 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS V 173 " --> pdb=" O LYS V 182 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LYS V 182 " --> pdb=" O LYS V 173 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 194 through 197 removed outlier: 5.402A pdb=" N GLY V 214 " --> pdb=" O LEU V 218 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N LEU V 218 " --> pdb=" O GLY V 214 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU V 223 " --> pdb=" O GLN V 233 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLN V 233 " --> pdb=" O GLU V 223 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 253 through 258 removed outlier: 6.161A pdb=" N ILE V 278 " --> pdb=" O MET V 254 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU V 256 " --> pdb=" O ALA V 276 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA V 276 " --> pdb=" O LEU V 256 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE V 258 " --> pdb=" O GLN V 274 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N GLN V 274 " --> pdb=" O PHE V 258 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N HIS V 283 " --> pdb=" O THR V 279 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA V 297 " --> pdb=" O LYS V 286 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'V' and resid 308 through 314 removed outlier: 5.350A pdb=" N GLN V 310 " --> pdb=" O THR V 341 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR V 341 " --> pdb=" O GLN V 310 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN V 337 " --> pdb=" O PHE V 314 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL V 347 " --> pdb=" O LYS V 359 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LYS V 359 " --> pdb=" O VAL V 347 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS V 349 " --> pdb=" O LEU V 357 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 374 through 375 removed outlier: 6.477A pdb=" N ASP V 393 " --> pdb=" O MET V 399 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N MET V 399 " --> pdb=" O ASP V 393 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'W' and resid 25 through 31 Processing sheet with id=AF6, first strand: chain 'W' and resid 90 through 96 removed outlier: 6.900A pdb=" N ASN W 74 " --> pdb=" O GLU W 128 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU W 128 " --> pdb=" O ASN W 74 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY W 76 " --> pdb=" O VAL W 126 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL W 126 " --> pdb=" O GLY W 76 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP W 78 " --> pdb=" O LEU W 124 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 145 through 147 removed outlier: 6.109A pdb=" N GLY Y 146 " --> pdb=" O ILE Y 169 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE Y 117 " --> pdb=" O LEU Y 168 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA Y 170 " --> pdb=" O ILE Y 117 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL Y 119 " --> pdb=" O ALA Y 170 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE Y 118 " --> pdb=" O ILE Y 194 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL Y 82 " --> pdb=" O LEU Y 226 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU Y 83 " --> pdb=" O ILE Y 250 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 269 through 270 removed outlier: 7.197A pdb=" N VAL Y 269 " --> pdb=" O LEU Y 394 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'Y' and resid 341 through 345 removed outlier: 6.563A pdb=" N ILE Y 292 " --> pdb=" O LEU Y 343 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N CYS Y 345 " --> pdb=" O ILE Y 292 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL Y 294 " --> pdb=" O CYS Y 345 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 50 through 55 removed outlier: 3.643A pdb=" N TYR Z 50 " --> pdb=" O LYS Z 65 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 60 through 61 removed outlier: 5.720A pdb=" N THR a 33 " --> pdb=" O ARG a 60 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU a 87 " --> pdb=" O LEU a 34 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE a 36 " --> pdb=" O LEU a 87 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 109 through 111 removed outlier: 6.110A pdb=" N ILE a 226 " --> pdb=" O ILE a 236 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 115 through 118 removed outlier: 5.869A pdb=" N ASN a 116 " --> pdb=" O VAL a 220 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL a 220 " --> pdb=" O ASN a 116 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 115 through 118 removed outlier: 5.869A pdb=" N ASN a 116 " --> pdb=" O VAL a 220 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL a 220 " --> pdb=" O ASN a 116 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL a 136 " --> pdb=" O MET a 177 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N PHE a 179 " --> pdb=" O VAL a 136 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER a 138 " --> pdb=" O PHE a 179 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N ILE a 181 " --> pdb=" O SER a 138 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASP a 140 " --> pdb=" O ILE a 181 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU a 137 " --> pdb=" O VAL b 223 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N SER b 225 " --> pdb=" O LEU a 137 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N PHE a 139 " --> pdb=" O SER b 225 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 33 through 34 removed outlier: 3.603A pdb=" N ALA c 33 " --> pdb=" O LEU c 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 94 through 98 removed outlier: 6.613A pdb=" N VAL c 85 " --> pdb=" O ILE c 97 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLN c 81 " --> pdb=" O SER c 71 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LYS c 69 " --> pdb=" O ASP c 83 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL c 85 " --> pdb=" O GLU c 67 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N GLU c 67 " --> pdb=" O VAL c 85 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLU c 55 " --> pdb=" O THR c 107 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'i' and resid 72 through 76 Processing sheet with id=AG9, first strand: chain 'j' and resid 64 through 67 removed outlier: 3.576A pdb=" N ARG j 99 " --> pdb=" O ALA j 50 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N VAL j 52 " --> pdb=" O SER j 97 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER j 97 " --> pdb=" O VAL j 52 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU j 29 " --> pdb=" O LEU j 14 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N TYR j 16 " --> pdb=" O VAL j 27 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL j 27 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N ARG j 18 " --> pdb=" O PRO j 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG j 73 " --> pdb=" O ARG j 82 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'n' and resid 16 through 17 1892 hydrogen bonds defined for protein. 5376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1304 hydrogen bonds 2148 hydrogen bond angles 0 basepair planarities 523 basepair parallelities 769 stacking parallelities Total time for adding SS restraints: 59.88 Time building geometry restraints manager: 38.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 19342 1.33 - 1.47: 35866 1.47 - 1.61: 35656 1.61 - 1.75: 108 1.75 - 1.89: 170 Bond restraints: 91142 Sorted by residual: bond pdb=" CA TYR n 39 " pdb=" C TYR n 39 " ideal model delta sigma weight residual 1.526 1.470 0.056 1.14e-02 7.69e+03 2.42e+01 bond pdb=" C ALA Z 138 " pdb=" N PRO Z 139 " ideal model delta sigma weight residual 1.335 1.285 0.050 1.30e-02 5.92e+03 1.47e+01 bond pdb=" CB TRP X 156 " pdb=" CG TRP X 156 " ideal model delta sigma weight residual 1.498 1.382 0.116 3.10e-02 1.04e+03 1.41e+01 bond pdb=" CB ARG j 82 " pdb=" CG ARG j 82 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.36e+01 bond pdb=" CB ASN U 45 " pdb=" CG ASN U 45 " ideal model delta sigma weight residual 1.516 1.428 0.088 2.50e-02 1.60e+03 1.23e+01 ... (remaining 91137 not shown) Histogram of bond angle deviations from ideal: 96.82 - 105.26: 9351 105.26 - 113.70: 56372 113.70 - 122.15: 47691 122.15 - 130.59: 17062 130.59 - 139.03: 933 Bond angle restraints: 131409 Sorted by residual: angle pdb=" C ALA M 58 " pdb=" N PRO M 59 " pdb=" CA PRO M 59 " ideal model delta sigma weight residual 119.84 133.65 -13.81 1.25e+00 6.40e-01 1.22e+02 angle pdb=" C LYS a 103 " pdb=" N PRO a 104 " pdb=" CA PRO a 104 " ideal model delta sigma weight residual 120.38 130.02 -9.64 1.03e+00 9.43e-01 8.77e+01 angle pdb=" N PRO O 119 " pdb=" CA PRO O 119 " pdb=" CB PRO O 119 " ideal model delta sigma weight residual 103.25 111.63 -8.38 1.05e+00 9.07e-01 6.36e+01 angle pdb=" N PRO D 224 " pdb=" CA PRO D 224 " pdb=" C PRO D 224 " ideal model delta sigma weight residual 112.47 96.84 15.63 2.06e+00 2.36e-01 5.76e+01 angle pdb=" C LEU Z 97 " pdb=" N LEU Z 98 " pdb=" CA LEU Z 98 " ideal model delta sigma weight residual 121.90 113.53 8.37 1.26e+00 6.30e-01 4.41e+01 ... (remaining 131404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 52356 35.80 - 71.60: 4462 71.60 - 107.41: 482 107.41 - 143.21: 34 143.21 - 179.01: 39 Dihedral angle restraints: 57373 sinusoidal: 39355 harmonic: 18018 Sorted by residual: dihedral pdb=" CA LYS Y 110 " pdb=" C LYS Y 110 " pdb=" N PRO Y 111 " pdb=" CA PRO Y 111 " ideal model delta harmonic sigma weight residual -180.00 -118.62 -61.38 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA VAL Y 186 " pdb=" C VAL Y 186 " pdb=" N PHE Y 187 " pdb=" CA PHE Y 187 " ideal model delta harmonic sigma weight residual 180.00 -129.17 -50.83 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" O4' U A3214 " pdb=" C1' U A3214 " pdb=" N1 U A3214 " pdb=" C2 U A3214 " ideal model delta sinusoidal sigma weight residual -160.00 19.01 -179.01 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 57370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 12935 0.074 - 0.149: 2832 0.149 - 0.223: 370 0.223 - 0.297: 46 0.297 - 0.372: 6 Chirality restraints: 16189 Sorted by residual: chirality pdb=" C1' G A1346 " pdb=" O4' G A1346 " pdb=" C2' G A1346 " pdb=" N9 G A1346 " both_signs ideal model delta sigma weight residual False 2.46 2.09 0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CB THR P 76 " pdb=" CA THR P 76 " pdb=" OG1 THR P 76 " pdb=" CG2 THR P 76 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C1' U A1405 " pdb=" O4' U A1405 " pdb=" C2' U A1405 " pdb=" N1 U A1405 " both_signs ideal model delta sigma weight residual False 2.47 2.13 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 16186 not shown) Planarity restraints: 10241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 39 " 0.064 2.00e-02 2.50e+03 2.85e-02 2.44e+01 pdb=" N9 G B 39 " -0.067 2.00e-02 2.50e+03 pdb=" C8 G B 39 " 0.000 2.00e-02 2.50e+03 pdb=" N7 G B 39 " 0.004 2.00e-02 2.50e+03 pdb=" C5 G B 39 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G B 39 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G B 39 " 0.024 2.00e-02 2.50e+03 pdb=" N1 G B 39 " -0.007 2.00e-02 2.50e+03 pdb=" C2 G B 39 " -0.012 2.00e-02 2.50e+03 pdb=" N2 G B 39 " 0.012 2.00e-02 2.50e+03 pdb=" N3 G B 39 " -0.014 2.00e-02 2.50e+03 pdb=" C4 G B 39 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU X 157 " 0.079 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO X 158 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO X 158 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO X 158 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 56 " 0.026 2.00e-02 2.50e+03 2.65e-02 2.11e+01 pdb=" N9 G B 56 " -0.012 2.00e-02 2.50e+03 pdb=" C8 G B 56 " -0.007 2.00e-02 2.50e+03 pdb=" N7 G B 56 " -0.007 2.00e-02 2.50e+03 pdb=" C5 G B 56 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G B 56 " -0.061 2.00e-02 2.50e+03 pdb=" O6 G B 56 " 0.052 2.00e-02 2.50e+03 pdb=" N1 G B 56 " 0.021 2.00e-02 2.50e+03 pdb=" C2 G B 56 " -0.024 2.00e-02 2.50e+03 pdb=" N2 G B 56 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 56 " 0.011 2.00e-02 2.50e+03 pdb=" C4 G B 56 " 0.001 2.00e-02 2.50e+03 ... (remaining 10238 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 474 2.30 - 2.95: 46539 2.95 - 3.60: 146426 3.60 - 4.25: 228228 4.25 - 4.90: 334008 Nonbonded interactions: 755675 Sorted by model distance: nonbonded pdb=" O GLU V 236 " pdb=" NH2 ARG V 293 " model vdw 1.653 2.520 nonbonded pdb=" O2 U A3332 " pdb=" O6 G A3371 " model vdw 1.845 2.432 nonbonded pdb=" O2' C A3002 " pdb=" OE2 GLU F 180 " model vdw 1.938 2.440 nonbonded pdb=" O6 G A 754 " pdb=" O2 U A 778 " model vdw 1.970 2.432 nonbonded pdb=" O6 G A 974 " pdb=" O4 U A1108 " model vdw 1.972 2.432 ... (remaining 755670 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 13.720 Check model and map are aligned: 0.940 Set scattering table: 0.620 Process input model: 220.170 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 243.