Starting phenix.real_space_refine on Mon Jan 20 11:37:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xyi_6788/01_2025/5xyi_6788_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xyi_6788/01_2025/5xyi_6788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5xyi_6788/01_2025/5xyi_6788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xyi_6788/01_2025/5xyi_6788.map" model { file = "/net/cci-nas-00/data/ceres_data/5xyi_6788/01_2025/5xyi_6788_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xyi_6788/01_2025/5xyi_6788_neut.cif" } resolution = 3.35 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1490 5.49 5 S 159 5.16 5 C 35713 2.51 5 N 12093 2.21 5 O 16469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 196 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 65924 Number of models: 1 Model: "" Number of chains: 34 Chain: "2" Number of atoms: 31820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1490, 31820 Classifications: {'RNA': 1490} Modifications used: {'rna2p_pur': 135, 'rna2p_pyr': 109, 'rna3p_pur': 665, 'rna3p_pyr': 581} Link IDs: {'rna2p': 243, 'rna3p': 1246} Chain breaks: 17 Chain: "A" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1603 Classifications: {'peptide': 204} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 194} Chain breaks: 3 Chain: "B" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1747 Classifications: {'peptide': 219} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 213} Chain breaks: 1 Chain: "C" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1685 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 10, 'TRANS': 206} Chain breaks: 1 Chain: "D" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1655 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 6, 'TRANS': 201} Chain breaks: 1 Chain: "E" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1935 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 10, 'TRANS': 235} Chain breaks: 1 Chain: "F" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1476 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 179} Chain breaks: 1 Chain: "G" Number of atoms: 155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 155 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "H" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1276 Classifications: {'peptide': 163} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 155} Chain breaks: 1 Chain: "I" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1300 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "J" Number of atoms: 1321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1321 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 157} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "K" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 731 Classifications: {'peptide': 90} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 84} Chain breaks: 1 Chain: "L" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1160 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 133} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 509 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'CIS': 2, 'PTRANS': 1, 'TRANS': 99} Chain breaks: 2 Unresolved non-hydrogen bonds: 298 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 144 Chain: "N" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1190 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 143} Chain: "O" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1005 Classifications: {'peptide': 135} Link IDs: {'CIS': 2, 'PTRANS': 5, 'TRANS': 127} Chain: "P" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 962 Classifications: {'peptide': 118} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 110} Chain breaks: 1 Chain: "Q" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1043 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 2 Chain: "R" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 961 Classifications: {'peptide': 118} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 112} Chain: "S" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1077 Classifications: {'peptide': 135} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 128} Chain: "T" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1148 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "U" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 777 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain breaks: 2 Chain: "V" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 671 Classifications: {'peptide': 87} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 81} Chain: "W" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 124} Chain breaks: 1 Chain: "X" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1062 Classifications: {'peptide': 140} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 133} Chain: "Y" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 792 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 102} Chain breaks: 2 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "Z" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 560 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "a" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 815 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "b" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 632 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 8, 'TRANS': 73} Chain: "c" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 475 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "d" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "e" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 337 Classifications: {'peptide': 42} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 37} Chain: "g" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2380 Classifications: {'peptide': 305} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain breaks: 2 Chain: "n" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 225 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Time building chain proxies: 25.95, per 1000 atoms: 0.39 Number of scatterers: 65924 At special positions: 0 Unit cell: (216.48, 223.08, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 159 16.00 P 1490 15.00 O 16469 8.00 N 12093 7.00 C 35713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 26 " distance=2.36 Simple disulfide: pdb=" SG CYS a 23 " - pdb=" SG CYS a 77 " distance=2.66 Simple disulfide: pdb=" SG CYS a 26 " - pdb=" SG CYS a 77 " distance=1.53 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 43 " distance=2.86 Simple disulfide: pdb=" SG CYS d 25 " - pdb=" SG CYS d 43 " distance=2.95 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 10.69 Conformation dependent library (CDL) restraints added in 3.8 seconds 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8152 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 57 sheets defined 35.0% alpha, 15.3% beta 367 base pairs and 759 stacking pairs defined. Time for finding SS restraints: 19.81 Creating SS restraints... Processing helix chain 'A' and resid 14 through 22 removed outlier: 4.570A pdb=" N VAL A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 63 removed outlier: 3.653A pdb=" N TYR A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 129 through 136 removed outlier: 4.052A pdb=" N ALA A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 185 removed outlier: 4.327A pdb=" N GLY A 170 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.960A pdb=" N LYS A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.946A pdb=" N VAL B 71 " --> pdb=" O HIS B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 110 removed outlier: 3.942A pdb=" N MET B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 175 removed outlier: 3.841A pdb=" N VAL B 160 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.023A pdb=" N VAL B 185 " --> pdb=" O CYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.627A pdb=" N ASN B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 194 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 196 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 230 through 237 removed outlier: 3.668A pdb=" N ALA B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 236 " --> pdb=" O ASP B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 removed outlier: 3.560A pdb=" N ARG C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 74 removed outlier: 4.272A pdb=" N ILE C 70 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 removed outlier: 4.240A pdb=" N VAL C 83 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N HIS C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 150 removed outlier: 3.728A pdb=" N ALA C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 removed outlier: 3.852A pdb=" N LEU C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 239 removed outlier: 4.578A pdb=" N PHE C 237 " --> pdb=" O MET C 233 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.604A pdb=" N ASN C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.537A pdb=" N THR D 15 " --> pdb=" O ARG D 11 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 79 removed outlier: 3.676A pdb=" N VAL D 60 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N HIS D 63 " --> pdb=" O PHE D 59 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ARG D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU D 67 " --> pdb=" O HIS D 63 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN D 68 " --> pdb=" O GLY D 64 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 70 " --> pdb=" O ARG D 66 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET D 72 " --> pdb=" O GLN D 68 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 112 removed outlier: 3.553A pdb=" N GLU D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 132 removed outlier: 3.640A pdb=" N ILE D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG D 125 " --> pdb=" O TYR D 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D 132 " --> pdb=" O MET D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 169 removed outlier: 3.789A pdb=" N GLN D 167 " --> pdb=" O ASP D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 50 removed outlier: 3.983A pdb=" N LEU E 48 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG E 49 " --> pdb=" O ASN E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 67 removed outlier: 3.556A pdb=" N ILE E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL E 65 " --> pdb=" O ALA E 61 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS E 66 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.895A pdb=" N SER E 120 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE E 121 " --> pdb=" O GLU E 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 121' Processing helix chain 'F' and resid 7 through 9 No H-bonds generated for 'chain 'F' and resid 7 through 9' Processing helix chain 'F' and resid 16 through 21 removed outlier: 3.775A pdb=" N ASP F 21 " --> pdb=" O PHE F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 removed outlier: 4.172A pdb=" N LYS F 52 " --> pdb=" O ARG F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 65 Processing helix chain 'F' and resid 74 through 94 removed outlier: 4.269A pdb=" N ARG F 80 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE F 88 " --> pdb=" O HIS F 84 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA F 90 " --> pdb=" O PHE F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 108 removed outlier: 4.132A pdb=" N THR F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 104 " --> pdb=" O THR F 100 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS F 108 " --> pdb=" O GLY F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 152 removed outlier: 3.513A pdb=" N ILE F 136 " --> pdb=" O PRO F 132 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 140 " --> pdb=" O ILE F 136 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU F 142 " --> pdb=" O GLN F 138 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY F 146 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 172 removed outlier: 3.616A pdb=" N GLU F 165 " --> pdb=" O CYS F 161 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA F 168 " --> pdb=" O ASP F 164 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER F 170 " --> pdb=" O LEU F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 193 removed outlier: 4.160A pdb=" N ASP F 183 " --> pdb=" O CYS F 179 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG F 187 " --> pdb=" O ASP F 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 208 removed outlier: 3.934A pdb=" N TYR G 206 " --> pdb=" O LYS G 202 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA G 208 " --> pdb=" O GLU G 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 13 removed outlier: 3.633A pdb=" N GLU H 11 " --> pdb=" O ALA H 7 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE H 12 " --> pdb=" O ALA H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 52 Processing helix chain 'H' and resid 57 through 66 Processing helix chain 'H' and resid 97 through 110 removed outlier: 3.828A pdb=" N LEU H 106 " --> pdb=" O ASN H 102 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP H 107 " --> pdb=" O ASP H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 144 Processing helix chain 'H' and resid 145 through 157 removed outlier: 3.627A pdb=" N PHE H 149 " --> pdb=" O ARG H 145 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN H 154 " --> pdb=" O ALA H 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 106 through 117 removed outlier: 3.883A pdb=" N GLU I 114 " --> pdb=" O LYS I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 158 removed outlier: 3.758A pdb=" N ALA I 155 " --> pdb=" O PRO I 151 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP I 158 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 174 Processing helix chain 'I' and resid 183 through 194 removed outlier: 3.616A pdb=" N ALA I 187 " --> pdb=" O GLY I 183 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 33 removed outlier: 4.252A pdb=" N GLN J 27 " --> pdb=" O HIS J 23 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU J 31 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 60 removed outlier: 3.501A pdb=" N TRP J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL J 43 " --> pdb=" O GLU J 39 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS J 49 " --> pdb=" O TYR J 45 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA J 53 " --> pdb=" O LYS J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 82 removed outlier: 3.590A pdb=" N PHE J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA J 72 " --> pdb=" O ILE J 68 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU J 81 " --> pdb=" O ARG J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 95 Processing helix chain 'J' and resid 98 through 105 removed outlier: 3.610A pdb=" N ASP J 104 " --> pdb=" O ASN J 100 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG J 105 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 115 Processing helix chain 'J' and resid 119 through 129 Processing helix chain 'J' and resid 158 through 163 Processing helix chain 'K' and resid 4 through 19 removed outlier: 3.540A pdb=" N CYS K 14 " --> pdb=" O ARG K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 52 removed outlier: 3.813A pdb=" N TYR K 42 " --> pdb=" O ASN K 38 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE K 44 " --> pdb=" O TYR K 40 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA K 47 " --> pdb=" O GLN K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 80 removed outlier: 3.598A pdb=" N ILE K 72 " --> pdb=" O THR K 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG K 76 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 48 removed outlier: 3.503A pdb=" N ALA L 46 " --> pdb=" O PRO L 43 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU L 48 " --> pdb=" O THR L 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 13 removed outlier: 3.501A pdb=" N GLY M 8 " --> pdb=" O VAL M 4 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN M 11 " --> pdb=" O HIS M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 31 Processing helix chain 'M' and resid 46 through 60 removed outlier: 3.952A pdb=" N LYS M 58 " --> pdb=" O GLY M 54 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 76 removed outlier: 3.780A pdb=" N ALA M 75 " --> pdb=" O LEU M 71 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU M 76 " --> pdb=" O LEU M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 113 Processing helix chain 'N' and resid 29 through 43 removed outlier: 3.641A pdb=" N VAL N 34 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN N 35 " --> pdb=" O GLU N 31 