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 : 0.013 0.116 91142 Z= 0.828 Angle : 1.257 17.530 131409 Z= 0.645 Chirality : 0.062 0.372 16189 Planarity : 0.008 0.119 10241 Dihedral : 21.967 179.009 45667 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 36.22 Ramachandran Plot: Outliers : 0.66 % Allowed : 11.79 % Favored : 87.55 % Rotamer: Outliers : 0.29 % Allowed : 2.32 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.30 % Twisted Proline : 1.71 % Twisted General : 0.59 % 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: -5.05 (0.08), residues: 5921 helix: -4.20 (0.07), residues: 1959 sheet: -2.53 (0.14), residues: 867 loop : -3.02 (0.09), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.006 TRP Z 100 HIS 0.021 0.004 HIS G 243 PHE 0.048 0.005 PHE M 32 TYR 0.064 0.005 TYR n 39 ARG 0.023 0.002 ARG a 189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1083 time to evaluate : 5.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 170 GLU cc_start: 0.7119 (mp0) cc_final: 0.6892 (mp0) REVERT: D 176 PHE cc_start: 0.6536 (m-80) cc_final: 0.6130 (m-80) REVERT: E 206 GLU cc_start: 0.5693 (tt0) cc_final: 0.5464 (pt0) REVERT: F 278 ILE cc_start: 0.7787 (tp) cc_final: 0.7341 (tt) REVERT: G 55 LYS cc_start: 0.7928 (ttpp) cc_final: 0.7577 (ttmm) REVERT: H 110 TRP cc_start: 0.7668 (t-100) cc_final: 0.7171 (t-100) REVERT: H 228 LYS cc_start: 0.8119 (tttt) cc_final: 0.7602 (tttt) REVERT: H 299 ASP cc_start: 0.7270 (m-30) cc_final: 0.6854 (m-30) REVERT: K 85 ASN cc_start: 0.8511 (t0) cc_final: 0.8048 (t0) REVERT: K 165 PHE cc_start: 0.8909 (p90) cc_final: 0.8692 (p90) REVERT: L 118 LEU cc_start: 0.7220 (mp) cc_final: 0.7010 (mp) REVERT: L 120 ASP cc_start: 0.7549 (m-30) cc_final: 0.6472 (p0) REVERT: L 162 GLN cc_start: 0.7648 (pt0) cc_final: 0.7446 (tp40) REVERT: M 83 HIS cc_start: 0.7693 (t-90) cc_final: 0.7480 (t-90) REVERT: M 112 TYR cc_start: 0.6302 (p90) cc_final: 0.6033 (p90) REVERT: M 460 TRP cc_start: 0.5730 (m-90) cc_final: 0.5240 (m-90) REVERT: N 61 ARG cc_start: 0.1524 (mmt-90) cc_final: 0.0836 (ptp-170) REVERT: O 157 VAL cc_start: 0.8993 (m) cc_final: 0.8588 (t) REVERT: O 254 VAL cc_start: 0.6868 (t) cc_final: 0.6612 (m) REVERT: O 295 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7607 (pp) REVERT: R 6 TYR cc_start: 0.8355 (m-80) cc_final: 0.7982 (m-80) REVERT: R 29 GLU cc_start: 0.6664 (mp0) cc_final: 0.6155 (mp0) REVERT: S 48 PHE cc_start: 0.7752 (t80) cc_final: 0.7505 (t80) REVERT: S 54 TYR cc_start: 0.7899 (t80) cc_final: 0.7697 (t80) REVERT: S 87 MET cc_start: 0.8262 (mtt) cc_final: 0.8045 (mtt) REVERT: S 91 LYS cc_start: 0.8614 (mptt) cc_final: 0.8371 (mppt) REVERT: T 62 ARG cc_start: 0.7281 (mmt90) cc_final: 0.6888 (mpt-90) REVERT: U 50 LYS cc_start: 0.8160 (tptt) cc_final: 0.7886 (ttpt) REVERT: U 56 LYS cc_start: 0.8273 (tttm) cc_final: 0.7972 (tttp) REVERT: V 228 PHE cc_start: 0.6960 (m-10) cc_final: 0.6653 (m-10) REVERT: V 325 LEU cc_start: 0.7662 (pp) cc_final: 0.7422 (mt) REVERT: W 134 ASP cc_start: 0.6590 (m-30) cc_final: 0.6038 (t0) REVERT: W 147 ASP cc_start: 0.5759 (t70) cc_final: 0.5516 (t0) REVERT: X 44 LYS cc_start: 0.8873 (mptt) cc_final: 0.8453 (mtmt) REVERT: Y 475 LYS cc_start: 0.8601 (tptp) cc_final: 0.8366 (ttpt) REVERT: a 33 THR cc_start: 0.7586 (p) cc_final: 0.7353 (p) REVERT: a 120 MET cc_start: 0.2869 (tpt) cc_final: 0.1445 (tmm) REVERT: a 154 GLU cc_start: 0.6505 (mm-30) cc_final: 0.6160 (mm-30) REVERT: b 201 MET cc_start: 0.4785 (ttm) cc_final: 0.4571 (ttm) REVERT: b 258 ARG cc_start: 0.5664 (ttp-170) cc_final: 0.5422 (ttp-170) REVERT: c 54 ASP cc_start: 0.8296 (p0) cc_final: 0.8041 (p0) REVERT: m 82 ARG cc_start: 0.7990 (mtt180) cc_final: 0.7729 (mtm-85) REVERT: n 46 SER cc_start: 0.8710 (p) cc_final: 0.8470 (p) outliers start: 15 outliers final: 5 residues processed: 1096 average time/residue: 0.8507 time to fit residues: 1549.4722 Evaluate side-chains 719 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 713 time to evaluate : 5.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain V residue 293 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 654 optimal weight: 5.9990 chunk 587 optimal weight: 1.9990 chunk 325 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 396 optimal weight: 7.9990 chunk 313 optimal weight: 5.9990 chunk 607 optimal weight: 0.8980 chunk 235 optimal weight: 8.9990 chunk 369 optimal weight: 40.0000 chunk 452 optimal weight: 7.9990 chunk 703 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 HIS D 269 GLN D 291 GLN E 113 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 GLN F 211 GLN ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 GLN G 48 GLN G 114 ASN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 ASN ** H 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 295 GLN I 57 HIS J 52 GLN K 95 ASN K 137 ASN ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 HIS ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 GLN L 50 ASN ** L 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 156 GLN L 163 GLN ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 20 GLN M 53 ASN ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 410 GLN N 178 GLN O 208 GLN O 215 GLN O 221 ASN O 233 HIS O 262 GLN Q 41 GLN Q 62 GLN R 15 GLN R 37 HIS ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 139 HIS R 182 ASN S 42 ASN ** S 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 97 ASN T 101 ASN ** U 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** V 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 229 GLN ** V 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 337 ASN W 3 HIS ** W 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 62 ASN W 74 ASN ** W 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 GLN X 172 HIS ** X 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 51 GLN Y 266 GLN Y 288 GLN Y 300 ASN Y 330 ASN Z 33 ASN Z 47 ASN Z 85 ASN Z 96 HIS Z 117 GLN ** a 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 195 HIS ** a 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 66 GLN c 120 GLN i 49 ASN j 42 GLN j 75 HIS ** j 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 104 GLN m 35 ASN Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 91142 Z= 0.262 Angle : 0.781 12.187 131409 Z= 0.401 Chirality : 0.043 0.274 16189 Planarity : 0.006 0.125 10241 Dihedral : 23.896 179.946 33431 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 19.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.72 % Favored : 92.10 % Rotamer: Outliers : 2.70 % Allowed : 8.49 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.30 % Twisted Proline : 1.28 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.09), residues: 5921 helix: -2.21 (0.09), residues: 2080 sheet: -1.97 (0.15), residues: 878 loop : -2.50 (0.10), residues: 2963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP V 252 HIS 0.013 0.002 HIS I 172 PHE 0.037 0.002 PHE M 32 TYR 0.044 0.002 TYR H 230 ARG 0.016 0.001 ARG W 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1053 time to evaluate : 5.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 170 GLU cc_start: 0.7024 (mp0) cc_final: 0.6790 (mp0) REVERT: D 233 ASN cc_start: 0.4977 (OUTLIER) cc_final: 0.4689 (m-40) REVERT: E 154 ASN cc_start: 0.7527 (t0) cc_final: 0.7097 (t0) REVERT: E 193 VAL cc_start: 0.5406 (m) cc_final: 0.5014 (m) REVERT: E 195 GLN cc_start: 0.7334 (tt0) cc_final: 0.6800 (tp40) REVERT: E 206 GLU cc_start: 0.5664 (tt0) cc_final: 0.5261 (pt0) REVERT: F 147 GLU cc_start: 0.6723 (mp0) cc_final: 0.6469 (mp0) REVERT: F 332 ARG cc_start: 0.7325 (mpt180) cc_final: 0.7070 (mpt90) REVERT: G 8 VAL cc_start: 0.9243 (t) cc_final: 0.9035 (m) REVERT: G 52 VAL cc_start: 0.8976 (p) cc_final: 0.8696 (m) REVERT: H 140 LEU cc_start: 0.7994 (tt) cc_final: 0.7320 (tp) REVERT: H 299 ASP cc_start: 0.7239 (m-30) cc_final: 0.6805 (m-30) REVERT: I 101 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.6222 (p90) REVERT: J 62 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8264 (mm) REVERT: K 85 ASN cc_start: 0.8105 (t0) cc_final: 0.7894 (t0) REVERT: K 104 GLU cc_start: 0.6272 (tm-30) cc_final: 0.5524 (tm-30) REVERT: K 165 PHE cc_start: 0.8491 (p90) cc_final: 0.8287 (p90) REVERT: L 118 LEU cc_start: 0.7111 (mp) cc_final: 0.6895 (mp) REVERT: L 120 ASP cc_start: 0.7082 (m-30) cc_final: 0.6661 (p0) REVERT: M 38 PHE cc_start: 0.5277 (OUTLIER) cc_final: 0.4907 (m-80) REVERT: M 112 TYR cc_start: 0.6133 (p90) cc_final: 0.5873 (p90) REVERT: M 133 ASP cc_start: 0.7043 (p0) cc_final: 0.6835 (p0) REVERT: M 393 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6261 (mmm) REVERT: M 427 ILE cc_start: 0.4141 (OUTLIER) cc_final: 0.3408 (pp) REVERT: N 53 ILE cc_start: 0.3225 (OUTLIER) cc_final: 0.2699 (tt) REVERT: O 114 LEU cc_start: 0.9138 (mt) cc_final: 0.8872 (tp) REVERT: O 271 GLN cc_start: 0.8019 (pt0) cc_final: 0.7756 (pt0) REVERT: O 295 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7295 (pp) REVERT: P 121 SER cc_start: 0.8539 (p) cc_final: 0.8206 (m) REVERT: R 6 TYR cc_start: 0.7880 (m-80) cc_final: 0.7630 (m-80) REVERT: R 50 ARG cc_start: 0.7707 (ttm-80) cc_final: 0.7034 (mtt-85) REVERT: R 175 ASN cc_start: 0.8155 (p0) cc_final: 0.7904 (p0) REVERT: S 87 MET cc_start: 0.8513 (mtt) cc_final: 0.8312 (mtt) REVERT: T 11 PRO cc_start: 0.8093 (Cg_endo) cc_final: 0.7843 (Cg_exo) REVERT: T 26 PHE cc_start: 0.8080 (t80) cc_final: 0.7793 (t80) REVERT: T 30 ARG cc_start: 0.7255 (ttt90) cc_final: 0.6943 (ttt-90) REVERT: U 50 LYS cc_start: 0.7995 (tptt) cc_final: 0.7750 (ttpt) REVERT: V 325 LEU cc_start: 0.7414 (pp) cc_final: 0.7196 (mt) REVERT: W 27 MET cc_start: 0.7720 (mmt) cc_final: 0.7507 (mmp) REVERT: W 90 MET cc_start: 0.7724 (tmm) cc_final: 0.7207 (tmm) REVERT: W 118 PHE cc_start: 0.7532 (t80) cc_final: 0.7256 (t80) REVERT: W 134 ASP cc_start: 0.6671 (m-30) cc_final: 0.6341 (t0) REVERT: W 147 ASP cc_start: 0.6268 (t70) cc_final: 0.5854 (t0) REVERT: X 44 LYS cc_start: 0.8410 (mptt) cc_final: 0.8141 (mtmt) REVERT: X 205 ILE cc_start: 0.5584 (mm) cc_final: 0.5197 (mm) REVERT: Y 121 THR cc_start: 0.6568 (OUTLIER) cc_final: 0.5601 (p) REVERT: Y 145 PHE cc_start: 0.5795 (OUTLIER) cc_final: 0.5248 (p90) REVERT: Y 355 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6623 (tp) REVERT: Y 440 HIS cc_start: -0.0130 (OUTLIER) cc_final: -0.0820 (p-80) REVERT: a 120 MET cc_start: 0.2555 (tpt) cc_final: 0.1347 (tmm) REVERT: a 154 GLU cc_start: 0.6280 (mm-30) cc_final: 0.6042 (mm-30) REVERT: b 201 MET cc_start: 0.4478 (ttm) cc_final: 0.4171 (ttm) REVERT: c 19 TYR cc_start: 0.9080 (t80) cc_final: 0.8594 (t80) REVERT: c 54 ASP cc_start: 0.8078 (p0) cc_final: 0.7512 (p0) REVERT: i 75 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8119 (tt) REVERT: j 57 LYS cc_start: 0.7652 (ttpt) cc_final: 0.7324 (ttpp) REVERT: j 66 VAL cc_start: 0.9313 (t) cc_final: 0.9089 (m) REVERT: m 86 LYS cc_start: 0.7564 (mmtt) cc_final: 0.6795 (mmtt) outliers start: 141 outliers final: 75 residues processed: 1142 average time/residue: 0.8109 time to fit residues: 1572.6828 Evaluate side-chains 885 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 797 time to evaluate : 5.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 123 THR Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain M residue 38 PHE Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 393 MET Chi-restraints excluded: chain M residue 427 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 49 GLU Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 120 ASN Chi-restraints excluded: chain T residue 151 THR Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain U residue 40 THR Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain X residue 107 CYS Chi-restraints excluded: chain X residue 114 ASP Chi-restraints excluded: chain X residue 176 ILE Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Y residue 145 PHE Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 278 LEU Chi-restraints excluded: chain Y residue 279 LEU Chi-restraints excluded: chain Y residue 355 ILE Chi-restraints excluded: chain Y residue 440 HIS Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 55 CYS Chi-restraints excluded: chain Z residue 83 SER Chi-restraints excluded: chain Z residue 167 MET Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 220 VAL Chi-restraints excluded: chain a residue 221 MET Chi-restraints excluded: chain b residue 244 LEU Chi-restraints excluded: chain c residue 112 ASP Chi-restraints excluded: chain i residue 14 THR Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 81 VAL Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain m residue 47 ILE Chi-restraints excluded: chain m residue 61 ILE Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 71 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 391 optimal weight: 8.9990 chunk 218 optimal weight: 4.9990 chunk 585 optimal weight: 8.9990 chunk 479 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 705 optimal weight: 0.4980 chunk 761 optimal weight: 5.9990 chunk 627 optimal weight: 5.9990 chunk 699 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 565 optimal weight: 7.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 GLN J 159 GLN K 79 GLN ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 ASN ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 200 ASN O 201 ASN O 220 GLN ** O 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 262 GLN ** P 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 118 GLN ** U 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 114 HIS X 43 ASN ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 181 ASN ** Z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 ASN a 82 ASN a 115 GLN b 197 ASN c 120 GLN j 87 ASN j 88 ASN l 104 GLN m 35 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 91142 Z= 0.289 Angle : 0.737 11.889 131409 Z= 0.379 Chirality : 0.042 0.282 16189 Planarity : 0.006 0.109 10241 Dihedral : 23.619 179.566 33427 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.24 % Favored : 90.68 % Rotamer: Outliers : 4.04 % Allowed : 11.57 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.30 % Twisted Proline : 1.28 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.10), residues: 5921 helix: -1.20 (0.10), residues: 2088 sheet: -1.77 (0.16), residues: 891 loop : -2.31 (0.10), residues: 2942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 166 HIS 0.009 0.002 HIS F 13 PHE 0.035 0.002 PHE M 32 TYR 0.033 0.002 TYR R 30 ARG 0.009 0.001 ARG c 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 877 time to evaluate : 5.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 170 GLU cc_start: 0.6915 (mp0) cc_final: 0.6683 (mp0) REVERT: D 233 ASN cc_start: 0.4453 (OUTLIER) cc_final: 0.4245 (m-40) REVERT: D 257 MET cc_start: 0.7190 (tpp) cc_final: 0.6424 (mmm) REVERT: E 102 PHE cc_start: 0.7636 (OUTLIER) cc_final: 0.6499 (t80) REVERT: E 154 ASN cc_start: 0.7581 (t0) cc_final: 0.7373 (t0) REVERT: E 158 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.7499 (mtm) REVERT: E 195 GLN cc_start: 0.7524 (tt0) cc_final: 0.7093 (tp40) REVERT: F 190 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7373 (pm20) REVERT: H 140 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7517 (tp) REVERT: H 231 MET cc_start: 0.6917 (mpp) cc_final: 0.5936 (ttt) REVERT: H 274 TYR cc_start: 0.5021 (OUTLIER) cc_final: 0.4820 (t80) REVERT: I 101 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.6265 (p90) REVERT: J 62 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8165 (mm) REVERT: K 144 GLU cc_start: 0.3295 (tp30) cc_final: 0.3075 (tp30) REVERT: L 118 LEU cc_start: 0.7131 (mp) cc_final: 0.6915 (mp) REVERT: L 162 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7599 (tp-100) REVERT: M 38 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.5151 (m-80) REVERT: M 112 TYR cc_start: 0.6399 (p90) cc_final: 0.5947 (p90) REVERT: M 393 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6416 (mmm) REVERT: M 431 TRP cc_start: 0.5679 (t60) cc_final: 0.4494 (t60) REVERT: M 460 TRP cc_start: 0.3963 (p90) cc_final: 0.3539 (m-90) REVERT: N 53 ILE cc_start: 0.3290 (OUTLIER) cc_final: 0.2797 (tt) REVERT: N 173 LEU cc_start: 0.6318 (OUTLIER) cc_final: 0.5449 (mt) REVERT: O 271 GLN cc_start: 0.7799 (pt0) cc_final: 0.7545 (pt0) REVERT: O 280 TRP cc_start: 0.8356 (t60) cc_final: 0.7398 (t60) REVERT: O 295 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7420 (pp) REVERT: P 121 SER cc_start: 0.8572 (p) cc_final: 0.8259 (m) REVERT: R 6 TYR cc_start: 0.7892 (m-80) cc_final: 0.7397 (m-80) REVERT: S 87 MET cc_start: 0.8511 (mtt) cc_final: 0.8310 (mtt) REVERT: T 26 PHE cc_start: 0.8338 (t80) cc_final: 0.8090 (t80) REVERT: T 30 ARG cc_start: 0.7688 (ttt90) cc_final: 0.7029 (ttt-90) REVERT: T 47 TYR cc_start: 0.8342 (t80) cc_final: 0.7714 (t80) REVERT: U 50 LYS cc_start: 0.8016 (tptt) cc_final: 0.7777 (ttpt) REVERT: W 27 MET cc_start: 0.7687 (mmt) cc_final: 0.7394 (mmp) REVERT: W 90 MET cc_start: 0.7798 (tmm) cc_final: 0.7416 (tmm) REVERT: W 134 ASP cc_start: 0.6942 (m-30) cc_final: 0.6542 (t0) REVERT: W 147 ASP cc_start: 0.6198 (t70) cc_final: 0.5854 (t0) REVERT: X 44 LYS cc_start: 0.8468 (mptt) cc_final: 0.8265 (mtmt) REVERT: X 178 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8261 (tt) REVERT: Y 76 LEU cc_start: 0.7145 (tp) cc_final: 0.6889 (tp) REVERT: Y 121 THR cc_start: 0.6698 (OUTLIER) cc_final: 0.5817 (p) REVERT: Y 145 PHE cc_start: 0.6303 (OUTLIER) cc_final: 0.5401 (p90) REVERT: Y 159 GLU cc_start: 0.7479 (tt0) cc_final: 0.7130 (tt0) REVERT: Y 174 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5923 (ptm-80) REVERT: Y 181 ASN cc_start: 0.4826 (m-40) cc_final: 0.4597 (m-40) REVERT: Y 322 LYS cc_start: 0.8068 (mmmm) cc_final: 0.7859 (mmtt) REVERT: Y 363 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7581 (mp10) REVERT: Y 433 ILE cc_start: 0.2977 (OUTLIER) cc_final: 0.2684 (mt) REVERT: Y 440 HIS cc_start: 0.0336 (OUTLIER) cc_final: -0.0334 (p-80) REVERT: Z 4 GLU cc_start: 0.8174 (pm20) cc_final: 0.7764 (pm20) REVERT: a 28 MET cc_start: 0.6377 (tmm) cc_final: 0.6102 (tpt) REVERT: a 120 MET cc_start: 0.2240 (tpt) cc_final: 0.1370 (tmm) REVERT: a 214 GLU cc_start: 0.3775 (tp30) cc_final: 0.1079 (mt-10) REVERT: b 201 MET cc_start: 0.4687 (ttm) cc_final: 0.4381 (ttm) REVERT: b 215 HIS cc_start: 0.4702 (t-90) cc_final: 0.4258 (t-90) REVERT: c 80 VAL cc_start: 0.9250 (p) cc_final: 0.9033 (m) REVERT: i 49 ASN cc_start: 0.7723 (m110) cc_final: 0.7345 (m110) REVERT: j 57 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7718 (ttpp) REVERT: j 66 VAL cc_start: 0.9356 (t) cc_final: 0.9041 (m) outliers start: 211 outliers final: 124 residues processed: 1016 average time/residue: 0.8563 time to fit residues: 1508.2205 Evaluate side-chains 922 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 779 time to evaluate : 5.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 222 VAL Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 283 THR Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 274 TYR Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain I residue 88 SER Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain M residue 38 PHE Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 393 MET Chi-restraints excluded: chain M residue 412 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain Q residue 98 SER Chi-restraints excluded: chain Q residue 103 ILE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 89 SER Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 49 GLU Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 120 ASN Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 151 THR Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain U residue 26 LEU Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain U residue 111 ARG Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 138 ARG Chi-restraints excluded: chain V residue 356 MET Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain X residue 107 CYS Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Y residue 145 PHE Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 174 ARG Chi-restraints excluded: chain Y residue 260 THR Chi-restraints excluded: chain Y residue 278 LEU Chi-restraints excluded: chain Y residue 279 LEU Chi-restraints excluded: chain Y residue 316 VAL Chi-restraints excluded: chain Y residue 331 THR Chi-restraints excluded: chain Y residue 348 VAL Chi-restraints excluded: chain Y residue 433 ILE Chi-restraints excluded: chain Y residue 440 HIS Chi-restraints excluded: chain Z residue 23 ASN Chi-restraints excluded: chain Z residue 26 ASN Chi-restraints excluded: chain Z residue 33 ASN Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 55 CYS Chi-restraints excluded: chain Z residue 167 MET Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain a residue 186 ILE Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 220 VAL Chi-restraints excluded: chain a residue 221 MET Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 91 ASN Chi-restraints excluded: chain i residue 14 THR Chi-restraints excluded: chain i residue 50 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 66 LEU Chi-restraints excluded: chain i residue 82 LEU Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 115 LEU Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 56 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 81 VAL Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain m residue 47 ILE Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain n residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 696 optimal weight: 10.0000 chunk 530 optimal weight: 5.9990 chunk 365 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 336 optimal weight: 1.9990 chunk 473 optimal weight: 8.9990 chunk 707 optimal weight: 9.9990 chunk 749 optimal weight: 0.7980 chunk 369 optimal weight: 20.0000 chunk 670 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 159 GLN ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 157 ASN ** M 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 221 ASN P 25 HIS R 15 GLN ** S 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 375 HIS ** W 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 46 GLN ** X 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 229 ASN ** X 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 143 GLN Z 33 ASN Z 146 GLN a 128 ASN a 239 ASN j 87 ASN j 88 ASN m 35 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 91142 Z= 0.253 Angle : 0.693 11.442 131409 Z= 0.356 Chirality : 0.040 0.274 16189 Planarity : 0.005 0.110 10241 Dihedral : 23.470 179.793 33426 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.75 % Favored : 91.13 % Rotamer: Outliers : 4.23 % Allowed : 13.91 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.30 % Twisted Proline : 1.28 % Twisted General : 0.12 % 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: -2.38 (0.10), residues: 5921 helix: -0.76 (0.11), residues: 2105 sheet: -1.71 (0.16), residues: 888 loop : -2.15 (0.11), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP M 166 HIS 0.009 0.001 HIS F 13 PHE 0.035 0.002 PHE M 32 TYR 0.047 0.002 TYR R 30 ARG 0.008 0.001 ARG T 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 861 time to evaluate : 5.