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR N 40 " --> pdb=" O MET N 36 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS N 43 " --> pdb=" O ASP N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 57 removed outlier: 3.783A pdb=" N GLY N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALA N 52 " --> pdb=" O SER N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 68 Processing helix chain 'N' and resid 70 through 79 Processing helix chain 'N' and resid 85 through 105 removed outlier: 3.544A pdb=" N LEU N 91 " --> pdb=" O GLU N 87 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN N 97 " --> pdb=" O LYS N 93 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS N 104 " --> pdb=" O LYS N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 116 Processing helix chain 'N' and resid 118 through 132 removed outlier: 3.604A pdb=" N HIS N 123 " --> pdb=" O GLU N 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG N 127 " --> pdb=" O HIS N 123 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 151 removed outlier: 3.560A pdb=" N LEU N 149 " --> pdb=" O THR N 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 97 removed outlier: 3.874A pdb=" N ALA O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG O 92 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS O 94 " --> pdb=" O ALA O 90 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU O 95 " --> pdb=" O ALA O 91 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY O 97 " --> pdb=" O LEU O 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 129 removed outlier: 4.532A pdb=" N GLN O 121 " --> pdb=" O ALA O 117 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER O 122 " --> pdb=" O GLN O 118 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG O 125 " --> pdb=" O GLN O 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 18 through 25 removed outlier: 3.525A pdb=" N LEU P 22 " --> pdb=" O THR P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 31 removed outlier: 4.311A pdb=" N ASP P 29 " --> pdb=" O MET P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 34 No H-bonds generated for 'chain 'P' and resid 32 through 34' Processing helix chain 'P' and resid 38 through 44 removed outlier: 3.563A pdb=" N ILE P 42 " --> pdb=" O ARG P 38 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 64 removed outlier: 3.886A pdb=" N LEU P 53 " --> pdb=" O LYS P 49 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE P 54 " --> pdb=" O HIS P 50 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG P 61 " --> pdb=" O LEU P 57 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL P 64 " --> pdb=" O ALA P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 89 Processing helix chain 'P' and resid 107 through 111 Processing helix chain 'P' and resid 114 through 119 removed outlier: 3.682A pdb=" N PHE P 118 " --> pdb=" O LEU P 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 46 removed outlier: 3.514A pdb=" N LEU Q 46 " --> pdb=" O ARG Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 46 through 52 Processing helix chain 'Q' and resid 70 through 93 removed outlier: 3.661A pdb=" N VAL Q 75 " --> pdb=" O HIS Q 71 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE Q 78 " --> pdb=" O GLN Q 74 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN Q 80 " --> pdb=" O TYR Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 97 through 110 removed outlier: 3.638A pdb=" N GLU Q 101 " --> pdb=" O ALA Q 97 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU Q 106 " --> pdb=" O ILE Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 114 removed outlier: 3.579A pdb=" N LEU Q 114 " --> pdb=" O ARG Q 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 111 through 114' Processing helix chain 'R' and resid 6 through 20 removed outlier: 3.554A pdb=" N LEU R 15 " --> pdb=" O ARG R 11 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG R 19 " --> pdb=" O LEU R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 27 through 38 removed outlier: 3.697A pdb=" N ASN R 31 " --> pdb=" O ASP R 27 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG R 33 " --> pdb=" O GLN R 29 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 62 removed outlier: 4.180A pdb=" N ARG R 47 " --> pdb=" O SER R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 84 removed outlier: 3.525A pdb=" N LYS R 80 " --> pdb=" O GLN R 76 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 109 Processing helix chain 'S' and resid 31 through 35 Processing helix chain 'S' and resid 39 through 49 removed outlier: 3.537A pdb=" N TYR S 44 " --> pdb=" O ARG S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 75 removed outlier: 3.596A pdb=" N GLU S 66 " --> pdb=" O THR S 62 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU S 68 " --> pdb=" O LYS S 64 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE S 69 " --> pdb=" O GLU S 65 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER S 71 " --> pdb=" O GLU S 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 120 removed outlier: 3.796A pdb=" N ALA S 107 " --> pdb=" O THR S 103 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG S 110 " --> pdb=" O GLY S 106 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA S 111 " --> pdb=" O ALA S 107 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU S 112 " --> pdb=" O ASN S 108 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N MET S 116 " --> pdb=" O GLU S 112 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS S 117 " --> pdb=" O ILE S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 130 removed outlier: 3.599A pdb=" N ARG S 126 " --> pdb=" O LYS S 122 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY S 128 " --> pdb=" O GLY S 124 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 31 removed outlier: 4.051A pdb=" N ASN T 23 " --> pdb=" O ASP T 19 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE T 29 " --> pdb=" O LEU T 25 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN T 30 " --> pdb=" O ALA T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 74 removed outlier: 4.089A pdb=" N THR T 62 " --> pdb=" O ASN T 58 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE T 68 " --> pdb=" O ALA T 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS T 74 " --> pdb=" O GLN T 70 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 87 Processing helix chain 'T' and resid 104 through 114 removed outlier: 3.555A pdb=" N ILE T 110 " --> pdb=" O VAL T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 130 through 147 removed outlier: 3.507A pdb=" N ARG T 135 " --> pdb=" O PRO T 131 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP T 138 " --> pdb=" O GLN T 134 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR T 142 " --> pdb=" O ASP T 138 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS T 146 " --> pdb=" O THR T 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS T 147 " --> pdb=" O SER T 143 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 51 removed outlier: 3.999A pdb=" N VAL U 39 " --> pdb=" O ASN U 35 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU U 47 " --> pdb=" O LEU U 43 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS U 48 " --> pdb=" O MET U 44 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS U 49 " --> pdb=" O GLY U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 99 through 107 removed outlier: 3.606A pdb=" N LYS U 103 " --> pdb=" O ALA U 99 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN U 104 " --> pdb=" O GLU U 100 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL U 105 " --> pdb=" O ALA U 101 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN U 107 " --> pdb=" O LYS U 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 62 removed outlier: 3.528A pdb=" N ARG V 59 " --> pdb=" O SER V 55 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY V 62 " --> pdb=" O VAL V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 63 through 76 Processing helix chain 'W' and resid 6 through 21 removed outlier: 3.655A pdb=" N LEU W 11 " --> pdb=" O LEU W 7 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS W 12 " --> pdb=" O ALA W 8 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG W 20 " --> pdb=" O ASN W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 44 removed outlier: 3.576A pdb=" N MET W 41 " --> pdb=" O PHE W 37 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 94 removed outlier: 4.280A pdb=" N TRP W 89 " --> pdb=" O ASP W 85 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA W 91 " --> pdb=" O GLU W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 112 through 120 removed outlier: 3.675A pdb=" N LYS W 118 " --> pdb=" O GLU W 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 24 removed outlier: 3.541A pdb=" N SER X 21 " --> pdb=" O LEU X 17 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TRP X 24 " --> pdb=" O LYS X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 35 removed outlier: 3.828A pdb=" N THR X 35 " --> pdb=" O ARG X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 96 removed outlier: 4.416A pdb=" N ASP X 96 " --> pdb=" O LEU X 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 130 through 137 Processing helix chain 'Y' and resid 35 through 47 Processing helix chain 'Y' and resid 78 through 84 removed outlier: 3.922A pdb=" N LYS Y 82 " --> pdb=" O LEU Y 78 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS Y 83 " --> pdb=" O ASP Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 94 removed outlier: 4.006A pdb=" N LEU Y 90 " --> pdb=" O PRO Y 86 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS Y 92 " --> pdb=" O HIS Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 116 removed outlier: 3.943A pdb=" N ARG Y 111 " --> pdb=" O LYS Y 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN Y 112 " --> pdb=" O ASN Y 108 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS Y 113 " --> pdb=" O ALA Y 109 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL Y 114 " --> pdb=" O ARG Y 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 27 through 38 removed outlier: 3.967A pdb=" N ALA Z 32 " --> pdb=" O PRO Z 28 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP Z 33 " --> pdb=" O GLU Z 29 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS Z 36 " --> pdb=" O ALA Z 32 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL Z 38 " --> pdb=" O MET Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 53 removed outlier: 3.552A pdb=" N ALA Z 50 " --> pdb=" O ALA Z 46 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU Z 51 " --> pdb=" O GLY Z 47 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG Z 52 " --> pdb=" O LYS Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 71 removed outlier: 3.612A pdb=" N LYS Z 62 " --> pdb=" O THR Z 58 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU Z 64 " --> pdb=" O ALA Z 60 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA Z 69 " --> pdb=" O GLU Z 65 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU Z 70 " --> pdb=" O ALA Z 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 49 through 54 Processing helix chain 'a' and resid 74 through 81 Processing helix chain 'b' and resid 12 through 19 removed outlier: 3.591A pdb=" N LEU b 17 " --> pdb=" O VAL b 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 33 through 37 removed outlier: 3.727A pdb=" N LEU d 37 " --> pdb=" O GLN d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 47 removed outlier: 3.558A pdb=" N GLU d 46 " --> pdb=" O ARG d 42 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG d 47 " --> pdb=" O CYS d 43 " (cutoff:3.500A) Processing helix chain 'e' and resid 12 through 17 removed outlier: 3.794A pdb=" N SER e 16 " --> pdb=" O GLY e 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 44 removed outlier: 3.643A pdb=" N LEU e 36 " --> pdb=" O GLY e 32 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 23 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39 removed outlier: 4.273A pdb=" N VAL A 46 " --> pdb=" O PHE A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 73 removed outlier: 7.403A pdb=" N VAL A 72 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N CYS A 142 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL A 158 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA A 144 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 27 Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 66 removed outlier: 5.394A pdb=" N ARG B 84 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE B 96 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ILE B 86 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR B 94 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 12.179A pdb=" N GLN B 95 " --> pdb=" O LYS B 215 " (cutoff:3.500A) removed outlier: 11.553A pdb=" N LYS B 215 " --> pdb=" O GLN B 95 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ALA B 97 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 213 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE B 130 " --> pdb=" O ILE B 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.657A pdb=" N PHE B 138 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY B 205 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 103 removed outlier: 3.501A pdb=" N GLY C 129 " --> pdb=" O ALA C 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 173 through 177 Processing sheet with id=AA8, first strand: chain 'D' and resid 35 through 42 removed outlier: 4.212A pdb=" N GLY D 37 " --> pdb=" O LYS D 52 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR D 47 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE D 88 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE D 49 " --> pdb=" O PHE D 88 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP D 90 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE D 51 " --> pdb=" O ASP D 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 151 through 155 removed outlier: 3.527A pdb=" N SER D 151 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY D 134 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 210 through 211 removed outlier: 3.637A pdb=" N LYS D 210 " --> pdb=" O ASP R 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 70 through 72 Processing sheet with id=AB3, first strand: chain 'E' and resid 102 through 103 removed outlier: 4.122A pdb=" N ILE E 102 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 147 through 148 removed outlier: 3.799A pdb=" N GLN E 128 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 191 through 193 removed outlier: 3.855A pdb=" N ARG E 191 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL E 180 " --> pdb=" O ILE E 228 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 197 through 199 removed outlier: 3.552A pdb=" N LYS E 197 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE E 218 " --> pdb=" O LEU E 210 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AB8, first strand: chain 'F' and resid 113 through 115 Processing sheet with id=AB9, first strand: chain 'H' and resid 26 through 31 removed outlier: 3.998A pdb=" N SER H 26 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL H 39 " --> pdb=" O LYS H 28 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL H 37 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN H 68 " --> pdb=" O THR H 36 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 115 through 117 removed outlier: 3.547A pdb=" N GLY H 117 " --> pdb=" O ILE H 133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 120 through 122 Processing sheet with id=AC3, first strand: chain 'I' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'I' and resid 47 through 48 removed outlier: 3.816A pdb=" N GLY I 51 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 62 through 67 removed outlier: 4.222A pdb=" N ASN I 80 " --> pdb=" O SER I 103 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL I 101 " --> pdb=" O THR I 82 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER I 100 " --> pdb=" O ILE I 166 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 132 through 133 Processing sheet with id=AC7, first strand: chain 'K' and resid 20 through 24 removed outlier: 3.791A pdb=" N LEU K 21 " --> pdb=" O TYR K 65 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 68 through 73 removed outlier: 16.692A pdb=" N VAL L 68 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 14.284A pdb=" N LEU L 89 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N ARG L 70 " --> pdb=" O ASP L 87 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP L 87 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL L 72 " --> pdb=" O ARG L 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG L 97 " --> pdb=" O ILE L 92 