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 179 LEU cc_start: 0.6807 (tt) cc_final: 0.6398 (tp) REVERT: E 132 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7353 (ttm-80) REVERT: E 154 ASN cc_start: 0.7510 (t0) cc_final: 0.6804 (t0) REVERT: E 155 TYR cc_start: 0.7804 (t80) cc_final: 0.7503 (t80) REVERT: E 158 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7550 (mtm) REVERT: E 195 GLN cc_start: 0.7567 (tt0) cc_final: 0.6997 (tp40) REVERT: F 71 GLU cc_start: 0.6154 (pt0) cc_final: 0.4872 (mm-30) REVERT: F 90 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8354 (m) REVERT: H 140 LEU cc_start: 0.8049 (tt) cc_final: 0.7490 (tp) REVERT: H 274 TYR cc_start: 0.6644 (OUTLIER) cc_final: 0.5015 (t80) REVERT: I 101 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.6244 (p90) REVERT: L 162 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7639 (tp-100) REVERT: M 38 PHE cc_start: 0.5914 (OUTLIER) cc_final: 0.5224 (m-80) REVERT: M 112 TYR cc_start: 0.6434 (p90) cc_final: 0.6031 (p90) REVERT: M 133 ASP cc_start: 0.6110 (p0) cc_final: 0.5839 (p0) REVERT: M 460 TRP cc_start: 0.4153 (p90) cc_final: 0.3733 (m-90) REVERT: N 173 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5160 (mt) REVERT: N 177 LEU cc_start: 0.4676 (tp) cc_final: 0.4226 (tp) REVERT: O 280 TRP cc_start: 0.8324 (t60) cc_final: 0.7498 (t60) REVERT: O 295 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7351 (pp) REVERT: P 121 SER cc_start: 0.8471 (p) cc_final: 0.8175 (m) REVERT: R 6 TYR cc_start: 0.7805 (m-80) cc_final: 0.7365 (m-80) REVERT: T 47 TYR cc_start: 0.8407 (t80) cc_final: 0.7912 (t80) REVERT: W 90 MET cc_start: 0.7808 (tmm) cc_final: 0.7189 (tmm) REVERT: W 134 ASP cc_start: 0.6864 (m-30) cc_final: 0.6481 (t0) REVERT: W 147 ASP cc_start: 0.6202 (t70) cc_final: 0.5932 (t0) REVERT: X 44 LYS cc_start: 0.8421 (mptt) cc_final: 0.8212 (mtmt) REVERT: X 175 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5893 (p0) REVERT: X 178 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8281 (tt) REVERT: Y 76 LEU cc_start: 0.7411 (tp) cc_final: 0.7187 (tp) REVERT: Y 121 THR cc_start: 0.6801 (OUTLIER) cc_final: 0.5917 (p) REVERT: Y 145 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5346 (p90) REVERT: Y 159 GLU cc_start: 0.7177 (tt0) cc_final: 0.6896 (tt0) REVERT: Y 227 PHE cc_start: 0.5543 (m-80) cc_final: 0.5124 (m-80) REVERT: Y 322 LYS cc_start: 0.8104 (mmmm) cc_final: 0.7899 (mmtt) REVERT: Y 433 ILE cc_start: 0.3049 (OUTLIER) cc_final: 0.2730 (mt) REVERT: Y 440 HIS cc_start: 0.0325 (OUTLIER) cc_final: -0.0334 (p-80) REVERT: Z 4 GLU cc_start: 0.7845 (pm20) cc_final: 0.7525 (pm20) REVERT: a 120 MET cc_start: 0.1918 (tpt) cc_final: 0.1125 (tmm) REVERT: a 223 VAL cc_start: 0.7509 (t) cc_final: 0.7296 (m) REVERT: a 231 PHE cc_start: 0.6177 (m-80) cc_final: 0.5878 (m-10) REVERT: b 201 MET cc_start: 0.4366 (ttm) cc_final: 0.4161 (ttm) REVERT: c 54 ASP cc_start: 0.7972 (p0) cc_final: 0.7654 (p0) REVERT: c 80 VAL cc_start: 0.9128 (p) cc_final: 0.8887 (m) REVERT: i 49 ASN cc_start: 0.7685 (m110) cc_final: 0.7312 (m110) REVERT: j 63 LYS cc_start: 0.8408 (mmmm) cc_final: 0.8002 (mmtp) REVERT: m 86 LYS cc_start: 0.7542 (mmtt) cc_final: 0.6959 (mmtm) outliers start: 221 outliers final: 141 residues processed: 1003 average time/residue: 0.7975 time to fit residues: 1365.5738 Evaluate side-chains 930 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 776 time to evaluate : 5.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 129 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 158 SER Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 274 TYR Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 191 ASN Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain M residue 38 PHE Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 412 VAL Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 179 VAL Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 246 TYR Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 15 GLN Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 184 THR Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 GLN Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 120 ASN Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain U residue 26 LEU Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain U residue 111 ARG Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 138 ARG Chi-restraints excluded: chain V residue 268 LYS Chi-restraints excluded: chain V residue 342 ASP Chi-restraints excluded: chain V residue 346 ASN Chi-restraints excluded: chain V residue 356 MET Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain X residue 57 ASP Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 175 ASP Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Y residue 145 PHE Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 260 THR Chi-restraints excluded: chain Y residue 278 LEU Chi-restraints excluded: chain Y residue 279 LEU Chi-restraints excluded: chain Y residue 307 GLU Chi-restraints excluded: chain Y residue 316 VAL Chi-restraints excluded: chain Y residue 331 THR Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Y residue 348 VAL Chi-restraints excluded: chain Y residue 433 ILE Chi-restraints excluded: chain Y residue 440 HIS Chi-restraints excluded: chain Z residue 23 ASN Chi-restraints excluded: chain Z residue 26 ASN Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 167 MET Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain a residue 186 ILE Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 220 VAL Chi-restraints excluded: chain a residue 243 VAL Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 91 ASN Chi-restraints excluded: chain i residue 14 THR Chi-restraints excluded: chain i residue 50 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 66 LEU Chi-restraints excluded: chain i residue 73 THR Chi-restraints excluded: chain i residue 82 LEU Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 86 THR Chi-restraints excluded: chain i residue 115 LEU Chi-restraints excluded: chain j residue 22 VAL Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 81 VAL Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 109 ILE Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 46 SER Chi-restraints excluded: chain n residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 623 optimal weight: 6.9990 chunk 425 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 557 optimal weight: 5.9990 chunk 309 optimal weight: 0.0970 chunk 639 optimal weight: 8.9990 chunk 517 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 382 optimal weight: 10.0000 chunk 672 optimal weight: 0.7980 chunk 189 optimal weight: 20.0000 overall best weight: 3.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 101 ASN J 25 GLN ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 ASN M 14 ASN ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 GLN O 221 ASN P 106 GLN Q 41 GLN ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 GLN V 24 ASN ** V 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 330 ASN Z 33 ASN b 197 ASN j 87 ASN m 35 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 91142 Z= 0.293 Angle : 0.711 11.515 131409 Z= 0.364 Chirality : 0.041 0.308 16189 Planarity : 0.005 0.113 10241 Dihedral : 23.418 179.728 33426 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.71 % Favored : 90.19 % Rotamer: Outliers : 5.00 % Allowed : 14.83 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.30 % Twisted Proline : 1.28 % Twisted General : 0.10 % 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: -2.28 (0.10), residues: 5921 helix: -0.65 (0.11), residues: 2106 sheet: -1.73 (0.17), residues: 891 loop : -2.09 (0.11), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 166 HIS 0.010 0.001 HIS F 13 PHE 0.033 0.002 PHE M 32 TYR 0.060 0.002 TYR R 30 ARG 0.007 0.001 ARG L 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 826 time to evaluate : 5.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 PHE cc_start: 0.7750 (OUTLIER) cc_final: 0.6477 (t80) REVERT: E 158 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7360 (mtm) REVERT: E 165 ARG cc_start: 0.8079 (ptp90) cc_final: 0.7834 (mtm-85) REVERT: E 195 GLN cc_start: 0.7165 (tt0) cc_final: 0.6846 (tp40) REVERT: F 90 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8397 (m) REVERT: F 190 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: H 274 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.4803 (t80) REVERT: I 80 ASN cc_start: 0.8556 (t0) cc_final: 0.8203 (t0) REVERT: I 101 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.6323 (p90) REVERT: L 110 LYS cc_start: 0.7247 (ttpp) cc_final: 0.6961 (mttt) REVERT: L 162 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7585 (tp-100) REVERT: M 38 PHE cc_start: 0.5857 (OUTLIER) cc_final: 0.5606 (m-80) REVERT: M 112 TYR cc_start: 0.6651 (p90) cc_final: 0.6064 (p90) REVERT: M 133 ASP cc_start: 0.6160 (p0) cc_final: 0.5859 (p0) REVERT: M 199 TRP cc_start: 0.6818 (p90) cc_final: 0.6592 (p90) REVERT: M 431 TRP cc_start: 0.5625 (t60) cc_final: 0.5124 (t60) REVERT: M 442 VAL cc_start: -0.0168 (OUTLIER) cc_final: -0.0506 (p) REVERT: M 460 TRP cc_start: 0.4169 (p90) cc_final: 0.3669 (m-90) REVERT: N 53 ILE cc_start: 0.3014 (OUTLIER) cc_final: 0.2715 (tt) REVERT: N 173 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5153 (mt) REVERT: N 177 LEU cc_start: 0.4658 (tp) cc_final: 0.4186 (tp) REVERT: N 223 ARG cc_start: 0.3297 (tpt170) cc_final: 0.2560 (ppt170) REVERT: O 280 TRP cc_start: 0.8284 (t60) cc_final: 0.7458 (t60) REVERT: O 295 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7507 (pp) REVERT: P 121 SER cc_start: 0.8468 (p) cc_final: 0.8267 (m) REVERT: R 6 TYR cc_start: 0.7830 (m-80) cc_final: 0.7375 (m-80) REVERT: S 87 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8297 (mtt) REVERT: S 106 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: T 30 ARG cc_start: 0.7972 (ttt90) cc_final: 0.7407 (ttt90) REVERT: T 47 TYR cc_start: 0.8290 (t80) cc_final: 0.7773 (t80) REVERT: W 90 MET cc_start: 0.7858 (tmm) cc_final: 0.7166 (tmm) REVERT: W 134 ASP cc_start: 0.6907 (m-30) cc_final: 0.6541 (t0) REVERT: X 44 LYS cc_start: 0.8511 (mptt) cc_final: 0.8231 (mtmt) REVERT: X 137 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6662 (tp-100) REVERT: X 175 ASP cc_start: 0.5607 (OUTLIER) cc_final: 0.5376 (p0) REVERT: X 178 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8345 (tt) REVERT: Y 121 THR cc_start: 0.6781 (OUTLIER) cc_final: 0.5855 (p) REVERT: Y 145 PHE cc_start: 0.6433 (OUTLIER) cc_final: 0.5453 (p90) REVERT: Y 159 GLU cc_start: 0.7194 (tt0) cc_final: 0.6889 (tt0) REVERT: Y 227 PHE cc_start: 0.5681 (m-80) cc_final: 0.5269 (m-80) REVERT: Y 433 ILE cc_start: 0.2929 (OUTLIER) cc_final: 0.2590 (mt) REVERT: Y 440 HIS cc_start: 0.0220 (OUTLIER) cc_final: -0.0365 (p-80) REVERT: Z 4 GLU cc_start: 0.7816 (pm20) cc_final: 0.7528 (pm20) REVERT: a 120 MET cc_start: 0.1988 (tpt) cc_final: 0.1111 (tmm) REVERT: a 214 GLU cc_start: 0.3700 (tp30) cc_final: 0.1062 (mt-10) REVERT: a 231 PHE cc_start: 0.6183 (m-80) cc_final: 0.5728 (m-10) REVERT: c 54 ASP cc_start: 0.7959 (p0) cc_final: 0.7654 (p0) REVERT: c 80 VAL cc_start: 0.9141 (p) cc_final: 0.8886 (m) REVERT: i 49 ASN cc_start: 0.7728 (m110) cc_final: 0.7342 (m110) REVERT: j 63 LYS cc_start: 0.8490 (mmmm) cc_final: 0.7929 (mmmt) REVERT: l 64 GLU cc_start: 0.6943 (pp20) cc_final: 0.6686 (pp20) REVERT: m 86 LYS cc_start: 0.7690 (mmtt) cc_final: 0.7094 (mmtm) outliers start: 261 outliers final: 181 residues processed: 1000 average time/residue: 0.7792 time to fit residues: 1353.4726 Evaluate side-chains 970 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 769 time to evaluate : 5.