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE L 135 " --> pdb=" O PRO L 106 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL L 137 " --> pdb=" O ALA L 124 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA L 124 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS L 139 " --> pdb=" O THR L 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 34 through 39 Processing sheet with id=AD1, first strand: chain 'O' and resid 35 through 38 removed outlier: 6.456A pdb=" N VAL O 35 " --> pdb=" O GLY O 100 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS O 102 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY O 37 " --> pdb=" O HIS O 102 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS O 104 " --> pdb=" O GLY O 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 35 through 38 removed outlier: 6.456A pdb=" N VAL O 35 " --> pdb=" O GLY O 100 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N HIS O 102 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY O 37 " --> pdb=" O HIS O 102 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LYS O 104 " --> pdb=" O GLY O 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 75 through 77 removed outlier: 3.563A pdb=" N TYR P 96 " --> pdb=" O THR P 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 4 through 8 removed outlier: 3.529A pdb=" N VAL Q 4 " --> pdb=" O CYS Q 19 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU Q 25 " --> pdb=" O ILE Q 62 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL Q 64 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS Q 27 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL Q 66 " --> pdb=" O LYS Q 27 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 16 through 17 removed outlier: 3.610A pdb=" N THR S 20 " --> pdb=" O MET S 17 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 76 through 77 removed outlier: 3.526A pdb=" N LYS T 121 " --> pdb=" O GLN T 128 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 88 through 89 Processing sheet with id=AD8, first strand: chain 'U' and resid 60 through 67 removed outlier: 5.788A pdb=" N LYS U 90 " --> pdb=" O PRO U 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU U 86 " --> pdb=" O LEU U 65 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 94 through 95 removed outlier: 3.510A pdb=" N LYS d 54 " --> pdb=" O GLU U 85 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 32 through 33 Processing sheet with id=AE2, first strand: chain 'V' and resid 36 through 40 removed outlier: 7.192A pdb=" N ILE V 36 " --> pdb=" O GLU V 48 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLU V 48 " --> pdb=" O ILE V 36 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LYS V 38 " --> pdb=" O THR V 46 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR V 46 " --> pdb=" O LYS V 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 24 through 27 removed outlier: 3.501A pdb=" N VAL W 25 " --> pdb=" O ILE W 63 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 71 through 73 removed outlier: 3.748A pdb=" N VAL W 73 " --> pdb=" O MET W 128 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET W 128 " --> pdb=" O VAL W 73 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 80 through 81 removed outlier: 3.574A pdb=" N LYS W 124 " --> pdb=" O SER W 105 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 47 through 56 removed outlier: 7.137A pdb=" N ARG X 72 " --> pdb=" O VAL X 53 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYS X 55 " --> pdb=" O ALA X 70 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA X 70 " --> pdb=" O LYS X 55 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N PHE X 121 " --> pdb=" O THR X 83 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU X 102 " --> pdb=" O ILE X 124 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL X 126 " --> pdb=" O ARG X 100 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ARG X 100 " --> pdb=" O VAL X 126 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 7 through 14 removed outlier: 5.874A pdb=" N ILE Y 8 " --> pdb=" O ASP Y 25 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP Y 25 " --> pdb=" O ILE Y 8 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS Y 10 " --> pdb=" O VAL Y 23 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL Y 23 " --> pdb=" O LYS Y 10 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE Y 71 " --> pdb=" O GLY Y 58 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLY Y 58 " --> pdb=" O PHE Y 71 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N PHE Y 73 " --> pdb=" O ILE Y 56 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE Y 56 " --> pdb=" O PHE Y 73 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N TYR Y 75 " --> pdb=" O VAL Y 54 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL Y 54 " --> pdb=" O TYR Y 75 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 44 through 45 removed outlier: 7.055A pdb=" N CYS Z 84 " --> pdb=" O VAL Z 76 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'a' and resid 20 through 22 Processing sheet with id=AF1, first strand: chain 'a' and resid 37 through 43 Processing sheet with id=AF2, first strand: chain 'b' and resid 33 through 36 Processing sheet with id=AF3, first strand: chain 'b' and resid 65 through 66 Processing sheet with id=AF4, first strand: chain 'c' and resid 40 through 45 removed outlier: 3.863A pdb=" N GLY c 18 " --> pdb=" O GLN c 28 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARG c 30 " --> pdb=" O VAL c 16 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL c 16 " --> pdb=" O ARG c 30 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLU c 32 " --> pdb=" O LYS c 14 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS c 14 " --> pdb=" O GLU c 32 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'd' and resid 31 through 32 removed outlier: 3.602A pdb=" N ILE d 39 " --> pdb=" O ILE d 32 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 24 through 29 removed outlier: 7.246A pdb=" N GLU g 331 " --> pdb=" O PRO g 25 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA g 27 " --> pdb=" O ALA g 329 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS g 308 " --> pdb=" O GLY g 321 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'g' and resid 36 through 41 removed outlier: 3.850A pdb=" N SER g 38 " --> pdb=" O ALA g 51 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU g 48 " --> pdb=" O TRP g 60 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER g 50 " --> pdb=" O LEU g 58 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU g 58 " --> pdb=" O SER g 50 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA g 57 " --> pdb=" O ARG g 75 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG g 75 " --> pdb=" O ALA g 57 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL g 59 " --> pdb=" O PHE g 73 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N TRP g 69 " --> pdb=" O ASN g 63 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'g' and resid 83 through 87 removed outlier: 3.601A pdb=" N ASP g 85 " --> pdb=" O SER g 98 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU g 95 " --> pdb=" O TRP g 107 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU g 104 " --> pdb=" O LEU g 117 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU g 117 " --> pdb=" O LEU g 104 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU g 106 " --> pdb=" O LYS g 115 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP g 108 " --> pdb=" O THR g 113 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N THR g 113 " --> pdb=" O ASP g 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 125 through 127 removed outlier: 4.248A pdb=" N GLY g 141 " --> pdb=" O GLN g 145 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLN g 145 " --> pdb=" O GLY g 141 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL g 146 " --> pdb=" O GLU g 158 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU g 158 " --> pdb=" O VAL g 146 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE g 148 " --> pdb=" O LYS g 156 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 165 through 170 removed outlier: 3.711A pdb=" N SER g 167 " --> pdb=" O GLY g 185 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS g 204 " --> pdb=" O ILE g 193 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 215 through 218 removed outlier: 3.650A pdb=" N SER g 215 " --> pdb=" O GLY g 228 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY g 228 " --> pdb=" O SER g 215 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE g 246 " --> pdb=" O MET g 236 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU g 238 " --> pdb=" O LYS g 244 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N LYS g 244 " --> pdb=" O LEU g 238 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 257 through 259 removed outlier: 3.613A pdb=" N CYS g 267 " --> pdb=" O ALA g 258 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA g 268 " --> pdb=" O ALA g 275 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL g 276 " --> pdb=" O ILE g 285 " (cutoff:3.500A) 1130 hydrogen bonds defined for protein. 3183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 858 hydrogen bonds 1420 hydrogen bond angles 0 basepair planarities 367 basepair parallelities 759 stacking parallelities Total time for adding SS restraints: 39.70 Time building geometry restraints manager: 13.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13413 1.33 - 1.46: 23740 1.46 - 1.58: 29896 1.58 - 1.71: 2962 1.71 - 1.83: 243 Bond restraints: 70254 Sorted by residual: bond pdb=" C ASP Q 117 " pdb=" N PRO Q 118 " ideal model delta sigma weight residual 1.332 1.386 -0.054 8.90e-03 1.26e+04 3.66e+01 bond pdb=" CA VAL R 93 " pdb=" CB VAL R 93 " ideal model delta sigma weight residual 1.534 1.570 -0.036 6.80e-03 2.16e+04 2.75e+01 bond pdb=" C THR H 81 " pdb=" N PRO H 82 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.20e-02 6.94e+03 2.41e+01 bond pdb=" C LEU K 81 " pdb=" N PRO K 82 " ideal model delta sigma weight residual 1.330 1.388 -0.058 1.22e-02 6.72e+03 2.30e+01 bond pdb=" C ALA g 171 " pdb=" N PRO g 172 " ideal model delta sigma weight residual 1.330 1.388 -0.058 1.22e-02 6.72e+03 2.22e+01 ... (remaining 70249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 99977 3.38 - 6.75: 1989 6.75 - 10.13: 89 10.13 - 13.51: 29 13.51 - 16.88: 7 Bond angle restraints: 102091 Sorted by residual: angle pdb=" N VAL Q 115 " pdb=" CA VAL Q 115 " pdb=" C VAL Q 115 " ideal model delta sigma weight residual 110.72 122.23 -11.51 1.01e+00 9.80e-01 1.30e+02 angle pdb=" C4' A 2 92 " pdb=" C3' A 2 92 " pdb=" O3' A 2 92 " ideal model delta sigma weight residual 109.40 122.64 -13.24 1.50e+00 4.44e-01 7.79e+01 angle pdb=" N VAL M 18 " pdb=" CA VAL M 18 " pdb=" C VAL M 18 " ideal model delta sigma weight residual 108.35 119.56 -11.21 1.32e+00 5.74e-01 7.22e+01 angle pdb=" C4' G 21374 " pdb=" C3' G 21374 " pdb=" O3' G 21374 " ideal model delta sigma weight residual 109.40 121.92 -12.52 1.50e+00 4.44e-01 6.97e+01 angle pdb=" N HIS F 31 " pdb=" CA HIS F 31 " pdb=" C HIS F 31 " ideal model delta sigma weight residual 109.62 121.71 -12.09 1.50e+00 4.44e-01 6.50e+01 ... (remaining 102086 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 40212 35.82 - 71.63: 3621 71.63 - 107.45: 449 107.45 - 143.27: 9 143.27 - 179.08: 44 Dihedral angle restraints: 44335 sinusoidal: 31760 harmonic: 12575 Sorted by residual: dihedral pdb=" O4' U 2 684 " pdb=" C1' U 2 684 " pdb=" N1 U 2 684 " pdb=" C2 U 2 684 " ideal model delta sinusoidal sigma weight residual -160.00 14.37 -174.37 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U 2 615 " pdb=" C1' U 2 615 " pdb=" N1 U 2 615 " pdb=" C2 U 2 615 " ideal model delta sinusoidal sigma weight residual 200.00 29.10 170.90 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U 21174 " pdb=" C1' U 21174 " pdb=" N1 U 21174 " pdb=" C2 U 21174 " ideal model delta sinusoidal sigma weight residual 200.00 34.39 165.61 1 1.50e+01 4.44e-03 8.40e+01 ... (remaining 44332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 10486 0.128 - 0.256: 2177 0.256 - 0.383: 44 0.383 - 0.511: 7 0.511 - 0.639: 6 Chirality restraints: 12720 Sorted by residual: chirality pdb=" C3' G 21374 " pdb=" C4' G 21374 " pdb=" O3' G 21374 " pdb=" C2' G 21374 " both_signs ideal model delta sigma weight residual False -2.74 -2.11 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C3' A 21150 " pdb=" C4' A 21150 " pdb=" O3' A 21150 " pdb=" C2' A 21150 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.57 2.00e-01 2.50e+01 8.02e+00 chirality pdb=" C3' G 2 24 " pdb=" C4' G 2 24 " pdb=" O3' G 2 24 " pdb=" C2' G 2 24 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.56 2.00e-01 2.50e+01 7.94e+00 ... (remaining 12717 not shown) Planarity restraints: 7439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS H 16 " -0.062 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO H 17 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO H 17 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO H 17 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU Q 114 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.24e+00 pdb=" C LEU Q 114 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU Q 114 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL Q 115 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 26 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.84e+00 pdb=" C ASP F 26 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP F 26 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR F 27 " -0.016 2.00e-02 2.50e+03 ... (remaining 7436 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 18 1.87 - 2.63: 1121 2.63 - 3.39: 78394 3.39 - 4.14: 185475 4.14 - 4.90: 285375 Nonbonded interactions: 550383 Sorted by model distance: nonbonded pdb=" NH1 ARG O 129 " pdb=" NH2 ARG c 39 " model vdw 1.113 3.200 nonbonded pdb=" CE1 PHE S 11 " pdb=" CD1 ILE Z 25 " model vdw 1.205 3.760 nonbonded pdb=" O TYR P 14 " pdb=" O ARG S 92 " model vdw 1.235 3.040 nonbonded pdb=" CE1 HIS g 32 " pdb=" OG SER g 52 " model vdw 1.388 3.260 nonbonded pdb=" OP1 A 21154 " pdb=" O ARG U 55 " model vdw 1.460 3.040 ... (remaining 550378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.820 Check model and map are aligned: 0.370 Set scattering table: 0.450 Process input model: 129.490 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.170 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: 0.010 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 70254 Z= 0.427 Angle : 1.113 16.884 102091 Z= 0.746 Chirality : 0.091 0.639 12720 Planarity : 0.004 0.095 7439 Dihedral : 22.951 179.084 36168 Min Nonbonded Distance : 1.113 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 2.71 % Allowed : 8.28 % Favored : 89.01 % Rotamer: Outliers : 5.14 % Allowed : 9.91 % Favored : 84.95 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.11), residues: 4250 helix: -2.23 (0.12), residues: 1268 sheet: -2.55 (0.18), residues: 651 loop : -2.52 (0.11), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 84 HIS 0.007 0.001 HIS S 99 PHE 0.014 0.001 PHE d 44 TYR 0.017 0.001 TYR E 80 ARG 0.011 0.001 ARG n 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1674 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 1491 time to evaluate : 3.578 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: A 16 MET cc_start: 0.8493 (mmt) cc_final: 0.8232 (mmt) REVERT: A 40 ARG cc_start: 0.6541 (ttp80) cc_final: 0.6206 (ptm-80) REVERT: A 41 LYS cc_start: 0.6293 (ttmt) cc_final: 0.5699 (mttt) REVERT: A 44 THR cc_start: 0.7403 (OUTLIER) cc_final: 0.7039 (m) REVERT: A 47 ILE cc_start: 0.6728 (pp) cc_final: 0.6470 (mm) REVERT: A 51 MET cc_start: 0.6139 (mtm) cc_final: 0.5803 (mtp) REVERT: A 79 SER cc_start: 0.8229 (m) cc_final: 0.7550 (t) REVERT: A 102 THR cc_start: 0.7774 (OUTLIER) cc_final: 0.7560 (t) REVERT: A 126 ASN cc_start: 0.8159 (t0) cc_final: 0.7825 (t0) REVERT: A 128 ASP cc_start: 0.7110 (t70) cc_final: 0.6237 (p0) REVERT: A 153 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7374 (p0) REVERT: A 161 CYS cc_start: 0.7750 (t) cc_final: 0.7344 (t) REVERT: A 163 THR cc_start: 0.8456 (p) cc_final: 0.8237 (p) REVERT: A 173 MET cc_start: 0.8127 (mmm) cc_final: 0.7699 (tpp) REVERT: A 202 TYR cc_start: 0.7934 (t80) cc_final: 0.7502 (t80) REVERT: A 210 LYS cc_start: 0.7790 (mttt) cc_final: 0.7408 (tppt) REVERT: B 27 HIS cc_start: 0.7905 (m-70) cc_final: 0.7627 (m-70) REVERT: B 34 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.5389 (p90) REVERT: B 61 ARG cc_start: 0.7221 (mtt180) cc_final: 0.6860 (mtt180) REVERT: B 73 ASP cc_start: 0.5289 (m-30) cc_final: 0.4713 (t70) REVERT: B 74 LEU cc_start: 