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 274 TYR Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 191 ASN Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain M residue 38 PHE Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 412 VAL Chi-restraints excluded: chain M residue 442 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 179 VAL Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 221 ASN Chi-restraints excluded: chain O residue 246 TYR Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 103 ILE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain S residue 89 SER Chi-restraints excluded: chain S residue 106 GLU Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 45 GLN Chi-restraints excluded: chain T residue 49 GLU Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 120 ASN Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 151 THR Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 26 LEU Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain U residue 111 ARG Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain V residue 38 PHE Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 138 ARG Chi-restraints excluded: chain V residue 268 LYS Chi-restraints excluded: chain V residue 342 ASP Chi-restraints excluded: chain V residue 346 ASN Chi-restraints excluded: chain V residue 356 MET Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain X residue 57 ASP Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 137 GLN Chi-restraints excluded: chain X residue 156 TRP Chi-restraints excluded: chain X residue 175 ASP Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Y residue 145 PHE Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 174 ARG Chi-restraints excluded: chain Y residue 260 THR Chi-restraints excluded: chain Y residue 278 LEU Chi-restraints excluded: chain Y residue 279 LEU Chi-restraints excluded: chain Y residue 296 LEU Chi-restraints excluded: chain Y residue 307 GLU Chi-restraints excluded: chain Y residue 316 VAL Chi-restraints excluded: chain Y residue 331 THR Chi-restraints excluded: chain Y residue 348 VAL Chi-restraints excluded: chain Y residue 433 ILE Chi-restraints excluded: chain Y residue 440 HIS Chi-restraints excluded: chain Z residue 10 ILE Chi-restraints excluded: chain Z residue 16 SER Chi-restraints excluded: chain Z residue 23 ASN Chi-restraints excluded: chain Z residue 26 ASN Chi-restraints excluded: chain Z residue 33 ASN Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 55 CYS Chi-restraints excluded: chain Z residue 167 MET Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain a residue 182 VAL Chi-restraints excluded: chain a residue 186 ILE Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 220 VAL Chi-restraints excluded: chain a residue 243 VAL Chi-restraints excluded: chain b residue 233 ILE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 91 ASN Chi-restraints excluded: chain i residue 14 THR Chi-restraints excluded: chain i residue 50 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 66 LEU Chi-restraints excluded: chain i residue 73 THR Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 82 LEU Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 86 THR Chi-restraints excluded: chain i residue 115 LEU Chi-restraints excluded: chain j residue 22 VAL Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 56 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 81 VAL Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain l residue 20 GLN Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 109 ILE Chi-restraints excluded: chain m residue 47 ILE Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 46 SER Chi-restraints excluded: chain n residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 252 optimal weight: 0.9990 chunk 674 optimal weight: 7.9990 chunk 148 optimal weight: 40.0000 chunk 439 optimal weight: 5.9990 chunk 184 optimal weight: 30.0000 chunk 749 optimal weight: 0.3980 chunk 622 optimal weight: 10.0000 chunk 347 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 393 optimal weight: 0.4980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 ASN F 371 GLN ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 25 GLN ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 221 ASN ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 ASN ** V 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 197 ASN j 87 ASN m 35 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 91142 Z= 0.179 Angle : 0.642 19.021 131409 Z= 0.328 Chirality : 0.038 0.288 16189 Planarity : 0.005 0.114 10241 Dihedral : 23.243 179.621 33426 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.09 % Favored : 91.79 % Rotamer: Outliers : 4.14 % Allowed : 16.72 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.30 % Twisted Proline : 1.28 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.11), residues: 5921 helix: -0.29 (0.11), residues: 2089 sheet: -1.59 (0.17), residues: 926 loop : -1.94 (0.11), residues: 2906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 166 HIS 0.009 0.001 HIS F 13 PHE 0.032 0.002 PHE M 32 TYR 0.064 0.002 TYR R 30 ARG 0.017 0.000 ARG L 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 906 time to evaluate : 5.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 95 VAL cc_start: 0.8442 (t) cc_final: 0.8088 (p) REVERT: E 102 PHE cc_start: 0.7542 (OUTLIER) cc_final: 0.6404 (t80) REVERT: E 155 TYR cc_start: 0.7511 (t80) cc_final: 0.7282 (t80) REVERT: E 200 MET cc_start: 0.2722 (ttt) cc_final: 0.2250 (ptm) REVERT: F 136 LYS cc_start: 0.7434 (pptt) cc_final: 0.6992 (ptmm) REVERT: F 190 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: H 274 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.4597 (t80) REVERT: I 13 GLU cc_start: 0.8146 (mp0) cc_final: 0.7888 (mp0) REVERT: I 80 ASN cc_start: 0.8488 (t0) cc_final: 0.8208 (t0) REVERT: I 101 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6165 (p90) REVERT: L 154 VAL cc_start: 0.5806 (m) cc_final: 0.5427 (m) REVERT: L 162 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7635 (tp-100) REVERT: M 20 GLN cc_start: 0.6346 (OUTLIER) cc_final: 0.5757 (mm-40) REVERT: M 133 ASP cc_start: 0.5951 (p0) cc_final: 0.5557 (p0) REVERT: M 199 TRP cc_start: 0.6547 (p90) cc_final: 0.6261 (p90) REVERT: M 431 TRP cc_start: 0.5426 (t60) cc_final: 0.4510 (t60) REVERT: M 460 TRP cc_start: 0.3872 (p90) cc_final: 0.3488 (m-90) REVERT: N 173 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5375 (mt) REVERT: N 177 LEU cc_start: 0.4539 (tp) cc_final: 0.4069 (tp) REVERT: N 223 ARG cc_start: 0.3136 (tpt170) cc_final: 0.2591 (ppt170) REVERT: O 280 TRP cc_start: 0.8135 (t60) cc_final: 0.7372 (t60) REVERT: O 286 MET cc_start: 0.7775 (ttm) cc_final: 0.7566 (ttm) REVERT: O 295 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7159 (pp) REVERT: R 6 TYR cc_start: 0.7704 (m-80) cc_final: 0.7367 (m-80) REVERT: S 87 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8279 (mtt) REVERT: S 167 TYR cc_start: 0.8719 (t80) cc_final: 0.8388 (t80) REVERT: T 11 PRO cc_start: 0.7937 (Cg_endo) cc_final: 0.7661 (Cg_exo) REVERT: T 30 ARG cc_start: 0.7839 (ttt90) cc_final: 0.7422 (ttt-90) REVERT: T 47 TYR cc_start: 0.8226 (t80) cc_final: 0.7861 (t80) REVERT: W 90 MET cc_start: 0.7931 (tmm) cc_final: 0.7347 (tmm) REVERT: W 134 ASP cc_start: 0.6869 (m-30) cc_final: 0.6465 (t0) REVERT: X 175 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.5676 (p0) REVERT: Y 121 THR cc_start: 0.6751 (OUTLIER) cc_final: 0.5866 (p) REVERT: Y 145 PHE cc_start: 0.6114 (OUTLIER) cc_final: 0.5400 (p90) REVERT: Y 157 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6555 (pt0) REVERT: Y 159 GLU cc_start: 0.7198 (tt0) cc_final: 0.6985 (tt0) REVERT: Y 162 MET cc_start: 0.8263 (mmp) cc_final: 0.7858 (mmp) REVERT: Y 433 ILE cc_start: 0.2585 (OUTLIER) cc_final: 0.2303 (mt) REVERT: Y 440 HIS cc_start: 0.0197 (OUTLIER) cc_final: -0.0612 (p-80) REVERT: Z 4 GLU cc_start: 0.7525 (pm20) cc_final: 0.7098 (pm20) REVERT: a 231 PHE cc_start: 0.5861 (m-80) cc_final: 0.5557 (m-10) REVERT: b 197 ASN cc_start: 0.4204 (OUTLIER) cc_final: 0.3798 (t0) REVERT: b 268 PHE cc_start: 0.4628 (OUTLIER) cc_final: 0.4316 (t80) REVERT: c 54 ASP cc_start: 0.7882 (p0) cc_final: 0.7537 (p0) REVERT: i 49 ASN cc_start: 0.7629 (m110) cc_final: 0.7229 (m110) REVERT: m 46 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6725 (mm-30) REVERT: m 86 LYS cc_start: 0.7488 (mmtt) cc_final: 0.7022 (mmtm) outliers start: 216 outliers final: 142 residues processed: 1042 average time/residue: 0.7801 time to fit residues: 1399.8555 Evaluate side-chains 950 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 792 time to evaluate : 5.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 274 TYR Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 191 ASN Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 393 MET Chi-restraints excluded: chain M residue 412 VAL Chi-restraints excluded: chain M residue 432 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain Q residue 12 TRP Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain S residue 89 SER Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 120 ASN Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain U residue 26 LEU Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain U residue 111 ARG Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain V residue 38 PHE Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 346 ASN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain X residue 57 ASP Chi-restraints excluded: chain X residue 175 ASP Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Y residue 145 PHE Chi-restraints excluded: chain Y residue 157 GLU Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 174 ARG Chi-restraints excluded: chain Y residue 278 LEU Chi-restraints excluded: chain Y residue 279 LEU Chi-restraints excluded: chain Y residue 296 LEU Chi-restraints excluded: chain Y residue 307 GLU Chi-restraints excluded: chain Y residue 316 VAL Chi-restraints excluded: chain Y residue 348 VAL Chi-restraints excluded: chain Y residue 433 ILE Chi-restraints excluded: chain Y residue 440 HIS Chi-restraints excluded: chain Z residue 16 SER Chi-restraints excluded: chain Z residue 23 ASN Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 55 CYS Chi-restraints excluded: chain Z residue 167 MET Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain a residue 182 VAL Chi-restraints excluded: chain a residue 186 ILE Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 220 VAL Chi-restraints excluded: chain a residue 243 VAL Chi-restraints excluded: chain b residue 197 ASN Chi-restraints excluded: chain b residue 233 ILE Chi-restraints excluded: chain b residue 268 PHE Chi-restraints excluded: chain c residue 91 ASN Chi-restraints excluded: chain i residue 66 LEU Chi-restraints excluded: chain i residue 73 THR Chi-restraints excluded: chain i residue 75 LEU Chi-restraints excluded: chain i residue 82 LEU Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 56 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 81 VAL Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 98 SER Chi-restraints excluded: chain l residue 109 ILE Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain n residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 722 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 427 optimal weight: 20.0000 chunk 547 optimal weight: 20.0000 chunk 424 optimal weight: 9.9990 chunk 631 optimal weight: 40.0000 chunk 418 optimal weight: 30.0000 chunk 746 optimal weight: 10.0000 chunk 467 optimal weight: 5.9990 chunk 455 optimal weight: 0.5980 chunk 344 optimal weight: 2.9990 overall best weight: 5.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 221 ASN ** O 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 HIS ** X 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 330 ASN Z 33 ASN a 29 ASN a 31 GLN a 150 GLN b 196 ASN ** i 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 87 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 91142 Z= 0.404 Angle : 0.780 11.962 131409 Z= 0.396 Chirality : 0.043 0.287 16189 Planarity : 0.006 0.119 10241 Dihedral : 23.349 179.872 33426 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.29 % Favored : 89.65 % Rotamer: Outliers : 5.23 % Allowed : 16.74 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.30 % Twisted Proline : 1.28 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.10), residues: 5921 helix: -0.58 (0.11), residues: 2113 sheet: -1.74 (0.17), residues: 887 loop : -2.07 (0.11), residues: 2921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP T 83 HIS 0.010 0.002 HIS F 13 PHE 0.031 0.002 PHE M 32 TYR 0.060 0.002 TYR R 30 ARG 0.016 0.001 ARG L 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 787 time to evaluate : 5.