0.5703 (mp) cc_final: 0.5351 (mp) REVERT: B 80 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6125 (mt) REVERT: B 91 GLU cc_start: 0.7443 (tt0) cc_final: 0.6757 (tt0) REVERT: B 103 HIS cc_start: 0.6849 (t-90) cc_final: 0.6641 (t-90) REVERT: B 111 ARG cc_start: 0.7762 (mtt90) cc_final: 0.7433 (mtm180) REVERT: B 114 ARG cc_start: 0.7369 (mmt-90) cc_final: 0.7061 (mmt90) REVERT: B 155 HIS cc_start: 0.6997 (t70) cc_final: 0.6787 (t-90) REVERT: B 166 LYS cc_start: 0.7590 (tttp) cc_final: 0.7315 (tppt) REVERT: B 170 ASP cc_start: 0.7926 (t70) cc_final: 0.7688 (t70) REVERT: B 178 GLU cc_start: 0.7957 (pt0) cc_final: 0.7146 (tm-30) REVERT: B 183 ASP cc_start: 0.6618 (m-30) cc_final: 0.6320 (m-30) REVERT: B 186 ASP cc_start: 0.7598 (m-30) cc_final: 0.7239 (m-30) REVERT: B 187 GLU cc_start: 0.7625 (pt0) cc_final: 0.7103 (pt0) REVERT: B 195 GLU cc_start: 0.8438 (tt0) cc_final: 0.8036 (tp30) REVERT: B 224 VAL cc_start: 0.7407 (t) cc_final: 0.7185 (p) REVERT: B 225 LYS cc_start: 0.6896 (tttp) cc_final: 0.6642 (tptp) REVERT: B 231 LYS cc_start: 0.7733 (mttt) cc_final: 0.7409 (mmtm) REVERT: B 232 ASP cc_start: 0.7143 (m-30) cc_final: 0.6896 (t0) REVERT: C 65 LYS cc_start: 0.7420 (mmmt) cc_final: 0.6454 (ptmm) REVERT: C 91 LEU cc_start: 0.7406 (pp) cc_final: 0.7106 (pt) REVERT: C 96 MET cc_start: 0.8375 (mmm) cc_final: 0.7948 (mmp) REVERT: C 98 ILE cc_start: 0.7979 (mt) cc_final: 0.7728 (mm) REVERT: C 109 GLN cc_start: 0.7779 (mt0) cc_final: 0.7482 (mt0) REVERT: C 110 ARG cc_start: 0.7090 (ttp-170) cc_final: 0.6756 (ttt180) REVERT: C 116 ILE cc_start: 0.7202 (OUTLIER) cc_final: 0.6954 (mt) REVERT: C 123 LYS cc_start: 0.7242 (mtmm) cc_final: 0.6826 (ptpp) REVERT: C 146 TYR cc_start: 0.7509 (m-80) cc_final: 0.7080 (m-10) REVERT: C 158 TYR cc_start: 0.7769 (m-80) cc_final: 0.7410 (m-80) REVERT: C 182 MET cc_start: 0.7606 (tpt) cc_final: 0.6971 (tpt) REVERT: C 201 LYS cc_start: 0.7061 (mmtp) cc_final: 0.6669 (tptt) REVERT: C 205 MET cc_start: 0.6499 (mtt) cc_final: 0.6203 (mtt) REVERT: C 235 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: C 246 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7248 (mp0) REVERT: C 252 GLU cc_start: 0.7934 (tp30) cc_final: 0.7327 (tp30) REVERT: D 10 ARG cc_start: 0.7543 (mtm180) cc_final: 0.7331 (mtp85) REVERT: D 21 GLU cc_start: 0.7820 (tt0) cc_final: 0.7437 (tt0) REVERT: D 27 THR cc_start: 0.7409 (m) cc_final: 0.7139 (p) REVERT: D 39 GLU cc_start: 0.7594 (mt-10) cc_final: 0.6569 (mp0) REVERT: D 65 ARG cc_start: 0.6638 (ttp80) cc_final: 0.5691 (mtm110) REVERT: D 69 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7492 (mp0) REVERT: D 76 LYS cc_start: 0.6840 (mmmt) cc_final: 0.5527 (mmtm) REVERT: D 79 ARG cc_start: 0.8078 (mtp180) cc_final: 0.7670 (mmt180) REVERT: D 86 GLU cc_start: 0.6348 (mt-10) cc_final: 0.6043 (mt-10) REVERT: D 107 ARG cc_start: 0.6801 (ttt180) cc_final: 0.6459 (ttp-170) REVERT: D 121 TYR cc_start: 0.7944 (m-80) cc_final: 0.7615 (m-80) REVERT: D 133 ARG cc_start: 0.7600 (mmm160) cc_final: 0.7212 (mmp80) REVERT: D 136 GLU cc_start: 0.7691 (tt0) cc_final: 0.6963 (tt0) REVERT: D 147 ARG cc_start: 0.5757 (ptp90) cc_final: 0.5023 (mmm160) REVERT: D 155 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7067 (tp30) REVERT: D 157 TYR cc_start: 0.7018 (p90) cc_final: 0.6745 (p90) REVERT: D 170 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7404 (t) REVERT: D 171 GLN cc_start: 0.7537 (pt0) cc_final: 0.7333 (pp30) REVERT: E 39 ARG cc_start: 0.7448 (mmm160) cc_final: 0.6932 (mmm160) REVERT: E 68 ARG cc_start: 0.7339 (mtp85) cc_final: 0.7095 (mtp180) REVERT: E 87 MET cc_start: 0.7012 (mmm) cc_final: 0.6372 (mpp) REVERT: E 99 PHE cc_start: 0.4973 (m-80) cc_final: 0.4504 (m-80) REVERT: E 101 ILE cc_start: 0.7260 (mt) cc_final: 0.6987 (tp) REVERT: E 106 LYS cc_start: 0.7615 (mmtp) cc_final: 0.6095 (tppt) REVERT: E 123 LEU cc_start: 0.8002 (mt) cc_final: 0.7764 (mt) REVERT: E 128 GLN cc_start: 0.7831 (tt0) cc_final: 0.7623 (tt0) REVERT: E 130 LYS cc_start: 0.7056 (pttm) cc_final: 0.6743 (tttp) REVERT: E 143 ASP cc_start: 0.8282 (m-30) cc_final: 0.7883 (t0) REVERT: E 158 ASP cc_start: 0.7497 (m-30) cc_final: 0.7206 (m-30) REVERT: E 163 ASN cc_start: 0.8571 (m-40) cc_final: 0.7764 (m110) REVERT: E 168 GLU cc_start: 0.8078 (tt0) cc_final: 0.7525 (tt0) REVERT: E 183 VAL cc_start: 0.8522 (t) cc_final: 0.8310 (p) REVERT: E 196 GLN cc_start: 0.8206 (mt0) cc_final: 0.7944 (mp10) REVERT: E 211 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7350 (tppt) REVERT: F 9 LYS cc_start: 0.8434 (mttp) cc_final: 0.8201 (mttt) REVERT: F 37 MET cc_start: 0.6964 (tpt) cc_final: 0.6649 (tpp) REVERT: F 48 LYS cc_start: 0.7071 (tptm) cc_final: 0.6493 (ptmt) REVERT: F 49 ARG cc_start: 0.6529 (ttp-170) cc_final: 0.6308 (mtp180) REVERT: F 50 PHE cc_start: 0.7229 (m-80) cc_final: 0.6420 (m-10) REVERT: F 97 PRO cc_start: 0.8374 (Cg_endo) cc_final: 0.8159 (Cg_exo) REVERT: F 112 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6572 (mt-10) REVERT: F 149 LYS cc_start: 0.7675 (mmmt) cc_final: 0.7299 (mtpp) REVERT: F 182 LYS cc_start: 0.4834 (ptmt) cc_final: 0.4299 (ttmt) REVERT: F 184 GLU cc_start: 0.7426 (tt0) cc_final: 0.7045 (tt0) REVERT: F 186 GLU cc_start: 0.6585 (tt0) cc_final: 0.6336 (mt-10) REVERT: H 20 LYS cc_start: 0.6946 (tttp) cc_final: 0.6509 (tptt) REVERT: H 46 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7883 (mm110) REVERT: H 50 PHE cc_start: 0.6495 (m-80) cc_final: 0.6125 (m-80) REVERT: H 68 GLN cc_start: 0.7164 (mp10) cc_final: 0.6869 (mp10) REVERT: H 69 ILE cc_start: 0.7340 (mm) cc_final: 0.7035 (tp) REVERT: H 122 TYR cc_start: 0.7832 (m-80) cc_final: 0.7514 (m-80) REVERT: H 127 LYS cc_start: 0.6983 (mttt) cc_final: 0.6516 (mmtt) REVERT: I 6 MET cc_start: 0.6995 (ttp) cc_final: 0.6694 (tmm) REVERT: I 17 ARG cc_start: 0.6621 (mmm160) cc_final: 0.5916 (mmt180) REVERT: I 24 LYS cc_start: 0.8131 (mttm) cc_final: 0.7526 (mttp) REVERT: I 37 ARG cc_start: 0.6950 (mtt180) cc_final: 0.6634 (mtt-85) REVERT: I 54 LYS cc_start: 0.7395 (mtpp) cc_final: 0.6980 (mtpt) REVERT: I 77 ARG cc_start: 0.7309 (ttp-110) cc_final: 0.6985 (ttp80) REVERT: I 92 ARG cc_start: 0.8151 (ttp-170) cc_final: 0.7744 (ttp-110) REVERT: I 115 ARG cc_start: 0.7039 (mmm160) cc_final: 0.6794 (tpt90) REVERT: I 152 GLU cc_start: 0.6671 (mt-10) cc_final: 0.6390 (mm-30) REVERT: I 161 ARG cc_start: 0.7202 (mtm-85) cc_final: 0.6993 (mmm-85) REVERT: I 189 TYR cc_start: 0.7328 (m-80) cc_final: 0.6949 (m-10) REVERT: J 10 PHE cc_start: 0.7324 (p90) cc_final: 0.7019 (p90) REVERT: J 11 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7976 (ttmm) REVERT: J 18 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6779 (mt-10) REVERT: J 34 LEU cc_start: 0.6604 (tp) cc_final: 0.6242 (mt) REVERT: J 38 ARG cc_start: 0.7484 (ptm-80) cc_final: 0.7224 (tmm-80) REVERT: J 39 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7270 (tp30) REVERT: J 85 ASP cc_start: 0.7309 (m-30) cc_final: 0.6891 (t0) REVERT: J 103 MET cc_start: 0.6705 (mmt) cc_final: 0.6395 (tpp) REVERT: J 106 ARG cc_start: 0.7039 (ptm160) cc_final: 0.6332 (ptp-110) REVERT: J 114 ARG cc_start: 0.6029 (OUTLIER) cc_final: 0.5029 (tpp-160) REVERT: J 147 TRP cc_start: 0.6538 (m-10) cc_final: 0.5889 (m-10) REVERT: J 149 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: K 18 ASN cc_start: 0.6077 (m110) cc_final: 0.5749 (m-40) REVERT: K 37 LEU cc_start: 0.6577 (mp) cc_final: 0.6276 (mt) REVERT: K 40 TYR cc_start: 0.7056 (m-80) cc_final: 0.6652 (m-10) REVERT: L 80 ARG cc_start: 0.6826 (mtm180) cc_final: 0.6229 (mtm180) REVERT: L 89 LEU cc_start: 0.8051 (mt) cc_final: 0.7811 (mm) REVERT: L 93 ARG cc_start: 0.7452 (ttt90) cc_final: 0.6428 (ttp-170) REVERT: L 98 PHE cc_start: 0.7794 (m-80) cc_final: 0.7552 (m-80) REVERT: L 100 LYS cc_start: 0.7740 (mtmm) cc_final: 0.7377 (mmtp) REVERT: L 103 THR cc_start: 0.7823 (m) cc_final: 0.7549 (p) REVERT: L 108 HIS cc_start: 0.8738 (t70) cc_final: 0.7956 (t70) REVERT: L 151 GLN cc_start: 0.8018 (tp40) cc_final: 0.7223 (tp40) REVERT: L 153 ARG cc_start: 0.7805 (mtp180) cc_final: 0.7422 (mtm180) REVERT: N 6 SER cc_start: 0.8648 (m) cc_final: 0.8404 (m) REVERT: N 11 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6678 (mm) REVERT: N 29 SER cc_start: 0.4957 (t) cc_final: 0.4707 (p) REVERT: N 31 GLU cc_start: 0.7526 (tt0) cc_final: 0.7284 (pm20) REVERT: N 37 ILE cc_start: 0.8053 (mm) cc_final: 0.7826 (mt) REVERT: N 62 MET cc_start: 0.7597 (mmt) cc_final: 0.7331 (mmt) REVERT: N 86 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6357 (mt-10) REVERT: N 97 ASN cc_start: 0.8073 (t0) cc_final: 0.7868 (t0) REVERT: N 100 LYS cc_start: 0.7708 (tttp) cc_final: 0.7505 (tttm) REVERT: N 103 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6382 (mm-30) REVERT: N 104 HIS cc_start: 0.8597 (t70) cc_final: 0.8094 (m170) REVERT: N 108 ASP cc_start: 0.7938 (p0) cc_final: 0.7705 (p0) REVERT: O 83 MET cc_start: 0.6835 (ttp) cc_final: 0.6429 (ptp) REVERT: O 99 ASP cc_start: 0.6880 (t0) cc_final: 0.6534 (m-30) REVERT: O 108 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7140 (tm-30) REVERT: O 125 ARG cc_start: 0.7367 (ttp-170) cc_final: 0.7048 (ttm-80) REVERT: O 136 ARG cc_start: 0.7576 (ttp80) cc_final: 0.6368 (ttp-170) REVERT: P 13 THR cc_start: 0.6989 (p) cc_final: 0.6785 (p) REVERT: P 51 VAL cc_start: 0.7458 (t) cc_final: 0.7248 (m) REVERT: P 55 GLU cc_start: 0.7633 (tt0) cc_final: 0.7202 (tt0) REVERT: P 56 LYS cc_start: 0.7576 (ttmm) cc_final: 0.7284 (mttm) REVERT: P 75 VAL cc_start: 0.7559 (t) cc_final: 0.7239 (p) REVERT: P 107 LYS cc_start: 0.7958 (mmtp) cc_final: 0.7529 (mppt) REVERT: Q 5 GLN cc_start: 0.8517 (tt0) cc_final: 0.8261 (tt0) REVERT: Q 21 GLU cc_start: 0.8865 (tt0) cc_final: 0.8125 (tp30) REVERT: Q 34 ASN cc_start: 0.7317 (m-40) cc_final: 0.6730 (m-40) REVERT: Q 59 ASN cc_start: 0.7534 (m110) cc_final: 0.6758 (t0) REVERT: Q 60 LEU cc_start: 0.6140 (mp) cc_final: 0.5533 (mm) REVERT: Q 111 ARG cc_start: 0.7712 (ttt90) cc_final: 0.7411 (ttt90) REVERT: Q 134 ARG cc_start: 0.7882 (mmt90) cc_final: 0.7513 (mmp80) REVERT: R 24 LEU cc_start: 0.7535 (mt) cc_final: 0.7111 (mt) REVERT: R 35 CYS cc_start: 0.8690 (m) cc_final: 0.8343 (m) REVERT: R 46 MET cc_start: 0.7202 (mmm) cc_final: 0.6878 (mmm) REVERT: R 49 LYS cc_start: 0.7235 (mtpt) cc_final: 0.6897 (mttt) REVERT: R 63 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7288 (mtp180) REVERT: R 81 ARG cc_start: 0.7436 (ttt180) cc_final: 0.6939 (mtm180) REVERT: R 85 MET cc_start: 0.7507 (ptm) cc_final: 0.7181 (ptm) REVERT: S 13 ASP cc_start: 0.8026 (p0) cc_final: 0.7794 (p0) REVERT: S 20 THR cc_start: 0.7867 (p) cc_final: 0.7595 (t) REVERT: S 21 ASN cc_start: 0.7684 (p0) cc_final: 0.6573 (t0) REVERT: S 48 ARG cc_start: 0.8167 (tpt90) cc_final: 0.7580 (ttt90) REVERT: S 62 THR cc_start: 0.8982 (m) cc_final: 0.8522 (m) REVERT: S 71 SER cc_start: 0.8650 (t) cc_final: 0.8376 (p) REVERT: S 108 ASN cc_start: 0.8570 (t0) cc_final: 0.8194 (t0) REVERT: S 112 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6684 (mm-30) REVERT: T 5 LYS cc_start: 0.6463 (ptmt) cc_final: 0.6212 (mtpt) REVERT: T 12 GLN cc_start: 0.6163 (mt0) cc_final: 0.5397 (pt0) REVERT: T 16 ILE cc_start: 0.8384 (pt) cc_final: 0.8165 (pt) REVERT: T 52 MET cc_start: 0.7304 (ttt) cc_final: 0.6591 (tpt) REVERT: T 121 LYS cc_start: 0.6959 (ptmt) cc_final: 0.6310 (pttt) REVERT: T 132 LYS cc_start: 0.7731 (ttmm) cc_final: 0.7392 (tttp) REVERT: T 140 VAL cc_start: 0.8470 (t) cc_final: 0.8152 (m) REVERT: T 146 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7787 (pptt) REVERT: U 21 VAL cc_start: 0.4392 (OUTLIER) cc_final: 0.4083 (p) REVERT: U 27 THR cc_start: 0.7788 (m) cc_final: 0.7579 (t) REVERT: U 40 VAL cc_start: 0.7857 (t) cc_final: 0.7619 (p) REVERT: U 52 LEU cc_start: 0.6230 (mt) cc_final: 0.5935 (mp) REVERT: U 53 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7263 (tp30) REVERT: U 66 ARG cc_start: 0.7855 (ttt180) cc_final: 0.7231 (ttm110) REVERT: U 71 ARG cc_start: 0.7607 (ptm160) cc_final: 0.7010 (ptm160) REVERT: U 82 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.6909 (m-30) REVERT: U 91 ARG cc_start: 0.6359 (mmt90) cc_final: 0.6090 (mmt-90) REVERT: U 104 GLN cc_start: 0.7600 (mt0) cc_final: 0.7280 (tt0) REVERT: V 51 THR cc_start: 0.8222 (p) cc_final: 0.8021 (p) REVERT: W 41 MET cc_start: 0.7226 (ptp) cc_final: 0.7017 (ptm) REVERT: W 47 ILE cc_start: 0.8331 (tt) cc_final: 0.8093 (tt) REVERT: W 49 ASP cc_start: 0.7964 (p0) cc_final: 0.7738 (p0) REVERT: W 51 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7420 (mt-10) REVERT: W 66 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8186 (mt) REVERT: W 81 VAL cc_start: 0.8223 (t) cc_final: 0.7765 (m) REVERT: W 88 MET cc_start: 0.7599 (ttp) cc_final: 0.7224 (tpt) REVERT: W 101 TYR cc_start: 0.8463 (m-80) cc_final: 0.7751 (m-80) REVERT: W 115 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7664 (mm-30) REVERT: W 118 LYS cc_start: 0.8380 (ttmm) cc_final: 0.8124 (ttpp) REVERT: W 128 MET cc_start: 0.8104 (ptp) cc_final: 0.7866 (ptp) REVERT: X 31 ARG cc_start: 0.6972 (ttp-170) cc_final: 0.6588 (ptt90) REVERT: Y 17 LEU cc_start: 0.7292 (mm) cc_final: 0.6846 (mm) REVERT: Y 19 ARG cc_start: 0.5388 (ptt180) cc_final: 0.5139 (ptt180) REVERT: Y 21 GLN cc_start: 0.7384 (pt0) cc_final: 0.6191 (pt0) REVERT: Y 40 LYS cc_start: 0.6013 (mttt) cc_final: 0.5584 (mttp) REVERT: Y 42 GLU cc_start: 0.6593 (mt-10) cc_final: 0.6011 (tm-30) REVERT: Y 56 ILE cc_start: 0.7767 (mt) cc_final: 0.7453 (mp) REVERT: Z 54 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7688 (mmmt) REVERT: Z 62 LYS cc_start: 0.8191 (mttt) cc_final: 0.7982 (mttt) REVERT: a 52 ASP cc_start: 0.7274 (m-30) cc_final: 0.7013 (m-30) REVERT: a 91 VAL cc_start: 0.7058 (m) cc_final: 0.6807 (p) REVERT: a 92 ARG cc_start: 0.6634 (mtt180) cc_final: 0.6201 (mtt180) REVERT: b 12 SER cc_start: 0.7798 (m) cc_final: 0.7579 (t) REVERT: b 20 ASN cc_start: 0.7776 (t0) cc_final: 0.7567 (t0) REVERT: b 31 SER cc_start: 0.6703 (p) cc_final: 0.6258 (p) REVERT: c 45 VAL cc_start: 0.7511 (m) cc_final: 0.7102 (p) REVERT: d 7 PRO cc_start: 0.7853 (Cg_endo) cc_final: 0.7537 (Cg_exo) REVERT: d 13 ASN cc_start: 0.7735 (m110) cc_final: 0.7482 (m-40) REVERT: d 36 ARG cc_start: 0.7217 (mtt180) cc_final: 0.7010 (ttm110) REVERT: e 10 GLN cc_start: 0.6931 (mt0) cc_final: 0.6411 (mm-40) REVERT: e 20 LYS cc_start: 0.8475 (pttp) cc_final: 0.7840 (tptp) REVERT: e 24 MET cc_start: 0.7051 (mtt) cc_final: 0.6623 (tmm) REVERT: g 73 PHE cc_start: 0.5871 (t80) cc_final: 0.4581 (t80) REVERT: g 115 LYS cc_start: 0.8019 (ttpt) cc_final: 0.7515 (tppt) REVERT: g 124 ASP cc_start: 0.7231 (p0) cc_final: 0.6960 (p0) REVERT: g 145 GLN cc_start: 0.6602 (pt0) cc_final: 0.5734 (mp10) REVERT: g 154 GLU cc_start: 0.7707 (pt0) cc_final: 0.7443 (pm20) REVERT: g 159 LEU cc_start: 0.7503 (mt) cc_final: 0.6602 (mp) REVERT: g 175 ASP cc_start: 0.7395 (t0) cc_final: 0.7100 (t0) REVERT: g 186 CYS cc_start: 0.7256 (m) cc_final: 0.6642 (m) REVERT: g 190 LYS cc_start: 0.5274 (mttt) cc_final: 0.5068 (mttt) REVERT: g 192 TYR cc_start: 0.4922 (m-80) cc_final: 0.4505 (m-80) REVERT: g 236 MET cc_start: 0.5189 (ttp) cc_final: 0.4025 (ttm) REVERT: g 241 ASN cc_start: 0.6767 (m-40) cc_final: 0.6488 (t0) REVERT: g 244 LYS cc_start: 0.7266 (ptpt) cc_final: 0.6691 (ttmt) REVERT: g 248 PHE cc_start: 0.6777 (m-80) cc_final: 0.6473 (m-80) REVERT: g 255 HIS cc_start: 0.8059 (m-70) cc_final: 0.7677 (m-70) REVERT: g 265 TRP cc_start: 0.5265 (m100) cc_final: 0.4487 (m100) REVERT: g 277 TRP cc_start: 0.6684 (m-90) cc_final: 0.6050 (m100) outliers start: 183 outliers final: 64 residues processed: 1595 average time/residue: 0.7212 time to fit residues: 1845.2908 Evaluate side-chains 1160 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 1078 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 208 PHE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 235 GLU Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain E residue 211 LYS Chi-restraints excluded: chain F residue 14 ASP Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 10 LYS Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain J residue 114 ARG Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 149 GLU Chi-restraints excluded: chain J residue 154 ILE Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 103 GLU Chi-restraints excluded: chain O residue 34 ILE Chi-restraints excluded: chain O residue 46 ASN Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 78 HIS Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 88 PHE Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 99 HIS Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 112 GLU Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 43 LEU Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 82 ASP Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain W residue 7 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 85 ASP Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain X residue 35 THR Chi-restraints excluded: chain X residue 89 ASP Chi-restraints excluded: chain Y residue 37 ASP Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 80 HIS Chi-restraints excluded: chain a residue 26 CYS Chi-restraints excluded: chain a residue 29 GLN Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 57 CYS Chi-restraints excluded: chain c residue 57 LEU Chi-restraints excluded: chain c residue 67 LEU Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 306 CYS Chi-restraints excluded: chain n residue 19 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 483 optimal weight: 2.9990 chunk 433 optimal weight: 10.0000 chunk 240 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 231 optimal weight: 0.0770 chunk 448 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 272 optimal weight: 1.9990 chunk 333 optimal weight: 3.9990 chunk 519 optimal weight: 1.9990 overall best weight: 1.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS B 76 HIS B 179 GLN C 73 HIS C 102 GLN C 167 HIS C 171 ASN C 218 HIS C 224 ASN D 75 GLN F 31 HIS ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 51 GLN ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 HIS I 11 HIS J 89 GLN J 100 ASN J 112 HIS J 129 HIS J 131 HIS J 141 GLN K 27 GLN K 62 HIS K 84 ASN L 13 GLN L 102 HIS ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 HIS O 73 GLN O 87 GLN P 105 GLN P 113 HIS R 83 ASN T 57 GLN T 134 GLN U 42 ASN U 115 HIS Y 88 HIS a 17 HIS b 50 HIS b 52 ASN ** c 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 32 HIS g 94 HIS g 150 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.119842 restraints weight = 109620.886| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.44 r_work: 0.3267 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 70254 Z= 0.232 Angle : 0.717 15.642 102091 Z= 0.376 Chirality : 0.043 0.342 12720 Planarity : 0.006 0.090 7439 Dihedral : 23.060 179.828 28069 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 1.46 % Allowed : 6.61 % Favored : 91.93 % Rotamer: Outliers : 6.07 % Allowed : 16.57 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.11), residues: 4250 helix: -0.90 (0.13), residues: 1351 sheet: -1.94 (0.17), residues: 764 loop : -2.26 (0.12), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 25 HIS 0.020 0.001 HIS g 32 PHE 0.034 0.002 PHE A 88 TYR 0.022 0.002 TYR F 12 ARG 0.019 0.001 ARG c 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1405 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1189 time to evaluate : 3.630 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: A 14 LYS cc_start: 0.7496 (ptpp) cc_final: 0.6658 (ptpp) REVERT: A 40 ARG cc_start: 0.7675 (ttp80) cc_final: 0.7430 (ttp80) REVERT: A 47 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7029 (mm) REVERT: A 53 TYR cc_start: 0.8097 (t80) cc_final: 0.7796 (t80) REVERT: A 79 SER cc_start: 0.8419 (m) cc_final: 0.7950 (t) REVERT: A 128 ASP cc_start: 0.7915 (t70) cc_final: 0.7700 (t0) REVERT: A 153 ASP cc_start: 0.8360 (p0) cc_final: 0.8123 (p0) REVERT: A 204 ASP cc_start: 0.7382 (m-30) cc_final: 0.7002 (t0) REVERT: A 210 LYS cc_start: 0.7310 (mttt) cc_final: 0.7077 (tppt) REVERT: A 213 GLU cc_start: 0.7106 (mp0) cc_final: 0.6628 (mp0) REVERT: B 34 PHE cc_start: 0.6663 (OUTLIER) cc_final: 0.5961 (p90) REVERT: B 70 MET cc_start: 0.5852 (ptp) cc_final: 0.5585 (ptp) REVERT: B 91 GLU cc_start: 0.7216 (tt0) cc_final: 0.6929 (tt0) REVERT: B 103 HIS cc_start: 0.8020 (t-90) cc_final: 0.7651 (t-170) REVERT: B 114 ARG cc_start: 0.8700 (mmt-90) cc_final: 0.8451 (mmt90) REVERT: B 159 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8037 (mm-40) REVERT: B 179 GLN cc_start: 0.8442 (mm110) cc_final: 0.7949 (mm-40) REVERT: C 96 MET cc_start: 0.8232 (mmm) cc_final: 0.8013 (mmt) REVERT: C 116 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8380 (tt) REVERT: D 21 GLU cc_start: 0.7988 (tt0) cc_final: 0.7567 (tt0) REVERT: D 33 GLU cc_start: 0.7054 (mp0) cc_final: 0.6747 (mp0) REVERT: D 39 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7463 (mp0) REVERT: D 65 ARG cc_start: 0.7244 (ttp80) cc_final: 0.6998 (mtm110) REVERT: D 105 SER cc_start: 0.8829 (t) cc_final: 0.8263 (p) REVERT: D 147 ARG cc_start: 0.6356 (ptp90) cc_final: 0.6029 (mmm160) REVERT: D 178 MET cc_start: 0.8443 (mtp) cc_final: 0.8232 (mtp) REVERT: E 106 LYS cc_start: 0.7517 (mmtp) cc_final: 0.6485 (tppt) REVERT: E 128 GLN cc_start: 0.7886 (tt0) cc_final: 0.7400 (mt0) REVERT: F 31 HIS cc_start: 0.8380 (OUTLIER) cc_final: 0.8121 (m170) REVERT: F 37 MET cc_start: 0.7946 (tpt) cc_final: 0.7683 (tpt) REVERT: F 41 THR cc_start: 0.8666 (m) cc_final: 0.8440 (p) REVERT: F 49 ARG cc_start: 0.7651 (ttp-170) cc_final: 0.7433 (mtp180) REVERT: F 50 PHE cc_start: 0.8166 (m-80) cc_final: 0.7529 (m-10) REVERT: F 97 PRO cc_start: 0.8793 (Cg_endo) cc_final: 0.8581 (Cg_exo) REVERT: F 181 LYS cc_start: 0.7619 (tppp) cc_final: 0.7374 (mmmt) REVERT: H 24 ILE cc_start: 0.8145 (mp) cc_final: 0.7936 (mm) REVERT: H 31 LYS cc_start: 0.7745 (ttmm) cc_final: 0.7527 (tptt) REVERT: H 36 THR cc_start: 0.7813 (p) cc_final: 0.7590 (t) REVERT: H 50 PHE cc_start: 0.7588 (m-80) cc_final: 0.7125 (m-80) REVERT: H 69 ILE cc_start: 0.8116 (mm) cc_final: 0.7819 (pt) REVERT: H 109 LEU cc_start: 0.9000 (tp) cc_final: 0.8700 (tp) REVERT: H 127 LYS cc_start: 0.8579 (mttt) cc_final: 0.7994 (mmtt) REVERT: H 134 LEU cc_start: 0.9114 (mm) cc_final: 0.8845 (mm) REVERT: H 143 GLU cc_start: 0.7713 (tt0) cc_final: 0.7465 (pt0) REVERT: I 17 ARG cc_start: 0.8017 (mmm160) cc_final: 0.7773 (mmt90) REVERT: I 24 LYS cc_start: 0.8779 (mttm) cc_final: 0.8546 (mttp) REVERT: I 46 VAL cc_start: 0.8820 (t) cc_final: 0.8415 (p) REVERT: I 92 ARG cc_start: 0.8477 (ttp-170) cc_final: 0.8237 (ttp-110) REVERT: I 114 GLU cc_start: 0.4227 (tt0) cc_final: 0.2754 (tm-30) REVERT: I 186 LEU cc_start: 0.8855 (tp) cc_final: 0.8583 (mt) REVERT: I 189 TYR cc_start: 0.7771 (m-80) cc_final: 0.7540 (m-80) REVERT: J 17 TYR cc_start: 0.8298 (m-80) cc_final: 0.5459 (t80) REVERT: J 18 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7343 (mt-10) REVERT: J 23 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.6957 (t70) REVERT: J 76 ARG cc_start: 0.8054 (ttp-110) cc_final: 0.7824 (mtm180) REVERT: J 89 GLN cc_start: 0.7496 (tt0) cc_final: 0.6991 (mt0) REVERT: J 106 ARG cc_start: 0.8069 (ptm160) cc_final: 0.7453 (ptp-170) REVERT: L 34 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7712 (tttm) REVERT: L 80 ARG cc_start: 0.7215 (mtm180) cc_final: 0.7007 (mmt90) REVERT: L 87 ASP cc_start: 0.8581 (m-30) cc_final: 0.8220 (m-30) REVERT: L 93 ARG cc_start: 0.8544 (ttt90) cc_final: 0.8330 (ttp-110) REVERT: L 103 THR cc_start: 0.8386 (m) cc_final: 0.8107 (m) REVERT: L 108 HIS cc_start: 0.8146 (t70) cc_final: 0.7754 (t-90) REVERT: N 11 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8244 (pt) REVERT: N 20 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6408 (mtt180) REVERT: N 104 HIS cc_start: 0.8046 (t70) cc_final: 0.7833 (m90) REVERT: N 129 TYR cc_start: 0.9267 (m-80) cc_final: 0.8907 (m-80) REVERT: O 129 ARG cc_start: 0.7546 (mtp85) cc_final: 0.7269 (mtm110) REVERT: O 136 ARG cc_start: 0.7622 (ttp80) cc_final: 0.6936 (ttm170) REVERT: P 14 TYR cc_start: 0.8054 (t80) cc_final: 0.7636 (t80) REVERT: P 36 THR cc_start: 0.8817 (t) cc_final: 0.8448 (m) REVERT: P 80 ARG cc_start: 0.8239 (mtp-110) cc_final: 0.7708 (mtm180) REVERT: P 88 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6742 (p90) REVERT: Q 18 TYR cc_start: 0.8954 (t80) cc_final: 0.7975 (t80) REVERT: Q 35 MET cc_start: 0.8786 (mmm) cc_final: 0.8507 (mmm) REVERT: Q 119 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8201 (ptt180) REVERT: S 21 ASN cc_start: 0.7795 (p0) cc_final: 0.7006 (t0) REVERT: S 30 LEU cc_start: 0.9271 (mt) cc_final: 0.9038 (mt) REVERT: S 52 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6843 (pp) REVERT: S 66 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8341 (tm-30) REVERT: S 86 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8821 (mp) REVERT: S 112 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6968 (mm-30) REVERT: S 118 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8398 (mtpp) REVERT: T 5 LYS cc_start: 0.8469 (ptmt) cc_final: 0.7974 (ptpt) REVERT: T 12 GLN cc_start: 0.7343 (mt0) cc_final: 0.6649 (pt0) REVERT: T 70 GLN cc_start: 0.8583 (tp40) cc_final: 0.8206 (mm-40) REVERT: U 52 LEU cc_start: 0.7784 (mt) cc_final: 0.7539 (mp) REVERT: U 98 THR cc_start: 0.7523 (t) cc_final: 0.7266 (m) REVERT: W 65 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8321 (mt) REVERT: W 83 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7714 (mt) REVERT: W 94 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8795 (mp) REVERT: W 101 TYR cc_start: 0.9200 (m-80) cc_final: 0.8848 (m-80) REVERT: X 9 ARG cc_start: 0.8556 (ttt90) cc_final: 0.8332 (ttm-80) REVERT: X 80 LYS cc_start: 0.8327 (tptp) cc_final: 0.8051 (tptp) REVERT: Y 27 GLN cc_start: 0.7707 (pm20) cc_final: 0.7198 (pm20) REVERT: Y 54 VAL cc_start: 0.7846 (t) cc_final: 0.7147 (p) REVERT: Z 54 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8488 (mmmt) REVERT: Z 74 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.7966 (p) REVERT: a 63 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7517 (mm-30) REVERT: a 91 VAL cc_start: 0.9256 (m) cc_final: 0.9004 (p) REVERT: d 13 ASN cc_start: 0.8363 (m110) cc_final: 0.8129 (m-40) REVERT: d 40 CYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7885 (p) REVERT: g 23 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6195 (p90) REVERT: g 73 PHE cc_start: 0.7160 (t80) cc_final: 0.6341 (t80) REVERT: g 115 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8164 (mmtp) REVERT: g 186 CYS cc_start: 0.8358 (m) cc_final: 0.7851 (m) REVERT: g 192 TYR cc_start: 0.7267 (m-80) cc_final: 0.6949 (m-80) REVERT: g 324 ASP cc_start: 0.8356 (p0) cc_final: 0.8149 (p0) outliers start: 216 outliers final: 113 residues processed: 1310 average time/residue: 0.7080 time to fit residues: 1516.8696 Evaluate side-chains 1119 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 987 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 31 HIS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 137 HIS Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 191 ASP Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 23 HIS Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 64 CYS Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 68 ILE Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 78 HIS Chi-restraints excluded: chain P residue 88 PHE Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 82 ASP Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 99 HIS Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 112 GLU Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 34 ILE Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 42 ASP Chi-restraints excluded: chain W residue 7 LEU Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain X residue 43 GLU Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 12 ILE Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 80 HIS Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 25 ASN Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 28 GLN Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 61 GLU Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 40 CYS Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 32 HIS Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 170 CYS Chi-restraints excluded: chain n residue 13 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 459 optimal weight: 0.9990 chunk 403 optimal weight: 0.9990 chunk 279 optimal weight: 6.9990 chunk 353 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 425 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 541 optimal weight: 10.0000 chunk 428 optimal weight: 0.0030 chunk 323 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 overall best weight: 2.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN B 59 ASN B 179 GLN C 109 GLN D 101 ASN E 112 HIS E 127 ASN ** E 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 ASN I 11 HIS J 100 ASN ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 43 GLN K 84 ASN L 134 HIS N 78 ASN ** O 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 GLN Q 5 GLN ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 57 GLN T 85 HIS T 99 HIS T 134 GLN U 35 ASN W 70 ASN ** W 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS X 98 ASN ** Y 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 43 ASN ** c 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 68 GLN ** g 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113062 restraints weight = 109867.129| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.33 r_work: 0.3190 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 70254 Z= 0.357 Angle : 0.757 13.581 102091 Z= 0.390 Chirality : 0.044 0.316 12720 Planarity : 0.006 0.062 7439 Dihedral : 23.018 179.976 27969 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 1.13 % Allowed : 7.74 % Favored : 91.13 % Rotamer: Outliers : 7.58 % Allowed : 19.32 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.12), residues: 4250 helix: -0.56 (0.13), residues: 1375 sheet: -1.64 (0.17), residues: 767 loop : -2.21 (0.12), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP g 277 HIS 0.043 0.002 HIS B 38 PHE 0.030 0.003 PHE A 200 TYR 0.031 0.002 TYR Q 93 ARG 0.013 0.001 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 270 poor density : 1088 time to evaluate : 3.633 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: A 44 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7744 (t) REVERT: A 62 MET cc_start: 0.8909 (mtp) cc_final: 0.8703 (mtp) REVERT: A 153 ASP cc_start: 0.8475 (p0) cc_final: 0.8191 (p0) REVERT: A 202 TYR cc_start: 0.7979 (t80) cc_final: 0.7460 (t80) REVERT: B 34 PHE cc_start: 0.6830 (OUTLIER) cc_final: 0.6049 (p90) REVERT: B 38 HIS cc_start: 0.6002 (OUTLIER) cc_final: 0.5656 (m-70) REVERT: B 103 HIS cc_start: 0.8116 (t-90) cc_final: 0.7889 (t-170) REVERT: B 155 HIS cc_start: 0.8532 (t70) cc_final: 0.8304 (t70) REVERT: B 159 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8153 (mm-40) REVERT: B 178 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7674 (tm-30) REVERT: B 187 GLU cc_start: 0.6459 (mm-30) cc_final: 0.5951 (mm-30) REVERT: B 190 GLU cc_start: 0.6668 (mt-10) cc_final: 0.6208 (mt-10) REVERT: C 116 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8709 (tt) REVERT: C 158 TYR cc_start: 0.8952 (m-80) cc_final: 0.8699 (m-80) REVERT: D 21 GLU cc_start: 0.7934 (tt0) cc_final: 0.7367 (tt0) REVERT: D 39 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7481 (mp0) REVERT: D 65 ARG cc_start: 0.7344 (ttp80) cc_final: 0.7065 (mtm110) REVERT: D 67 LEU cc_start: 0.8888 (tp) cc_final: 0.8656 (tt) REVERT: D 147 ARG cc_start: 0.6543 (ptp90) cc_final: 0.6025 (mtp180) REVERT: D 178 MET cc_start: 0.8527 (mtp) cc_final: 0.8227 (mtp) REVERT: E 51 ARG cc_start: 0.8363 (mmp80) cc_final: 0.7991 (mmp80) REVERT: E 118 GLU cc_start: 0.6832 (tm-30) cc_final: 0.6620 (tm-30) REVERT: E 128 GLN cc_start: 0.7829 (tt0) cc_final: 0.7510 (mt0) REVERT: E 158 ASP cc_start: 0.8508 (m-30) cc_final: 0.8015 (m-30) REVERT: E 232 GLU cc_start: 0.7666 (tp30) cc_final: 0.6959 (mm-30) REVERT: F 37 MET cc_start: 0.8109 (tpt) cc_final: 0.7593 (tpp) REVERT: F 50 PHE cc_start: 0.8320 (m-80) cc_final: 0.7784 (m-10) REVERT: F 97 PRO cc_start: 0.8891 (Cg_endo) cc_final: 0.8634 (Cg_exo) REVERT: H 50 PHE cc_start: 0.7999 (m-80) cc_final: 0.7202 (m-80) REVERT: H 69 ILE cc_start: 0.8174 (mm) cc_final: 0.7965 (pt) REVERT: H 127 LYS cc_start: 0.8878 (mttt) cc_final: 0.8241 (mmtt) REVERT: I 17 ARG cc_start: 0.8345 (mmm160) cc_final: 0.8115 (mmt90) REVERT: I 75 LYS cc_start: 0.8646 (ttpt) cc_final: 0.8147 (ttmt) REVERT: I 92 ARG cc_start: 0.8514 (ttp-170) cc_final: 0.8269 (ttp-110) REVERT: I 186 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8749 (mt) REVERT: J 18 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7484 (mt-10) REVERT: J 23 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7387 (t70) REVERT: J 49 LYS cc_start: 0.6745 (tttm) cc_final: 0.6260 (ttmm) REVERT: J 76 ARG cc_start: 0.8125 (ttp-110) cc_final: 0.7868 (mtm180) REVERT: J 89 GLN cc_start: 0.7446 (tt0) cc_final: 0.6945 (mt0) REVERT: J 103 MET cc_start: 0.7562 (tpp) cc_final: 0.7135 (tpp) REVERT: J 106 ARG cc_start: 0.7895 (ptm160) cc_final: 0.7480 (ptp-110) REVERT: K 34 LEU cc_start: 0.5364 (OUTLIER) cc_final: 0.5077 (pp) REVERT: K 72 ILE cc_start: 0.6492 (OUTLIER) cc_final: 0.6139 (mt) REVERT: K 91 ARG cc_start: 0.5619 (mtt180) cc_final: 0.4434 (ttp80) REVERT: L 39 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8043 (mtmm) REVERT: L 62 VAL cc_start: 0.8776 (t) cc_final: 0.8573 (m) REVERT: L 80 ARG cc_start: 0.7427 (mtm180) cc_final: 0.6838 (mmt90) REVERT: N 9 LYS cc_start: 0.8537 (mtmm) cc_final: 0.8294 (mtmm) REVERT: N 17 PRO cc_start: 0.8829 (Cg_exo) cc_final: 0.8571 (Cg_endo) REVERT: N 108 ASP cc_start: 0.8393 (p0) cc_final: 0.8177 (p0) REVERT: N 129 TYR cc_start: 0.9223 (m-80) cc_final: 0.8972 (m-80) REVERT: O 45 LYS cc_start: 0.8444 (ttpp) cc_final: 0.8129 (ptmm) REVERT: O 83 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7763 (ptp) REVERT: O 108 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: O 129 ARG cc_start: 0.7694 (mtp85) cc_final: 0.7340 (mtm110) REVERT: P 14 TYR cc_start: 0.7970 (t80) cc_final: 0.7747 (t80) REVERT: P 88 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7528 (p90) REVERT: P 102 PHE cc_start: 0.8378 (t80) cc_final: 0.8051 (t80) REVERT: P 113 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.7979 (m-70) REVERT: Q 18 TYR cc_start: 0.9175 (t80) cc_final: 0.8936 (t80) REVERT: Q 59 ASN cc_start: 0.5287 (t0) cc_final: 0.4913 (t0) REVERT: Q 102 ILE cc_start: 0.8527 (tt) cc_final: 0.8296 (mt) REVERT: Q 119 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8230 (ptt90) REVERT: Q 134 ARG cc_start: 0.9098 (mmp80) cc_final: 0.8571 (mmp-170) REVERT: R 62 GLU cc_start: 0.7707 (tp30) cc_final: 0.7302 (tp30) REVERT: S 21 ASN cc_start: 0.8376 (p0) cc_final: 0.7598 (t0) REVERT: S 25 ARG cc_start: 0.8229 (ptt90) cc_final: 0.7629 (ptp-170) REVERT: S 48 ARG cc_start: 0.8451 (tpt90) cc_final: 0.8064 (ttm-80) REVERT: S 52 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7246 (pp) REVERT: S 72 ILE cc_start: 0.8692 (mt) cc_final: 0.8449 (mt) REVERT: S 86 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9007 (mp) REVERT: S 112 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7446 (mm-30) REVERT: S 139 LYS cc_start: 0.9237 (tptt) cc_final: 0.9020 (tppt) REVERT: T 12 GLN cc_start: 0.7731 (mt0) cc_final: 0.6983 (pt0) REVERT: V 51 THR cc_start: 0.8605 (p) cc_final: 0.8218 (p) REVERT: W 31 SER cc_start: 0.9217 (p) cc_final: 0.8978 (p) REVERT: W 101 TYR cc_start: 0.9211 (m-80) cc_final: 0.8747 (m-80) REVERT: X 51 ILE cc_start: 0.8701 (mp) cc_final: 0.8371 (mp) REVERT: X 108 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7763 (ttt90) REVERT: Y 27 GLN cc_start: 0.7778 (pm20) cc_final: 0.7241 (pm20) REVERT: Y 53 LEU cc_start: 0.7444 (mt) cc_final: 0.7232 (mt) REVERT: Y 54 VAL cc_start: 0.8081 (t) cc_final: 0.7810 (p) REVERT: Z 18 GLU cc_start: 0.6090 (mp0) cc_final: 0.5870 (mp0) REVERT: Z 54 LYS cc_start: 0.8986 (mmtt) cc_final: 0.8528 (mmmt) REVERT: Z 74 VAL cc_start: 0.8361 (OUTLIER) cc_final: 0.8039 (p) REVERT: Z 80 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.7780 (p-80) REVERT: a 14 ASN cc_start: 0.9023 (t0) cc_final: 0.8628 (t0) REVERT: a 63 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7580 (mm-30) REVERT: d 13 ASN cc_start: 0.8356 (m110) cc_final: 0.8110 (m-40) REVERT: d 29 ARG cc_start: 0.8539 (mmm-85) cc_final: 0.8243 (mtt180) REVERT: g 23 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6778 (p90) REVERT: g 47 TYR cc_start: 0.6066 (m-80) cc_final: 0.5756 (m-80) REVERT: g 73 PHE cc_start: 0.7439 (t80) cc_final: 0.6862 (t80) REVERT: g 76 LEU cc_start: 0.7548 (mp) cc_final: 0.7327 (mp) REVERT: g 115 LYS cc_start: 0.8600 (ttpt) cc_final: 0.8183 (mmtp) REVERT: g 231 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7316 (p0) outliers start: 270 outliers final: 165 residues processed: 1235 average time/residue: 0.6728 time to fit residues: 1374.3948 Evaluate side-chains 1157 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 971 time to evaluate : 4.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 34 PHE Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 14 MET Chi-restraints excluded: chain J residue 23 HIS Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 48 SER Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 64 CYS Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 83 MET Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 108 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 77 THR Chi-restraints excluded: chain P residue 78 HIS Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 88 PHE Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain P residue 113 HIS Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 99 HIS Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 34 ILE Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain U residue 29 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain W residue 7 LEU Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 108 ARG Chi-restraints excluded: chain X residue 119 CYS Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 12 ILE Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 80 HIS Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 25 ASN Chi-restraints excluded: chain a residue 26 CYS Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 100 LEU Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain c residue 17 ILE Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 28 GLN Chi-restraints excluded: chain c residue 41 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 61 GLU Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 32 HIS Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 145 GLN Chi-restraints excluded: chain g residue 170 CYS Chi-restraints excluded: chain g residue 231 ASP Chi-restraints excluded: chain g residue 306 CYS Chi-restraints excluded: chain n residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 14 optimal weight: 9.9990 chunk 483 optimal weight: 3.9990 chunk 389 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 322 optimal weight: 6.9990 chunk 491 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 363 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 534 optimal weight: 0.6980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN E 188 ASN H 51 GLN ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 HIS I 94 ASN J 100 ASN J 141 GLN K 43 GLN K 84 ASN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 78 ASN ** Y 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 7 ASN c 28 GLN ** g 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 HIS g 263 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.114652 restraints weight = 109927.176| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.30 r_work: 0.3213 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 70254 Z= 0.261 Angle : 0.677 12.982 102091 Z= 0.348 Chirality : 0.040 0.293 12720 Planarity : 0.005 0.056 7439 Dihedral : 22.889 179.984 27962 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 1.06 % Allowed : 7.44 % Favored : 91.51 % Rotamer: Outliers : 7.61 % Allowed : 21.65 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.12), residues: 4250 helix: -0.20 (0.14), residues: 1373 sheet: -1.32 (0.18), residues: 780 loop : -2.12 (0.12), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP g 277 HIS 0.007 0.001 HIS V 29 PHE 0.022 0.002 PHE g 29 TYR 0.040 0.002 TYR Q 93 ARG 0.008 0.001 ARG d 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 271 poor density : 1038 time to evaluate : 3.709 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: A 40 ARG cc_start: 0.7684 (ttt-90) cc_final: 0.7354 (ttm-80) REVERT: A 44 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7680 (p) REVERT: A 49 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8828 (mm) REVERT: A 62 MET cc_start: 0.8763 (mtp) cc_final: 0.8546 (mtp) REVERT: A 100 ARG cc_start: 0.8427 (ptm-80) cc_final: 0.8062 (ttp80) REVERT: A 153 ASP cc_start: 0.8466 (p0) cc_final: 0.8162 (p0) REVERT: A 178 ARG cc_start: 0.8352 (ttp-170) cc_final: 0.8049 (ttt-90) REVERT: A 202 TYR cc_start: 0.7909 (t80) cc_final: 0.7409 (t80) REVERT: A 204 ASP cc_start: 0.7590 (m-30) cc_final: 0.6732 (t0) REVERT: B 155 HIS cc_start: 0.8509 (t70) cc_final: 0.8281 (t70) REVERT: B 159 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8177 (mm-40) REVERT: B 169 THR cc_start: 0.8126 (t) cc_final: 0.7835 (t) REVERT: B 178 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7710 (tm-30) REVERT: B 179 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8296 (mm110) REVERT: B 187 GLU cc_start: 0.6304 (mm-30) cc_final: 0.5709 (mm-30) REVERT: B 190 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6073 (mt-10) REVERT: B 199 GLN cc_start: 0.8493 (mp10) cc_final: 0.8259 (mp10) REVERT: C 96 MET cc_start: 0.8175 (mmm) cc_final: 0.7918 (mmm) REVERT: C 158 TYR cc_start: 0.8874 (m-80) cc_final: 0.8618 (m-80) REVERT: D 21 GLU cc_start: 0.7900 (tt0) cc_final: 0.7341 (tt0) REVERT: D 33 GLU cc_start: 0.7182 (mp0) cc_final: 0.6674 (mp0) REVERT: D 39 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7496 (mp0) REVERT: D 41 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.5704 (ttm110) REVERT: D 65 ARG cc_start: 0.7435 (ttp80) cc_final: 0.7125 (mtm110) REVERT: D 147 ARG cc_start: 0.6550 (ptp90) cc_final: 0.5979 (mtp180) REVERT: D 178 MET cc_start: 0.8554 (mtp) cc_final: 0.8288 (mtp) REVERT: E 51 ARG cc_start: 0.8236 (mmp80) cc_final: 0.7938 (mmp80) REVERT: E 118 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6718 (tm-30) REVERT: E 128 GLN cc_start: 0.7890 (tt0) cc_final: 0.7595 (mt0) REVERT: E 202 MET cc_start: 0.7786 (tpp) cc_final: 0.7181 (mmm) REVERT: E 206 ASP cc_start: 0.4414 (p0) cc_final: 0.3941 (p0) REVERT: E 232 GLU cc_start: 0.7705 (tp30) cc_final: 0.7075 (mm-30) REVERT: F 37 MET cc_start: 0.8107 (tpt) cc_final: 0.7606 (tpp) REVERT: F 50 PHE cc_start: 0.8125 (m-80) cc_final: 0.7697 (m-10) REVERT: F 66 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8656 (mtm) REVERT: F 138 GLN cc_start: 0.8335 (mm-40) cc_final: 0.8025 (mm-40) REVERT: H 50 PHE cc_start: 0.8103 (m-80) cc_final: 0.7451 (m-80) REVERT: H 127 LYS cc_start: 0.8721 (mttt) cc_final: 0.8233 (mmtt) REVERT: I 6 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7988 (ppp) REVERT: I 17 ARG cc_start: 0.8505 (mmm160) cc_final: 0.8192 (mmt180) REVERT: I 80 ASN cc_start: 0.8374 (p0) cc_final: 0.8058 (p0) REVERT: I 92 ARG cc_start: 0.8512 (ttp-170) cc_final: 0.8248 (ttp-110) REVERT: J 17 TYR cc_start: 0.8306 (m-10) cc_final: 0.5156 (t80) REVERT: J 23 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.7334 (t70) REVERT: J 36 ASN cc_start: 0.8207 (p0) cc_final: 0.7915 (p0) REVERT: J 49 LYS cc_start: 0.6847 (tttm) cc_final: 0.6509 (ttmm) REVERT: J 76 ARG cc_start: 0.8085 (ttp-110) cc_final: 0.7840 (mtm180) REVERT: J 89 GLN cc_start: 0.7441 (tt0) cc_final: 0.6954 (mt0) REVERT: J 103 MET cc_start: 0.7348 (tpp) cc_final: 0.6836 (tpp) REVERT: J 106 ARG cc_start: 0.8087 (ptm160) cc_final: 0.7328 (ptp-110) REVERT: K 34 LEU cc_start: 0.5334 (OUTLIER) cc_final: 0.4827 (pt) REVERT: K 54 CYS cc_start: 0.7425 (p) cc_final: 0.6926 (m) REVERT: K 91 ARG cc_start: 0.5793 (mtt180) cc_final: 0.4669 (ttp80) REVERT: L 80 ARG cc_start: 0.7213 (mtm180) cc_final: 0.7000 (mmt90) REVERT: N 9 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8295 (mtmm) REVERT: N 11 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8386 (pt) REVERT: N 17 PRO cc_start: 0.8764 (Cg_exo) cc_final: 0.8561 (Cg_endo) REVERT: N 129 TYR cc_start: 0.9251 (m-80) cc_final: 0.8627 (m-80) REVERT: O 29 LYS cc_start: 0.7284 (mttt) cc_final: 0.6918 (mttp) REVERT: O 129 ARG cc_start: 0.7693 (mtp85) cc_final: 0.7327 (mtm110) REVERT: O 133 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7728 (mmmt) REVERT: P 53 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7373 (tt) REVERT: P 102 PHE cc_start: 0.8416 (t80) cc_final: 0.8039 (t80) REVERT: Q 18 TYR cc_start: 0.9151 (t80) cc_final: 0.8915 (t80) REVERT: Q 59 ASN cc_start: 0.5298 (t0) cc_final: 0.4303 (t0) REVERT: Q 134 ARG cc_start: 0.9094 (mmp80) cc_final: 0.8672 (mmp-170) REVERT: R 111 LEU cc_start: 0.7464 (tp) cc_final: 0.7140 (tp) REVERT: S 21 ASN cc_start: 0.8458 (p0) cc_final: 0.7677 (t0) REVERT: S 25 ARG cc_start: 0.8207 (ptt90) cc_final: 0.7587 (ptp-170) REVERT: S 48 ARG cc_start: 0.8336 (tpt90) cc_final: 0.7931 (ttm-80) REVERT: S 52 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7468 (pp) REVERT: S 72 ILE cc_start: 0.8671 (mt) cc_final: 0.8348 (mt) REVERT: S 86 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9031 (mp) REVERT: S 112 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7341 (mm-30) REVERT: S 139 LYS cc_start: 0.9138 (tptt) cc_final: 0.8895 (tppt) REVERT: T 12 GLN cc_start: 0.7695 (mt0) cc_final: 0.6951 (pt0) REVERT: T 103 SER cc_start: 0.9117 (OUTLIER) cc_final: 0.8787 (t) REVERT: V 21 ASP cc_start: 0.8342 (t0) cc_final: 0.7713 (t70) REVERT: V 51 THR cc_start: 0.8595 (p) cc_final: 0.8175 (p) REVERT: W 31 SER cc_start: 0.9152 (p) cc_final: 0.8927 (p) REVERT: W 101 TYR cc_start: 0.9216 (m-80) cc_final: 0.8728 (m-80) REVERT: X 51 ILE cc_start: 0.8736 (mp) cc_final: 0.8339 (mp) REVERT: X 68 ARG cc_start: 0.7668 (mmt180) cc_final: 0.7442 (mpt180) REVERT: X 108 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8074 (mtp180) REVERT: Y 21 GLN cc_start: 0.7554 (mt0) cc_final: 0.7343 (mp10) REVERT: Y 27 GLN cc_start: 0.7845 (pm20) cc_final: 0.7218 (pm20) REVERT: Z 54 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8522 (mmmt) REVERT: Z 74 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8071 (p) REVERT: Z 80 HIS cc_start: 0.8633 (OUTLIER) cc_final: 0.7511 (p-80) REVERT: a 14 ASN cc_start: 0.9022 (t0) cc_final: 0.8548 (t0) REVERT: a 63 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7636 (mm-30) REVERT: c 59 GLU cc_start: 0.6371 (mp0) cc_final: 0.6130 (mp0) REVERT: d 13 ASN cc_start: 0.8293 (m110) cc_final: 0.8062 (m110) REVERT: d 40 CYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8050 (p) REVERT: e 26 LYS cc_start: 0.6837 (ttpp) cc_final: 0.6391 (tttm) REVERT: g 76 LEU cc_start: 0.7533 (mp) cc_final: 0.7231 (mp) REVERT: g 94 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.5813 (t-90) REVERT: g 115 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8036 (mmtp) REVERT: g 124 ASP cc_start: 0.7584 (p0) cc_final: 0.7321 (p0) REVERT: g 136 ARG cc_start: 0.7024 (mmm-85) cc_final: 0.6355 (mmp80) REVERT: g 192 TYR cc_start: 0.7668 (m-80) cc_final: 0.6988 (m-80) REVERT: g 292 PHE cc_start: 0.6117 (OUTLIER) cc_final: 0.5908 (p90) outliers start: 271 outliers final: 187 residues processed: 1194 average time/residue: 0.6750 time to fit residues: 1336.0523 Evaluate side-chains 1175 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 969 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 38 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 14 MET Chi-restraints excluded: chain J residue 23 HIS Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 149 GLU Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain O residue 41 ILE Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 83 MET Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 78 HIS Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 105 THR Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 99 HIS Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 46 THR Chi-restraints excluded: chain T residue 103 SER Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain U residue 29 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain V residue 9 VAL Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain W residue 7 LEU Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 108 ARG Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 12 ILE Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 80 HIS Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 25 ASN Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 12 SER Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain b residue 74 LEU Chi-restraints excluded: chain c residue 17 ILE Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 28 GLN Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 61 GLU Chi-restraints excluded: chain d residue 40 CYS Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain g residue 32 HIS Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 61 LYS Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 121 HIS Chi-restraints excluded: chain g residue 145 GLN Chi-restraints excluded: chain g residue 170 CYS Chi-restraints excluded: chain g residue 292 PHE Chi-restraints excluded: chain g residue 306 CYS Chi-restraints excluded: chain n residue 13 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 40 optimal weight: 10.0000 chunk 311 optimal weight: 0.9990 chunk 279 optimal weight: 7.9990 chunk 464 optimal