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6523 (t80) REVERT: E 149 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8288 (tm130) REVERT: E 155 TYR cc_start: 0.7034 (t80) cc_final: 0.6808 (t80) REVERT: E 200 MET cc_start: 0.3344 (ttt) cc_final: 0.2977 (ptm) REVERT: F 136 LYS cc_start: 0.7485 (pptt) cc_final: 0.7048 (ptmm) REVERT: F 190 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7164 (pm20) REVERT: H 194 MET cc_start: 0.7690 (tmm) cc_final: 0.7337 (ttp) REVERT: H 268 GLU cc_start: 0.6412 (mp0) cc_final: 0.5971 (mp0) REVERT: H 274 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.4397 (t80) REVERT: I 13 GLU cc_start: 0.8010 (mp0) cc_final: 0.7570 (mp0) REVERT: I 80 ASN cc_start: 0.8605 (t0) cc_final: 0.8265 (t0) REVERT: I 101 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.6149 (p90) REVERT: K 204 ARG cc_start: 0.7777 (ttm110) cc_final: 0.7555 (ptm160) REVERT: L 110 LYS cc_start: 0.6929 (ttpp) cc_final: 0.6674 (mttt) REVERT: L 162 GLN cc_start: 0.7928 (tp-100) cc_final: 0.7320 (tp-100) REVERT: L 179 ILE cc_start: 0.8672 (mm) cc_final: 0.8427 (mp) REVERT: M 20 GLN cc_start: 0.6420 (OUTLIER) cc_final: 0.5760 (mm-40) REVERT: M 133 ASP cc_start: 0.6221 (p0) cc_final: 0.5903 (p0) REVERT: M 431 TRP cc_start: 0.5665 (t60) cc_final: 0.4571 (t60) REVERT: M 442 VAL cc_start: -0.0372 (OUTLIER) cc_final: -0.0593 (p) REVERT: M 460 TRP cc_start: 0.4537 (p90) cc_final: 0.3617 (m-90) REVERT: N 173 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5312 (mt) REVERT: N 177 LEU cc_start: 0.4235 (tp) cc_final: 0.3694 (tp) REVERT: N 223 ARG cc_start: 0.3227 (tpt170) cc_final: 0.2619 (ppt170) REVERT: O 280 TRP cc_start: 0.8193 (t60) cc_final: 0.7414 (t60) REVERT: O 295 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7440 (pp) REVERT: R 6 TYR cc_start: 0.7924 (m-80) cc_final: 0.7483 (m-80) REVERT: S 27 LEU cc_start: 0.8097 (mt) cc_final: 0.7790 (mt) REVERT: S 46 GLU cc_start: 0.8152 (pm20) cc_final: 0.7905 (pm20) REVERT: S 87 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8260 (mtt) REVERT: T 30 ARG cc_start: 0.8135 (ttt90) cc_final: 0.7861 (ttt90) REVERT: T 47 TYR cc_start: 0.8212 (t80) cc_final: 0.7740 (t80) REVERT: W 90 MET cc_start: 0.8021 (tmm) cc_final: 0.7262 (tmm) REVERT: W 134 ASP cc_start: 0.7129 (m-30) cc_final: 0.6845 (t0) REVERT: X 137 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.6684 (tp-100) REVERT: X 178 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8492 (tt) REVERT: Y 121 THR cc_start: 0.6958 (OUTLIER) cc_final: 0.6052 (p) REVERT: Y 145 PHE cc_start: 0.6421 (OUTLIER) cc_final: 0.5594 (p90) REVERT: Y 157 GLU cc_start: 0.7262 (pt0) cc_final: 0.6898 (pt0) REVERT: Y 162 MET cc_start: 0.8427 (mmp) cc_final: 0.8046 (mmp) REVERT: Y 318 GLU cc_start: 0.7532 (pm20) cc_final: 0.7247 (pm20) REVERT: Y 433 ILE cc_start: 0.2912 (OUTLIER) cc_final: 0.2648 (mt) REVERT: Y 440 HIS cc_start: 0.0391 (OUTLIER) cc_final: -0.0068 (p-80) REVERT: Z 4 GLU cc_start: 0.7644 (pm20) cc_final: 0.7232 (pm20) REVERT: a 193 ILE cc_start: 0.1827 (OUTLIER) cc_final: 0.1197 (pp) REVERT: a 214 GLU cc_start: 0.3455 (tp30) cc_final: 0.0640 (mt-10) REVERT: c 54 ASP cc_start: 0.7987 (p0) cc_final: 0.7648 (p0) REVERT: i 49 ASN cc_start: 0.7822 (m110) cc_final: 0.7401 (m110) REVERT: m 86 LYS cc_start: 0.7635 (mmtt) cc_final: 0.7074 (mmtt) outliers start: 273 outliers final: 204 residues processed: 970 average time/residue: 0.7767 time to fit residues: 1306.3842 Evaluate side-chains 959 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 738 time to evaluate : 5.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 61 SER Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 274 TYR Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain J residue 188 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 191 ASN Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 138 MET Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 393 MET Chi-restraints excluded: chain M residue 412 VAL Chi-restraints excluded: chain M residue 432 ILE Chi-restraints excluded: chain M residue 442 VAL Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 53 ILE Chi-restraints excluded: chain N residue 56 THR Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 109 CYS Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 176 SER Chi-restraints excluded: chain O residue 221 ASN Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain Q residue 12 TRP Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 49 GLU Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 120 ASN Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 151 THR Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 26 LEU Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain U residue 111 ARG Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 129 VAL Chi-restraints excluded: chain V residue 18 ILE Chi-restraints excluded: chain V residue 38 PHE Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 342 ASP Chi-restraints excluded: chain V residue 346 ASN Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain W residue 16 THR Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain X residue 57 ASP Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 137 GLN Chi-restraints excluded: chain X residue 156 TRP Chi-restraints excluded: chain X residue 177 LEU Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Y residue 145 PHE Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 174 ARG Chi-restraints excluded: chain Y residue 225 MET Chi-restraints excluded: chain Y residue 260 THR Chi-restraints excluded: chain Y residue 278 LEU Chi-restraints excluded: chain Y residue 279 LEU Chi-restraints excluded: chain Y residue 307 GLU Chi-restraints excluded: chain Y residue 316 VAL Chi-restraints excluded: chain Y residue 331 THR Chi-restraints excluded: chain Y residue 364 PHE Chi-restraints excluded: chain Y residue 432 LEU Chi-restraints excluded: chain Y residue 433 ILE Chi-restraints excluded: chain Y residue 440 HIS Chi-restraints excluded: chain Z residue 17 HIS Chi-restraints excluded: chain Z residue 23 ASN Chi-restraints excluded: chain Z residue 26 ASN Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 55 CYS Chi-restraints excluded: chain Z residue 167 MET Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain a residue 182 VAL Chi-restraints excluded: chain a residue 186 ILE Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 193 ILE Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 220 VAL Chi-restraints excluded: chain a residue 243 VAL Chi-restraints excluded: chain b residue 197 ASN Chi-restraints excluded: chain b residue 233 ILE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 91 ASN Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain i residue 14 THR Chi-restraints excluded: chain i residue 50 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 66 LEU Chi-restraints excluded: chain i residue 73 THR Chi-restraints excluded: chain i residue 82 LEU Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 99 ASN Chi-restraints excluded: chain i residue 115 LEU Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 22 VAL Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 52 VAL Chi-restraints excluded: chain j residue 56 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 81 VAL Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 109 ILE Chi-restraints excluded: chain m residue 61 ILE Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 46 SER Chi-restraints excluded: chain n residue 70 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 462 optimal weight: 0.9980 chunk 298 optimal weight: 20.0000 chunk 446 optimal weight: 0.8980 chunk 225 optimal weight: 8.9990 chunk 146 optimal weight: 40.0000 chunk 144 optimal weight: 20.0000 chunk 474 optimal weight: 1.9990 chunk 508 optimal weight: 0.5980 chunk 369 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 587 optimal weight: 7.9990 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 215 GLN ** O 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 GLN ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 64 ASN ** V 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 142 GLN X 73 HIS X 132 GLN ** X 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 330 ASN Z 33 ASN a 115 GLN a 150 GLN b 197 ASN j 87 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 91142 Z= 0.218 Angle : 0.669 12.064 131409 Z= 0.341 Chirality : 0.039 0.250 16189 Planarity : 0.005 0.121 10241 Dihedral : 23.221 179.667 33426 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.71 % Favored : 91.22 % Rotamer: Outliers : 4.27 % Allowed : 18.26 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.30 % Twisted Proline : 1.28 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.11), residues: 5921 helix: -0.30 (0.11), residues: 2106 sheet: -1.69 (0.17), residues: 920 loop : -1.98 (0.11), residues: 2895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP M 166 HIS 0.009 0.001 HIS F 13 PHE 0.037 0.002 PHE Y 96 TYR 0.062 0.002 TYR R 30 ARG 0.019 0.000 ARG L 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1043 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 820 time to evaluate : 5.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 196 ILE cc_start: 0.7641 (mt) cc_final: 0.7395 (mp) REVERT: E 102 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.6417 (t80) REVERT: E 152 MET cc_start: 0.6167 (mmp) cc_final: 0.5242 (mmm) REVERT: E 162 LEU cc_start: 0.8638 (mt) cc_final: 0.8208 (mt) REVERT: F 190 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7150 (pm20) REVERT: H 194 MET cc_start: 0.7598 (tmm) cc_final: 0.7197 (ttp) REVERT: H 232 ASN cc_start: 0.5777 (t0) cc_final: 0.5475 (t0) REVERT: H 274 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.4380 (t80) REVERT: I 13 GLU cc_start: 0.8093 (mp0) cc_final: 0.7587 (mp0) REVERT: I 80 ASN cc_start: 0.8447 (t0) cc_final: 0.8136 (t0) REVERT: I 101 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.6242 (p90) REVERT: L 162 GLN cc_start: 0.8005 (tp-100) cc_final: 0.7471 (tp-100) REVERT: M 20 GLN cc_start: 0.6361 (OUTLIER) cc_final: 0.5750 (mm-40) REVERT: M 133 ASP cc_start: 0.6059 (p0) cc_final: 0.5687 (p0) REVERT: M 197 VAL cc_start: 0.7200 (m) cc_final: 0.6986 (m) REVERT: M 431 TRP cc_start: 0.5453 (t60) cc_final: 0.4764 (t60) REVERT: M 460 TRP cc_start: 0.4340 (p90) cc_final: 0.3876 (m-90) REVERT: N 62 MET cc_start: 0.5820 (OUTLIER) cc_final: 0.5570 (ttm) REVERT: N 173 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5244 (mt) REVERT: N 177 LEU cc_start: 0.4208 (tp) cc_final: 0.3891 (tp) REVERT: N 223 ARG cc_start: 0.3092 (tpt170) cc_final: 0.2619 (ppt170) REVERT: O 280 TRP cc_start: 0.8093 (t60) cc_final: 0.7344 (t60) REVERT: O 295 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7343 (pp) REVERT: R 6 TYR cc_start: 0.7801 (m-80) cc_final: 0.7469 (m-80) REVERT: S 46 GLU cc_start: 0.8126 (pm20) cc_final: 0.7900 (pm20) REVERT: S 87 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8313 (mtt) REVERT: T 30 ARG cc_start: 0.7954 (ttt90) cc_final: 0.7342 (ttt-90) REVERT: T 47 TYR cc_start: 0.8138 (t80) cc_final: 0.7705 (t80) REVERT: W 21 GLU cc_start: 0.5531 (tp30) cc_final: 0.5066 (tp30) REVERT: W 90 MET cc_start: 0.7965 (tmm) cc_final: 0.7369 (tmm) REVERT: W 134 ASP cc_start: 0.7078 (m-30) cc_final: 0.6510 (t0) REVERT: Y 121 THR cc_start: 0.6852 (OUTLIER) cc_final: 0.5979 (p) REVERT: Y 145 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5466 (p90) REVERT: Y 162 MET cc_start: 0.8184 (mmp) cc_final: 0.7851 (mmp) REVERT: Y 440 HIS cc_start: -0.0029 (OUTLIER) cc_final: -0.0589 (p-80) REVERT: Z 18 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6097 (mtm-85) REVERT: Z 39 THR cc_start: 0.7938 (p) cc_final: 0.7694 (p) REVERT: a 231 PHE cc_start: 0.5579 (m-80) cc_final: 0.5279 (m-10) REVERT: i 49 ASN cc_start: 0.7702 (m110) cc_final: 0.7273 (m110) REVERT: l 64 GLU cc_start: 0.6669 (pp20) cc_final: 0.6370 (pp20) REVERT: m 86 LYS cc_start: 0.7402 (mmtt) cc_final: 0.6785 (mmtm) outliers start: 223 outliers final: 173 residues processed: 966 average time/residue: 0.8674 time to fit residues: 1466.8977 Evaluate side-chains 962 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 776 time to evaluate : 5.