weight: 0.6980 chunk 253 optimal weight: 0.9990 chunk 328 optimal weight: 0.9990 chunk 342 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 241 optimal weight: 0.9990 chunk 364 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 HIS B 223 GLN C 125 HIS E 201 GLN F 31 HIS H 51 GLN ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 HIS I 94 ASN J 27 GLN J 100 ASN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 HIS ** O 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 67 HIS ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 99 HIS ** W 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 21 GLN c 28 GLN g 46 ASN ** g 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 263 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118183 restraints weight = 109468.089| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.42 r_work: 0.3235 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 70254 Z= 0.169 Angle : 0.619 12.302 102091 Z= 0.319 Chirality : 0.037 0.278 12720 Planarity : 0.004 0.054 7439 Dihedral : 22.778 179.729 27955 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.99 % Allowed : 7.11 % Favored : 91.91 % Rotamer: Outliers : 6.52 % Allowed : 23.67 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.12), residues: 4250 helix: 0.09 (0.14), residues: 1377 sheet: -1.07 (0.18), residues: 781 loop : -2.01 (0.12), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP g 277 HIS 0.013 0.001 HIS B 38 PHE 0.015 0.001 PHE P 88 TYR 0.034 0.002 TYR Q 93 ARG 0.009 0.001 ARG R 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 1044 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7480 (p) REVERT: A 202 TYR cc_start: 0.7900 (t80) cc_final: 0.7471 (t80) REVERT: A 204 ASP cc_start: 0.7420 (m-30) cc_final: 0.6696 (t0) REVERT: B 33 TYR cc_start: 0.7373 (m-80) cc_final: 0.7057 (m-80) REVERT: B 159 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8175 (mm-40) REVERT: B 169 THR cc_start: 0.8092 (t) cc_final: 0.7798 (t) REVERT: B 178 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7750 (tm-30) REVERT: B 179 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8324 (mm110) REVERT: B 199 GLN cc_start: 0.8505 (mp10) cc_final: 0.8285 (mp10) REVERT: C 116 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8754 (tt) REVERT: C 246 GLU cc_start: 0.7460 (pm20) cc_final: 0.7197 (pm20) REVERT: D 21 GLU cc_start: 0.7815 (tt0) cc_final: 0.7244 (tt0) REVERT: D 33 GLU cc_start: 0.7119 (mp0) cc_final: 0.6768 (mp0) REVERT: D 39 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7641 (mp0) REVERT: D 41 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.5392 (ttm110) REVERT: D 65 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7169 (mtm110) REVERT: D 93 GLN cc_start: 0.8066 (pm20) cc_final: 0.7110 (mm110) REVERT: D 147 ARG cc_start: 0.6559 (ptp90) cc_final: 0.5998 (mtp180) REVERT: D 178 MET cc_start: 0.8674 (mtp) cc_final: 0.8379 (mtp) REVERT: E 51 ARG cc_start: 0.8367 (mmp80) cc_final: 0.8028 (mmp80) REVERT: E 118 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6708 (tm-30) REVERT: E 128 GLN cc_start: 0.7956 (tt0) cc_final: 0.7714 (mt0) REVERT: E 202 MET cc_start: 0.7561 (tpp) cc_final: 0.6921 (mmm) REVERT: E 232 GLU cc_start: 0.7519 (tp30) cc_final: 0.6977 (mm-30) REVERT: F 31 HIS cc_start: 0.8512 (m-70) cc_final: 0.8284 (m170) REVERT: F 37 MET cc_start: 0.8190 (tpt) cc_final: 0.7713 (tpp) REVERT: F 50 PHE cc_start: 0.8039 (m-80) cc_final: 0.7545 (m-10) REVERT: F 66 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8617 (mtp) REVERT: F 160 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7135 (tt0) REVERT: H 50 PHE cc_start: 0.8150 (m-80) cc_final: 0.7514 (m-80) REVERT: H 127 LYS cc_start: 0.8690 (mttt) cc_final: 0.8226 (mmtt) REVERT: I 6 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8071 (ppp) REVERT: I 17 ARG cc_start: 0.8468 (mmm160) cc_final: 0.8101 (mmt180) REVERT: I 46 VAL cc_start: 0.8886 (t) cc_final: 0.8657 (p) REVERT: I 75 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8112 (ttmt) REVERT: I 80 ASN cc_start: 0.8296 (p0) cc_final: 0.7978 (p0) REVERT: I 92 ARG cc_start: 0.8467 (ttp-170) cc_final: 0.8200 (ttp-110) REVERT: J 23 HIS cc_start: 0.7626 (OUTLIER) cc_final: 0.7321 (t70) REVERT: J 49 LYS cc_start: 0.7252 (tttm) cc_final: 0.6934 (ttmt) REVERT: J 76 ARG cc_start: 0.8096 (ttp-110) cc_final: 0.7875 (mtm180) REVERT: J 89 GLN cc_start: 0.7423 (tt0) cc_final: 0.6989 (mt0) REVERT: K 34 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.5086 (pt) REVERT: K 54 CYS cc_start: 0.7520 (p) cc_final: 0.7019 (m) REVERT: K 91 ARG cc_start: 0.5848 (mtt180) cc_final: 0.4612 (ttp80) REVERT: L 80 ARG cc_start: 0.7329 (mtm180) cc_final: 0.6842 (mmt90) REVERT: N 9 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8307 (mtmm) REVERT: N 11 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8372 (pt) REVERT: N 17 PRO cc_start: 0.8686 (Cg_exo) cc_final: 0.8482 (Cg_endo) REVERT: O 129 ARG cc_start: 0.7738 (mtp85) cc_final: 0.7429 (mtm110) REVERT: O 133 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7685 (mmmt) REVERT: P 85 LEU cc_start: 0.8307 (mp) cc_final: 0.8100 (mp) REVERT: P 102 PHE cc_start: 0.8418 (t80) cc_final: 0.8048 (t80) REVERT: Q 18 TYR cc_start: 0.9055 (t80) cc_final: 0.8222 (t80) REVERT: Q 119 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8301 (ptt180) REVERT: Q 134 ARG cc_start: 0.9030 (mmp80) cc_final: 0.8631 (mmp-170) REVERT: R 81 ARG cc_start: 0.7935 (mmm-85) cc_final: 0.7643 (mtp85) REVERT: S 21 ASN cc_start: 0.8390 (p0) cc_final: 0.7642 (t0) REVERT: S 25 ARG cc_start: 0.8193 (ptt90) cc_final: 0.7643 (ptp-170) REVERT: S 48 ARG cc_start: 0.8383 (tpt90) cc_final: 0.7961 (ttm-80) REVERT: S 52 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7436 (pp) REVERT: S 72 ILE cc_start: 0.8652 (mt) cc_final: 0.8352 (mt) REVERT: S 112 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7353 (mm-30) REVERT: T 12 GLN cc_start: 0.7603 (mt0) cc_final: 0.6726 (pt0) REVERT: T 103 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8786 (t) REVERT: V 21 ASP cc_start: 0.8142 (t0) cc_final: 0.7642 (t70) REVERT: W 65 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8392 (mp) REVERT: W 94 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8808 (mp) REVERT: W 101 TYR cc_start: 0.9238 (m-80) cc_final: 0.8686 (m-80) REVERT: X 20 LYS cc_start: 0.9099 (mttt) cc_final: 0.8709 (mmtm) REVERT: X 51 ILE cc_start: 0.8675 (mp) cc_final: 0.8281 (mp) REVERT: Y 15 LYS cc_start: 0.8606 (mttp) cc_final: 0.8365 (mttm) REVERT: Y 27 GLN cc_start: 0.7976 (pm20) cc_final: 0.7455 (pm20) REVERT: Y 75 TYR cc_start: 0.5069 (OUTLIER) cc_final: 0.3095 (p90) REVERT: Z 54 LYS cc_start: 0.9002 (mmtt) cc_final: 0.8540 (mmmt) REVERT: Z 74 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8118 (p) REVERT: Z 80 HIS cc_start: 0.8408 (OUTLIER) cc_final: 0.7163 (p-80) REVERT: a 14 ASN cc_start: 0.8946 (t0) cc_final: 0.8534 (t0) REVERT: a 63 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7652 (mm-30) REVERT: d 13 ASN cc_start: 0.8271 (m110) cc_final: 0.8020 (m110) REVERT: d 40 CYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8120 (p) REVERT: e 26 LYS cc_start: 0.6823 (ttpp) cc_final: 0.6508 (tttm) REVERT: g 94 HIS cc_start: 0.6145 (OUTLIER) cc_final: 0.5576 (t-90) REVERT: g 115 LYS cc_start: 0.8661 (ttpt) cc_final: 0.7977 (mmtp) REVERT: g 116 LYS cc_start: 0.7733 (ptmt) cc_final: 0.7371 (pttt) REVERT: g 124 ASP cc_start: 0.7512 (p0) cc_final: 0.7280 (p0) REVERT: g 136 ARG cc_start: 0.7012 (mmm-85) cc_final: 0.5867 (mpp-170) outliers start: 232 outliers final: 148 residues processed: 1176 average time/residue: 0.6996 time to fit residues: 1380.5068 Evaluate side-chains 1122 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 953 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain F residue 160 GLU Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain I residue 6 MET Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain J residue 23 HIS Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 64 CYS Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 78 HIS Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 99 HIS Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 112 GLU Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 19 ASP Chi-restraints excluded: chain T residue 28 HIS Chi-restraints excluded: chain T residue 103 SER Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain T residue 128 GLN Chi-restraints excluded: chain U residue 29 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 75 TYR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 80 HIS Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 25 ASN Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain c residue 28 GLN Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 40 CYS Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 32 HIS Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 145 GLN Chi-restraints excluded: chain g residue 196 ILE Chi-restraints excluded: chain g residue 306 CYS Chi-restraints excluded: chain n residue 13 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 87 optimal weight: 5.9990 chunk 563 optimal weight: 0.0570 chunk 191 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 254 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 461 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 HIS D 75 GLN H 66 ASN I 11 HIS J 27 GLN J 100 ASN ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 139 HIS O 46 ASN P 78 HIS S 87 ASN ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 99 HIS ** W 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 28 HIS Z 80 HIS a 7 ASN a 43 ASN c 28 GLN g 32 HIS ** g 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 HIS g 155 ASN g 263 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110538 restraints weight = 110211.095| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.34 r_work: 0.3153 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 70254 Z= 0.499 Angle : 0.839 13.209 102091 Z= 0.423 Chirality : 0.047 0.324 12720 Planarity : 0.006 0.056 7439 Dihedral : 22.905 179.986 27953 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 1.13 % Allowed : 8.56 % Favored : 90.31 % Rotamer: Outliers : 8.96 % Allowed : 22.61 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.12), residues: 4250 helix: -0.30 (0.13), residues: 1384 sheet: -1.14 (0.18), residues: 781 loop : -2.16 (0.12), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP g 60 HIS 0.010 0.002 HIS C 218 PHE 0.024 0.003 PHE A 200 TYR 0.043 0.003 TYR Q 93 ARG 0.011 0.001 ARG g 302 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 319 poor density : 987 time to evaluate : 3.734 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: A 62 MET cc_start: 0.8994 (mtp) cc_final: 0.8751 (mtp) REVERT: A 153 ASP cc_start: 0.8658 (p0) cc_final: 0.8362 (p0) REVERT: A 202 TYR cc_start: 0.7962 (t80) cc_final: 0.7310 (t80) REVERT: A 204 ASP cc_start: 0.7514 (m-30) cc_final: 0.6357 (t0) REVERT: B 33 TYR cc_start: 0.7672 (m-80) cc_final: 0.7352 (m-80) REVERT: B 47 LYS cc_start: 0.7329 (ttpt) cc_final: 0.7117 (tttm) REVERT: B 159 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8359 (mm-40) REVERT: B 169 THR cc_start: 0.8270 (t) cc_final: 0.8014 (t) REVERT: B 178 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7669 (tm-30) REVERT: B 179 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8126 (mm110) REVERT: B 199 GLN cc_start: 0.8663 (mp10) cc_final: 0.8403 (mp10) REVERT: D 21 GLU cc_start: 0.7859 (tt0) cc_final: 0.7281 (tt0) REVERT: D 39 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7667 (mp0) REVERT: D 41 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7553 (ttm110) REVERT: D 93 GLN cc_start: 0.8220 (pm20) cc_final: 0.7215 (mm110) REVERT: D 178 MET cc_start: 0.8450 (mtp) cc_final: 0.8188 (mtp) REVERT: E 51 ARG cc_start: 0.8391 (mmp80) cc_final: 0.8069 (mmp80) REVERT: E 99 PHE cc_start: 0.6967 (m-80) cc_final: 0.6264 (m-80) REVERT: E 118 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6769 (tm-30) REVERT: E 128 GLN cc_start: 0.7890 (tt0) cc_final: 0.7645 (mt0) REVERT: E 202 MET cc_start: 0.7639 (tpp) cc_final: 0.7376 (mmm) REVERT: E 232 GLU cc_start: 0.7638 (tp30) cc_final: 0.6887 (mm-30) REVERT: F 34 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8093 (mm-40) REVERT: F 66 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8723 (ttp) REVERT: H 50 PHE cc_start: 0.8314 (m-80) cc_final: 0.7587 (m-80) REVERT: H 127 LYS cc_start: 0.8824 (mttt) cc_final: 0.8378 (mmtt) REVERT: H 134 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8823 (mm) REVERT: I 17 ARG cc_start: 0.8572 (mmm160) cc_final: 0.8224 (mmt180) REVERT: I 46 VAL cc_start: 0.8931 (t) cc_final: 0.8636 (p) REVERT: I 80 ASN cc_start: 0.8403 (p0) cc_final: 0.8044 (p0) REVERT: I 92 ARG cc_start: 0.8604 (ttp-170) cc_final: 0.8332 (ttp-110) REVERT: J 23 HIS cc_start: 0.7770 (OUTLIER) cc_final: 0.7473 (t70) REVERT: J 76 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7941 (mtm180) REVERT: J 89 GLN cc_start: 0.7393 (tt0) cc_final: 0.6895 (mt0) REVERT: J 100 ASN cc_start: 0.8562 (m110) cc_final: 0.8314 (m110) REVERT: K 54 CYS cc_start: 0.7589 (p) cc_final: 0.7224 (m) REVERT: K 91 ARG cc_start: 0.6073 (mtt180) cc_final: 0.4610 (ttp80) REVERT: L 80 ARG cc_start: 0.7514 (mtm180) cc_final: 0.7166 (mmt90) REVERT: L 100 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.9026 (mtpt) REVERT: N 3 ARG cc_start: 0.8067 (tpt170) cc_final: 0.7829 (tpt170) REVERT: N 9 LYS cc_start: 0.8833 (mtmm) cc_final: 0.8051 (mtmm) REVERT: O 129 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7313 (mtm110) REVERT: O 133 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7928 (mmmt) REVERT: P 53 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7527 (tt) REVERT: Q 119 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8352 (ptt180) REVERT: R 118 GLU cc_start: 0.7287 (mp0) cc_final: 0.7050 (mp0) REVERT: S 21 ASN cc_start: 0.8576 (p0) cc_final: 0.7874 (t0) REVERT: S 25 ARG cc_start: 0.8378 (ptt90) cc_final: 0.7800 (ptp-170) REVERT: S 48 ARG cc_start: 0.8402 (tpt90) cc_final: 0.8037 (ttt90) REVERT: S 52 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7810 (pp) REVERT: S 72 ILE cc_start: 0.8815 (mt) cc_final: 0.8444 (mt) REVERT: S 86 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9082 (mp) REVERT: S 112 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7580 (mm-30) REVERT: T 12 GLN cc_start: 0.7856 (mt0) cc_final: 0.7096 (pt0) REVERT: T 103 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8770 (t) REVERT: V 21 ASP cc_start: 0.8512 (t0) cc_final: 0.8293 (t0) REVERT: V 35 GLN cc_start: 0.8433 (mt0) cc_final: 0.8192 (mt0) REVERT: V 51 THR cc_start: 0.8526 (p) cc_final: 0.8060 (p) REVERT: W 71 LYS cc_start: 0.8856 (tttt) cc_final: 0.8536 (tttp) REVERT: W 101 TYR cc_start: 0.9242 (m-80) cc_final: 0.8898 (m-80) REVERT: X 20 LYS cc_start: 0.9109 (mttt) cc_final: 0.8768 (mmtm) REVERT: X 43 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6910 (mt-10) REVERT: X 51 ILE cc_start: 0.8734 (mp) cc_final: 0.8309 (mp) REVERT: Y 27 GLN cc_start: 0.7982 (pm20) cc_final: 0.7324 (pm20) REVERT: Y 75 TYR cc_start: 0.5375 (OUTLIER) cc_final: 0.2946 (p90) REVERT: Z 64 LEU cc_start: 0.9100 (mt) cc_final: 0.8891 (mt) REVERT: Z 74 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8182 (p) REVERT: Z 80 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.7807 (p90) REVERT: a 14 ASN cc_start: 0.9240 (t0) cc_final: 0.8797 (t0) REVERT: c 30 ARG cc_start: 0.7503 (ttm-80) cc_final: 0.7189 (ttp-170) REVERT: d 40 CYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8211 (p) REVERT: e 26 LYS cc_start: 0.6891 (ttpp) cc_final: 0.6400 (tttm) REVERT: g 76 LEU cc_start: 0.7520 (mp) cc_final: 0.7267 (mp) REVERT: g 94 HIS cc_start: 0.6219 (OUTLIER) cc_final: 0.5873 (t-90) REVERT: g 115 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8101 (mmtp) REVERT: g 136 ARG cc_start: 0.7178 (mmm-85) cc_final: 0.5707 (mpp-170) REVERT: g 292 PHE cc_start: 0.5904 (OUTLIER) cc_final: 0.5248 (p90) REVERT: g 331 GLU cc_start: 0.6764 (tp30) cc_final: 0.6289 (tp30) outliers start: 319 outliers final: 248 residues processed: 1177 average time/residue: 0.7019 time to fit residues: 1379.5754 Evaluate side-chains 1222 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 266 poor density : 956 time to evaluate : 3.