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 149 GLN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 274 TYR Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 191 ASN Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 393 MET Chi-restraints excluded: chain M residue 412 VAL Chi-restraints excluded: chain M residue 432 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 241 PHE Chi-restraints excluded: chain O residue 246 TYR Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain Q residue 11 ASN Chi-restraints excluded: chain Q residue 12 TRP Chi-restraints excluded: chain Q residue 103 ILE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 10 LEU Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 166 GLU Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 120 ASN Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 26 LEU Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain U residue 111 ARG Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain V residue 12 CYS Chi-restraints excluded: chain V residue 18 ILE Chi-restraints excluded: chain V residue 38 PHE Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 342 ASP Chi-restraints excluded: chain V residue 346 ASN Chi-restraints excluded: chain V residue 356 MET Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain X residue 57 ASP Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 156 TRP Chi-restraints excluded: chain X residue 177 LEU Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Y residue 145 PHE Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 174 ARG Chi-restraints excluded: chain Y residue 278 LEU Chi-restraints excluded: chain Y residue 279 LEU Chi-restraints excluded: chain Y residue 307 GLU Chi-restraints excluded: chain Y residue 316 VAL Chi-restraints excluded: chain Y residue 331 THR Chi-restraints excluded: chain Y residue 364 PHE Chi-restraints excluded: chain Y residue 440 HIS Chi-restraints excluded: chain Z residue 16 SER Chi-restraints excluded: chain Z residue 17 HIS Chi-restraints excluded: chain Z residue 18 ARG Chi-restraints excluded: chain Z residue 23 ASN Chi-restraints excluded: chain Z residue 33 ASN Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 167 MET Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain a residue 182 VAL Chi-restraints excluded: chain a residue 186 ILE Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 220 VAL Chi-restraints excluded: chain a residue 243 VAL Chi-restraints excluded: chain b residue 233 ILE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 91 ASN Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 66 LEU Chi-restraints excluded: chain i residue 73 THR Chi-restraints excluded: chain i residue 82 LEU Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 22 VAL Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain j residue 37 THR Chi-restraints excluded: chain j residue 56 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 92 LYS Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 109 ILE Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 46 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 679 optimal weight: 6.9990 chunk 715 optimal weight: 20.0000 chunk 652 optimal weight: 4.9990 chunk 696 optimal weight: 10.0000 chunk 418 optimal weight: 20.0000 chunk 303 optimal weight: 9.9990 chunk 546 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 629 optimal weight: 7.9990 chunk 658 optimal weight: 0.6980 chunk 693 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 149 GLN ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 ASN ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 221 ASN ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 330 ASN a 150 GLN b 197 ASN ** i 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 87 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 91142 Z= 0.371 Angle : 0.759 11.658 131409 Z= 0.386 Chirality : 0.042 0.320 16189 Planarity : 0.006 0.125 10241 Dihedral : 23.285 179.822 33426 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.49 % Favored : 89.44 % Rotamer: Outliers : 4.43 % Allowed : 18.39 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.30 % Twisted Proline : 0.85 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 5921 helix: -0.47 (0.11), residues: 2101 sheet: -1.80 (0.17), residues: 887 loop : -2.08 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP X 54 HIS 0.010 0.002 HIS F 13 PHE 0.032 0.002 PHE M 32 TYR 0.062 0.002 TYR R 30 ARG 0.019 0.001 ARG L 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 760 time to evaluate : 5.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: E 102 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.6591 (t80) REVERT: E 152 MET cc_start: 0.6566 (mmp) cc_final: 0.5197 (mmm) REVERT: F 190 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7197 (pm20) REVERT: H 194 MET cc_start: 0.7699 (tmm) cc_final: 0.7413 (ttp) REVERT: H 274 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.4316 (t80) REVERT: I 80 ASN cc_start: 0.8582 (t0) cc_final: 0.8255 (t0) REVERT: I 101 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.6417 (p90) REVERT: L 154 VAL cc_start: 0.5958 (m) cc_final: 0.5742 (m) REVERT: L 162 GLN cc_start: 0.7740 (tp-100) cc_final: 0.7165 (tp-100) REVERT: M 20 GLN cc_start: 0.6244 (OUTLIER) cc_final: 0.5644 (mm-40) REVERT: M 133 ASP cc_start: 0.6186 (p0) cc_final: 0.5822 (p0) REVERT: M 431 TRP cc_start: 0.5645 (t60) cc_final: 0.4514 (t60) REVERT: N 173 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.5302 (mt) REVERT: N 177 LEU cc_start: 0.4163 (tp) cc_final: 0.3822 (tp) REVERT: N 223 ARG cc_start: 0.3166 (tpt170) cc_final: 0.2660 (ppt170) REVERT: O 280 TRP cc_start: 0.8147 (t60) cc_final: 0.7481 (t60) REVERT: O 295 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7469 (pp) REVERT: R 6 TYR cc_start: 0.7898 (m-80) cc_final: 0.7542 (m-80) REVERT: S 46 GLU cc_start: 0.8160 (pm20) cc_final: 0.7936 (pm20) REVERT: S 54 TYR cc_start: 0.7680 (t80) cc_final: 0.7466 (t80) REVERT: S 87 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.8258 (mtt) REVERT: T 30 ARG cc_start: 0.8201 (ttt90) cc_final: 0.7878 (ttt90) REVERT: T 47 TYR cc_start: 0.8112 (t80) cc_final: 0.7692 (t80) REVERT: W 90 MET cc_start: 0.8020 (tmm) cc_final: 0.7299 (tmm) REVERT: X 137 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6747 (tp-100) REVERT: Y 121 THR cc_start: 0.7040 (OUTLIER) cc_final: 0.6154 (p) REVERT: Y 145 PHE cc_start: 0.6383 (OUTLIER) cc_final: 0.5630 (p90) REVERT: Y 157 GLU cc_start: 0.7185 (pt0) cc_final: 0.6907 (pt0) REVERT: Y 162 MET cc_start: 0.8310 (mmp) cc_final: 0.7923 (mmp) REVERT: Y 440 HIS cc_start: 0.0175 (OUTLIER) cc_final: -0.0200 (p-80) REVERT: Z 18 ARG cc_start: 0.7686 (OUTLIER) cc_final: 0.6962 (mtt-85) REVERT: Z 39 THR cc_start: 0.8253 (p) cc_final: 0.7969 (p) REVERT: a 214 GLU cc_start: 0.3111 (tp30) cc_final: 0.0176 (mt-10) REVERT: a 231 PHE cc_start: 0.5680 (m-80) cc_final: 0.5409 (m-10) REVERT: i 49 ASN cc_start: 0.7819 (m110) cc_final: 0.7390 (m110) REVERT: l 64 GLU cc_start: 0.6772 (pp20) cc_final: 0.6362 (pp20) REVERT: m 86 LYS cc_start: 0.7527 (mmtt) cc_final: 0.7072 (mmtt) outliers start: 231 outliers final: 194 residues processed: 917 average time/residue: 0.7753 time to fit residues: 1232.5943 Evaluate side-chains 946 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 739 time to evaluate : 5.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 274 TYR Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 191 ASN Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 179 ILE Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 393 MET Chi-restraints excluded: chain M residue 412 VAL Chi-restraints excluded: chain M residue 432 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 109 CYS Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 221 ASN Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 241 PHE Chi-restraints excluded: chain O residue 246 TYR Chi-restraints excluded: chain O residue 295 LEU Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain Q residue 11 ASN Chi-restraints excluded: chain Q residue 12 TRP Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 103 ILE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 120 ASN Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 151 THR Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 26 LEU Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain U residue 111 ARG Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain V residue 12 CYS Chi-restraints excluded: chain V residue 18 ILE Chi-restraints excluded: chain V residue 38 PHE Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 247 MET Chi-restraints excluded: chain V residue 342 ASP Chi-restraints excluded: chain V residue 346 ASN Chi-restraints excluded: chain V residue 356 MET Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain X residue 57 ASP Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 137 GLN Chi-restraints excluded: chain X residue 156 TRP Chi-restraints excluded: chain X residue 177 LEU Chi-restraints excluded: chain X residue 199 GLU Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Y residue 145 PHE Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 174 ARG Chi-restraints excluded: chain Y residue 260 THR Chi-restraints excluded: chain Y residue 278 LEU Chi-restraints excluded: chain Y residue 279 LEU Chi-restraints excluded: chain Y residue 296 LEU Chi-restraints excluded: chain Y residue 307 GLU Chi-restraints excluded: chain Y residue 316 VAL Chi-restraints excluded: chain Y residue 331 THR Chi-restraints excluded: chain Y residue 364 PHE Chi-restraints excluded: chain Y residue 440 HIS Chi-restraints excluded: chain Z residue 16 SER Chi-restraints excluded: chain Z residue 17 HIS Chi-restraints excluded: chain Z residue 18 ARG Chi-restraints excluded: chain Z residue 23 ASN Chi-restraints excluded: chain Z residue 26 ASN Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 64 MET Chi-restraints excluded: chain Z residue 167 MET Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain a residue 182 VAL Chi-restraints excluded: chain a residue 186 ILE Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 220 VAL Chi-restraints excluded: chain a residue 243 VAL Chi-restraints excluded: chain b residue 197 ASN Chi-restraints excluded: chain b residue 233 ILE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 91 ASN Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 66 LEU Chi-restraints excluded: chain i residue 73 THR Chi-restraints excluded: chain i residue 82 LEU Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 86 THR Chi-restraints excluded: chain i residue 115 LEU Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 22 VAL Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain j residue 56 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 92 LYS Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 109 ILE Chi-restraints excluded: chain l residue 118 ILE Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 46 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 457 optimal weight: 7.9990 chunk 736 optimal weight: 8.9990 chunk 449 optimal weight: 9.9990 chunk 349 optimal weight: 4.9990 chunk 511 optimal weight: 20.0000 chunk 772 optimal weight: 2.9990 chunk 710 optimal weight: 2.9990 chunk 614 optimal weight: 0.0010 chunk 63 optimal weight: 9.9990 chunk 474 optimal weight: 2.9990 chunk 376 optimal weight: 9.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 330 ASN Y 464 GLN a 150 GLN b 197 ASN ** i 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.170 91142 Z= 0.338 Angle : 0.809 59.110 131409 Z= 0.424 Chirality : 0.042 0.792 16189 Planarity : 0.006 0.130 10241 Dihedral : 23.288 179.826 33426 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.57 % Favored : 89.34 % Rotamer: Outliers : 4.41 % Allowed : 18.74 % Favored : 76.86 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.30 % Twisted Proline : 0.85 % Twisted General : 0.10 % 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: -2.21 (0.10), residues: 5921 helix: -0.48 (0.11), residues: 2101 sheet: -1.81 (0.17), residues: 887 loop : -2.09 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP X 54 HIS 0.017 0.001 HIS G 311 PHE 0.033 0.002 PHE F 209 TYR 0.058 0.002 TYR R 30 ARG 0.023 0.001 ARG L 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11842 Ramachandran restraints generated. 5921 Oldfield, 0 Emsley, 5921 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 742 time to evaluate : 5.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.6588 (t80) REVERT: E 152 MET cc_start: 0.6443 (mmp) cc_final: 0.5126 (mmt) REVERT: F 190 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7194 (pm20) REVERT: H 194 MET cc_start: 0.7695 (tmm) cc_final: 0.7401 (ttp) REVERT: H 268 GLU cc_start: 0.6110 (mp0) cc_final: 0.5718 (mp0) REVERT: H 274 TYR cc_start: 0.6556 (OUTLIER) cc_final: 0.4316 (t80) REVERT: I 80 ASN cc_start: 0.8568 (t0) cc_final: 0.8258 (t0) REVERT: I 101 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.6420 (p90) REVERT: L 162 GLN cc_start: 0.7737 (tp-100) cc_final: 0.7162 (tp-100) REVERT: M 20 GLN cc_start: 0.6410 (OUTLIER) cc_final: 0.5773 (mm-40) REVERT: M 133 ASP cc_start: 0.6192 (p0) cc_final: 0.5832 (p0) REVERT: M 431 TRP cc_start: 0.5637 (t60) cc_final: 0.4510 (t60) REVERT: N 173 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.5299 (mt) REVERT: N 177 LEU cc_start: 0.4156 (tp) cc_final: 0.3814 (tp) REVERT: N 223 ARG cc_start: 0.3162 (tpt170) cc_final: 0.2659 (ppt170) REVERT: O 280 TRP cc_start: 0.8150 (t60) cc_final: 0.7477 (t60) REVERT: R 6 TYR cc_start: 0.7892 (m-80) cc_final: 0.7534 (m-80) REVERT: S 46 GLU cc_start: 0.8155 (pm20) cc_final: 0.7932 (pm20) REVERT: S 54 TYR cc_start: 0.7683 (t80) cc_final: 0.7452 (t80) REVERT: S 87 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8250 (mtt) REVERT: T 30 ARG cc_start: 0.8190 (ttt90) cc_final: 0.7867 (ttt90) REVERT: T 47 TYR cc_start: 0.8113 (t80) cc_final: 0.7684 (t80) REVERT: W 90 MET cc_start: 0.8013 (tmm) cc_final: 0.7296 (tmm) REVERT: X 137 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.6737 (tp-100) REVERT: X 178 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8471 (tt) REVERT: Y 121 THR cc_start: 0.7037 (OUTLIER) cc_final: 0.6150 (p) REVERT: Y 145 PHE cc_start: 0.6384 (OUTLIER) cc_final: 0.5626 (p90) REVERT: Y 157 GLU cc_start: 0.7180 (pt0) cc_final: 0.6899 (pt0) REVERT: Y 162 MET cc_start: 0.8298 (mmp) cc_final: 0.7918 (mmp) REVERT: Y 440 HIS cc_start: 0.0175 (OUTLIER) cc_final: -0.0212 (p-80) REVERT: Z 18 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6931 (mtt-85) REVERT: Z 39 THR cc_start: 0.8224 (p) cc_final: 0.7944 (p) REVERT: i 49 ASN cc_start: 0.7814 (m110) cc_final: 0.7383 (m110) REVERT: l 64 GLU cc_start: 0.6762 (pp20) cc_final: 0.6350 (pp20) REVERT: m 86 LYS cc_start: 0.7516 (mmtt) cc_final: 0.7032 (mmtt) outliers start: 230 outliers final: 206 residues processed: 896 average time/residue: 0.7763 time to fit residues: 1207.1805 Evaluate side-chains 955 residues out of total 5227 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 736 time to evaluate : 5.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 233 ASN Chi-restraints excluded: chain D residue 267 PHE Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 141 ASN Chi-restraints excluded: chain E residue 147 ILE Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 24 SER Chi-restraints excluded: chain F residue 39 LYS Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain F residue 71 GLU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 190 GLU Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain G residue 7 THR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 55 LYS Chi-restraints excluded: chain G residue 71 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 230 VAL Chi-restraints excluded: chain G residue 269 SER Chi-restraints excluded: chain G residue 299 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 139 ASP Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 274 TYR Chi-restraints excluded: chain H residue 281 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 101 PHE Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 120 THR Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 181 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 161 GLU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 191 ASN Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain M residue 20 GLN Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 118 ILE Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain M residue 231 PHE Chi-restraints excluded: chain M residue 376 LEU Chi-restraints excluded: chain M residue 393 MET Chi-restraints excluded: chain M residue 412 VAL Chi-restraints excluded: chain M residue 432 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 62 MET Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 109 CYS Chi-restraints excluded: chain N residue 114 VAL Chi-restraints excluded: chain N residue 148 VAL Chi-restraints excluded: chain N residue 173 LEU Chi-restraints excluded: chain N residue 218 ILE Chi-restraints excluded: chain O residue 136 SER Chi-restraints excluded: chain O residue 146 ASP Chi-restraints excluded: chain O residue 221 ASN Chi-restraints excluded: chain O residue 223 ASP Chi-restraints excluded: chain O residue 241 PHE Chi-restraints excluded: chain O residue 246 TYR Chi-restraints excluded: chain P residue 51 LEU Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain Q residue 11 ASN Chi-restraints excluded: chain Q residue 12 TRP Chi-restraints excluded: chain Q residue 63 VAL Chi-restraints excluded: chain Q residue 103 ILE Chi-restraints excluded: chain R residue 8 GLU Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 29 GLU Chi-restraints excluded: chain R residue 34 ASN Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 180 PHE Chi-restraints excluded: chain S residue 87 MET Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 36 ILE Chi-restraints excluded: chain T residue 55 GLN Chi-restraints excluded: chain T residue 88 VAL Chi-restraints excluded: chain T residue 114 VAL Chi-restraints excluded: chain T residue 119 VAL Chi-restraints excluded: chain T residue 120 ASN Chi-restraints excluded: chain T residue 146 ILE Chi-restraints excluded: chain T residue 151 THR Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 26 LEU Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 63 SER Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 94 PHE Chi-restraints excluded: chain U residue 111 ARG Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain V residue 12 CYS Chi-restraints excluded: chain V residue 18 ILE Chi-restraints excluded: chain V residue 38 PHE Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 203 THR Chi-restraints excluded: chain V residue 247 MET Chi-restraints excluded: chain V residue 342 ASP Chi-restraints excluded: chain V residue 346 ASN Chi-restraints excluded: chain V residue 356 MET Chi-restraints excluded: chain V residue 366 THR Chi-restraints excluded: chain V residue 413 VAL Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain W residue 87 THR Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 145 THR Chi-restraints excluded: chain W residue 156 VAL Chi-restraints excluded: chain X residue 57 ASP Chi-restraints excluded: chain X residue 72 LEU Chi-restraints excluded: chain X residue 111 PHE Chi-restraints excluded: chain X residue 137 GLN Chi-restraints excluded: chain X residue 156 TRP Chi-restraints excluded: chain X residue 177 LEU Chi-restraints excluded: chain X residue 178 LEU Chi-restraints excluded: chain X residue 199 GLU Chi-restraints excluded: chain Y residue 121 THR Chi-restraints excluded: chain Y residue 145 PHE Chi-restraints excluded: chain Y residue 149 ILE Chi-restraints excluded: chain Y residue 171 THR Chi-restraints excluded: chain Y residue 174 ARG Chi-restraints excluded: chain Y residue 260 THR Chi-restraints excluded: chain Y residue 278 LEU Chi-restraints excluded: chain Y residue 279 LEU Chi-restraints excluded: chain Y residue 296 LEU Chi-restraints excluded: chain Y residue 307 GLU Chi-restraints excluded: chain Y residue 316 VAL Chi-restraints excluded: chain Y residue 331 THR Chi-restraints excluded: chain Y residue 364 PHE Chi-restraints excluded: chain Y residue 440 HIS Chi-restraints excluded: chain Z residue 16 SER Chi-restraints excluded: chain Z residue 17 HIS Chi-restraints excluded: chain Z residue 18 ARG Chi-restraints excluded: chain Z residue 23 ASN Chi-restraints excluded: chain Z residue 26 ASN Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 64 MET Chi-restraints excluded: chain Z residue 167 MET Chi-restraints excluded: chain a residue 136 VAL Chi-restraints excluded: chain a residue 176 VAL Chi-restraints excluded: chain a residue 179 PHE Chi-restraints excluded: chain a residue 182 VAL Chi-restraints excluded: chain a residue 186 ILE Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 219 PHE Chi-restraints excluded: chain a residue 220 VAL Chi-restraints excluded: chain a residue 243 VAL Chi-restraints excluded: chain b residue 233 ILE Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 91 ASN Chi-restraints excluded: chain c residue 106 ILE Chi-restraints excluded: chain i residue 59 SER Chi-restraints excluded: chain i residue 66 LEU Chi-restraints excluded: chain i residue 73 THR Chi-restraints excluded: chain i residue 82 LEU Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 86 THR Chi-restraints excluded: chain i residue 99 ASN Chi-restraints excluded: chain i residue 115 LEU Chi-restraints excluded: chain j residue 14 LEU Chi-restraints excluded: chain j residue 22 VAL Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain j residue 56 SER Chi-restraints excluded: chain j residue 59 VAL Chi-restraints excluded: chain j residue 62 SER Chi-restraints excluded: chain j residue 93 THR Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain l residue 58 ILE Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 93 THR Chi-restraints excluded: chain l residue 109 ILE Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 84 LYS Chi-restraints excluded: chain n residue 18 LEU Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 46 SER Chi-restraints excluded: chain n residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 488 optimal weight: 0.9980 chunk 654 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 566 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 chunk 615 optimal weight: 10.0000 chunk 257 optimal weight: 1.9990 chunk 632 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 113 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 330 ASN a 150 GLN b 197 ASN ** i 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.129402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097170 restraints weight = 218142.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.096992 restraints weight = 192184.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096947 restraints weight = 139548.599| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.360 91142 Z= 0.380 Angle : 0.812 59.199 131409 Z= 0.422 Chirality : 0.044 1.515 16189 Planarity : 0.006 0.131 10241 Dihedral : 23.288 179.874 33424 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.56 % Favored : 89.38 % Rotamer: Outliers : 4.75 % Allowed : 18.35 % Favored : 76.90 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 6.41 % Cis-general : 0.30 % Twisted Proline : 0.85 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.10), residues: 5921 helix: -0.49 (0.11), residues: 2101 sheet: -1.82 (0.17), residues: 887 loop : -2.09 (0.11), residues: 2933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP X 54 HIS 0.015 0.001 HIS G 311 PHE 0.031 0.002 PHE M 32 TYR 0.153 0.003 TYR a 43 ARG 0.028 0.001 ARG L 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19556.35 seconds wall clock time: 346 minutes 23.00 seconds (20783.00 seconds total)