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 135 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 75 GLN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 233 HIS Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 34 GLN Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 27 PHE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 153 LEU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 14 MET Chi-restraints excluded: chain J residue 23 HIS Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 56 GLU Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 146 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 100 LYS Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 64 CYS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 83 MET Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 25 MET Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 78 HIS Chi-restraints excluded: chain P residue 93 ILE Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 98 THR Chi-restraints excluded: chain Q residue 102 ILE Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 19 ASP Chi-restraints excluded: chain T residue 28 HIS Chi-restraints excluded: chain T residue 34 ILE Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 103 SER Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 121 LYS Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain U residue 29 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 120 VAL Chi-restraints excluded: chain V residue 10 ASP Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 65 ASP Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain X residue 119 CYS Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 12 ILE Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 75 TYR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 80 HIS Chi-restraints excluded: chain Z residue 81 ASP Chi-restraints excluded: chain a residue 7 ASN Chi-restraints excluded: chain a residue 20 THR Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 25 ASN Chi-restraints excluded: chain a residue 26 CYS Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 12 SER Chi-restraints excluded: chain b residue 28 ASN Chi-restraints excluded: chain b residue 53 VAL Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain c residue 17 ILE Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 28 GLN Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 61 GLU Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain d residue 40 CYS Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 32 HIS Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 121 HIS Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 145 GLN Chi-restraints excluded: chain g residue 170 CYS Chi-restraints excluded: chain g residue 196 ILE Chi-restraints excluded: chain g residue 205 GLU Chi-restraints excluded: chain g residue 292 PHE Chi-restraints excluded: chain g residue 306 CYS Chi-restraints excluded: chain n residue 13 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 106 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 455 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 235 optimal weight: 0.7980 chunk 279 optimal weight: 6.9990 chunk 508 optimal weight: 0.9980 chunk 245 optimal weight: 7.9990 chunk 310 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN J 27 GLN ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 ASN S 97 ASN ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 99 HIS U 107 GLN a 7 ASN c 28 GLN e 41 ASN g 32 HIS ** g 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 HIS g 263 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.144539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116187 restraints weight = 109589.337| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.36 r_work: 0.3213 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 70254 Z= 0.213 Angle : 0.654 11.615 102091 Z= 0.335 Chirality : 0.039 0.283 12720 Planarity : 0.005 0.054 7439 Dihedral : 22.771 179.968 27948 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 1.04 % Allowed : 7.27 % Favored : 91.69 % Rotamer: Outliers : 6.85 % Allowed : 25.33 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.12), residues: 4250 helix: -0.00 (0.14), residues: 1395 sheet: -0.99 (0.18), residues: 775 loop : -2.10 (0.12), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 91 HIS 0.016 0.001 HIS g 121 PHE 0.022 0.002 PHE g 29 TYR 0.026 0.002 TYR g 271 ARG 0.008 0.001 ARG T 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 979 time to evaluate : 3.660 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: A 100 ARG cc_start: 0.8373 (ptm-80) cc_final: 0.8034 (ttp80) REVERT: A 153 ASP cc_start: 0.8469 (p0) cc_final: 0.8118 (p0) REVERT: A 202 TYR cc_start: 0.7873 (t80) cc_final: 0.7477 (t80) REVERT: B 24 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6748 (mm-30) REVERT: B 159 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8156 (mm-40) REVERT: B 169 THR cc_start: 0.8203 (t) cc_final: 0.7938 (t) REVERT: B 178 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7645 (tm-30) REVERT: B 179 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8121 (mm110) REVERT: B 187 GLU cc_start: 0.6401 (mm-30) cc_final: 0.6033 (mm-30) REVERT: B 199 GLN cc_start: 0.8679 (mp10) cc_final: 0.8425 (mp10) REVERT: D 39 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7745 (mp0) REVERT: D 65 ARG cc_start: 0.7133 (ttp80) cc_final: 0.6747 (mtm110) REVERT: D 93 GLN cc_start: 0.8110 (pm20) cc_final: 0.7117 (mm110) REVERT: D 178 MET cc_start: 0.8552 (mtp) cc_final: 0.8281 (mtp) REVERT: E 39 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7921 (mmm160) REVERT: E 51 ARG cc_start: 0.8297 (mmp80) cc_final: 0.8046 (mmp80) REVERT: E 99 PHE cc_start: 0.6900 (m-80) cc_final: 0.6239 (m-80) REVERT: E 118 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6781 (tm-30) REVERT: E 128 GLN cc_start: 0.7936 (tt0) cc_final: 0.7698 (mt0) REVERT: F 16 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7469 (t70) REVERT: F 37 MET cc_start: 0.8061 (tpt) cc_final: 0.7773 (tpp) REVERT: F 66 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8679 (mtp) REVERT: F 138 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8088 (mm-40) REVERT: H 50 PHE cc_start: 0.8293 (m-80) cc_final: 0.7607 (m-80) REVERT: H 127 LYS cc_start: 0.8855 (mttt) cc_final: 0.8374 (mmtt) REVERT: I 17 ARG cc_start: 0.8469 (mmm160) cc_final: 0.8099 (mmt180) REVERT: I 80 ASN cc_start: 0.8332 (p0) cc_final: 0.7951 (p0) REVERT: I 92 ARG cc_start: 0.8548 (ttp-170) cc_final: 0.8294 (ttp-110) REVERT: J 23 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7330 (t70) REVERT: J 76 ARG cc_start: 0.8117 (ttp-110) cc_final: 0.7914 (mtm180) REVERT: J 89 GLN cc_start: 0.7372 (tt0) cc_final: 0.6954 (mt0) REVERT: J 100 ASN cc_start: 0.8593 (m110) cc_final: 0.8359 (m110) REVERT: K 54 CYS cc_start: 0.7706 (p) cc_final: 0.7372 (m) REVERT: K 76 ARG cc_start: 0.7567 (mmt90) cc_final: 0.7213 (mtt-85) REVERT: K 91 ARG cc_start: 0.5906 (mtt180) cc_final: 0.4407 (ttp80) REVERT: L 53 ASP cc_start: 0.8025 (m-30) cc_final: 0.7821 (m-30) REVERT: L 80 ARG cc_start: 0.7480 (mtm180) cc_final: 0.7256 (mtt-85) REVERT: N 9 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8386 (mtmm) REVERT: N 11 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8436 (pt) REVERT: N 56 ASP cc_start: 0.6950 (m-30) cc_final: 0.6685 (m-30) REVERT: O 129 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7409 (mtm110) REVERT: O 133 LYS cc_start: 0.7944 (mmmt) cc_final: 0.7669 (mmmt) REVERT: P 102 PHE cc_start: 0.8445 (t80) cc_final: 0.8209 (t80) REVERT: Q 18 TYR cc_start: 0.9123 (t80) cc_final: 0.8872 (t80) REVERT: Q 119 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8194 (ptt180) REVERT: Q 134 ARG cc_start: 0.8992 (mmp80) cc_final: 0.8539 (mmp-170) REVERT: R 3 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8746 (tpp-160) REVERT: R 104 GLU cc_start: 0.7952 (tt0) cc_final: 0.7734 (tt0) REVERT: S 21 ASN cc_start: 0.8527 (p0) cc_final: 0.7869 (t0) REVERT: S 25 ARG cc_start: 0.8321 (ptt90) cc_final: 0.7754 (ptp-170) REVERT: S 47 VAL cc_start: 0.9104 (t) cc_final: 0.8866 (m) REVERT: S 48 ARG cc_start: 0.8389 (tpt90) cc_final: 0.8011 (ttm-80) REVERT: S 52 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7828 (pp) REVERT: S 66 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8682 (tm-30) REVERT: S 72 ILE cc_start: 0.8783 (mt) cc_final: 0.8460 (mt) REVERT: S 86 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.9001 (mp) REVERT: S 112 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7361 (mm-30) REVERT: T 12 GLN cc_start: 0.7754 (mt0) cc_final: 0.6952 (pt0) REVERT: T 103 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8819 (t) REVERT: T 134 GLN cc_start: 0.8339 (pt0) cc_final: 0.8062 (pt0) REVERT: V 21 ASP cc_start: 0.8412 (t0) cc_final: 0.8020 (t0) REVERT: W 71 LYS cc_start: 0.8750 (tttt) cc_final: 0.8395 (tttp) REVERT: W 101 TYR cc_start: 0.9222 (m-80) cc_final: 0.8924 (m-80) REVERT: X 20 LYS cc_start: 0.9074 (mttt) cc_final: 0.8729 (mmtm) REVERT: X 51 ILE cc_start: 0.8691 (mp) cc_final: 0.8243 (mp) REVERT: Y 15 LYS cc_start: 0.8649 (mttp) cc_final: 0.8403 (mttm) REVERT: Y 27 GLN cc_start: 0.8063 (pm20) cc_final: 0.7528 (pm20) REVERT: Y 75 TYR cc_start: 0.5399 (OUTLIER) cc_final: 0.2919 (p90) REVERT: Z 54 LYS cc_start: 0.8967 (mmtt) cc_final: 0.8483 (mmmt) REVERT: Z 74 VAL cc_start: 0.8464 (OUTLIER) cc_final: 0.8139 (p) REVERT: Z 80 HIS cc_start: 0.8616 (OUTLIER) cc_final: 0.7746 (p90) REVERT: a 14 ASN cc_start: 0.9049 (t0) cc_final: 0.8602 (t0) REVERT: b 62 THR cc_start: 0.7439 (OUTLIER) cc_final: 0.7003 (p) REVERT: c 30 ARG cc_start: 0.7524 (ttm-80) cc_final: 0.7232 (ttp-170) REVERT: d 40 CYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8152 (p) REVERT: e 26 LYS cc_start: 0.6742 (ttpp) cc_final: 0.6311 (tttm) REVERT: e 41 ASN cc_start: 0.7476 (m110) cc_final: 0.7265 (m-40) REVERT: g 94 HIS cc_start: 0.6187 (OUTLIER) cc_final: 0.5869 (t-90) REVERT: g 115 LYS cc_start: 0.8742 (ttpt) cc_final: 0.8012 (mmtp) REVERT: g 116 LYS cc_start: 0.7754 (ptmt) cc_final: 0.7322 (pttt) REVERT: g 136 ARG cc_start: 0.7089 (mmm-85) cc_final: 0.5899 (mpp-170) REVERT: g 292 PHE cc_start: 0.5616 (OUTLIER) cc_final: 0.5113 (p90) REVERT: g 331 GLU cc_start: 0.6592 (tp30) cc_final: 0.6178 (tp30) outliers start: 244 outliers final: 189 residues processed: 1130 average time/residue: 0.6804 time to fit residues: 1279.9714 Evaluate side-chains 1155 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 949 time to evaluate : 3.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 14 MET Chi-restraints excluded: chain J residue 23 HIS Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 78 MET Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 64 CYS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 78 HIS Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain R residue 3 ARG Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 28 HIS Chi-restraints excluded: chain T residue 34 ILE Chi-restraints excluded: chain T residue 103 SER Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain U residue 29 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 27 HIS Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 119 CYS Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 75 TYR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 80 HIS Chi-restraints excluded: chain a residue 7 ASN Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 25 ASN Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 28 ASN Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain c residue 17 ILE Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 28 GLN Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 61 GLU Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain d residue 37 LEU Chi-restraints excluded: chain d residue 40 CYS Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 32 HIS Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 121 HIS Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 145 GLN Chi-restraints excluded: chain g residue 196 ILE Chi-restraints excluded: chain g residue 292 PHE Chi-restraints excluded: chain g residue 306 CYS Chi-restraints excluded: chain n residue 13 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 389 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 278 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 353 optimal weight: 20.0000 chunk 145 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 472 optimal weight: 0.6980 chunk 427 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 ASN ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 99 HIS a 7 ASN c 28 GLN g 32 HIS ** g 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 284 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.142530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114095 restraints weight = 109698.056| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.35 r_work: 0.3189 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 70254 Z= 0.301 Angle : 0.697 11.541 102091 Z= 0.356 Chirality : 0.040 0.296 12720 Planarity : 0.005 0.053 7439 Dihedral : 22.766 179.371 27948 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 1.06 % Allowed : 8.42 % Favored : 90.52 % Rotamer: Outliers : 7.75 % Allowed : 24.63 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.12), residues: 4250 helix: -0.05 (0.14), residues: 1396 sheet: -1.00 (0.18), residues: 782 loop : -2.12 (0.12), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP g 60 HIS 0.009 0.001 HIS g 121 PHE 0.022 0.002 PHE K 16 TYR 0.028 0.002 TYR g 271 ARG 0.008 0.001 ARG T 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 951 time to evaluate : 3.709 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: A 23 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5531 (mm) REVERT: A 44 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7461 (p) REVERT: A 100 ARG cc_start: 0.8415 (ptm-80) cc_final: 0.8027 (ttp80) REVERT: A 153 ASP cc_start: 0.8529 (p0) cc_final: 0.8211 (p0) REVERT: A 202 TYR cc_start: 0.7930 (t80) cc_final: 0.7483 (t80) REVERT: B 159 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8104 (mm-40) REVERT: B 169 THR cc_start: 0.8192 (t) cc_final: 0.7926 (t) REVERT: B 178 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7818 (tm-30) REVERT: B 179 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8077 (mm110) REVERT: B 190 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6524 (mt-10) REVERT: B 199 GLN cc_start: 0.8690 (mp10) cc_final: 0.8441 (mp10) REVERT: D 21 GLU cc_start: 0.7818 (tt0) cc_final: 0.7169 (tt0) REVERT: D 65 ARG cc_start: 0.7147 (ttp80) cc_final: 0.6701 (mtm110) REVERT: D 93 GLN cc_start: 0.8163 (pm20) cc_final: 0.7100 (mm110) REVERT: D 178 MET cc_start: 0.8569 (mtp) cc_final: 0.8275 (mtp) REVERT: E 39 ARG cc_start: 0.8230 (mmm160) cc_final: 0.7902 (mmm160) REVERT: E 51 ARG cc_start: 0.8256 (mmp80) cc_final: 0.7339 (mmp-170) REVERT: E 84 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8487 (p) REVERT: E 118 GLU cc_start: 0.7171 (tm-30) cc_final: 0.6791 (tm-30) REVERT: E 128 GLN cc_start: 0.7916 (tt0) cc_final: 0.7695 (mt0) REVERT: E 202 MET cc_start: 0.6631 (mmm) cc_final: 0.6281 (mmp) REVERT: F 16 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7349 (t70) REVERT: F 37 MET cc_start: 0.8065 (tpt) cc_final: 0.7747 (tpp) REVERT: F 66 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8687 (mtp) REVERT: F 138 GLN cc_start: 0.8642 (mm-40) cc_final: 0.8116 (mm-40) REVERT: F 180 ARG cc_start: 0.8004 (ttp-110) cc_final: 0.7756 (ttm-80) REVERT: H 50 PHE cc_start: 0.8322 (m-80) cc_final: 0.7643 (m-80) REVERT: H 127 LYS cc_start: 0.8853 (mttt) cc_final: 0.8386 (mmtt) REVERT: I 17 ARG cc_start: 0.8521 (mmm160) cc_final: 0.8114 (mmt180) REVERT: I 80 ASN cc_start: 0.8237 (p0) cc_final: 0.7841 (p0) REVERT: I 92 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.8321 (ttp-110) REVERT: J 23 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.7445 (t70) REVERT: J 89 GLN cc_start: 0.7496 (tt0) cc_final: 0.7068 (mt0) REVERT: K 54 CYS cc_start: 0.7518 (p) cc_final: 0.7111 (m) REVERT: K 76 ARG cc_start: 0.7528 (mmt90) cc_final: 0.7182 (mtt-85) REVERT: K 91 ARG cc_start: 0.6059 (mtt180) cc_final: 0.4477 (ttp80) REVERT: L 80 ARG cc_start: 0.7473 (mtm180) cc_final: 0.7264 (mtt-85) REVERT: L 100 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8902 (mtpt) REVERT: N 9 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8515 (mtmm) REVERT: N 11 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8349 (pt) REVERT: O 129 ARG cc_start: 0.7796 (mtp85) cc_final: 0.7476 (mtm110) REVERT: P 102 PHE cc_start: 0.8453 (t80) cc_final: 0.8163 (t80) REVERT: Q 119 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8241 (ptt180) REVERT: Q 134 ARG cc_start: 0.8988 (mmp80) cc_final: 0.8505 (mmp-170) REVERT: R 3 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8822 (tpp-160) REVERT: R 104 GLU cc_start: 0.7948 (tt0) cc_final: 0.7747 (tt0) REVERT: S 21 ASN cc_start: 0.8499 (p0) cc_final: 0.7821 (t0) REVERT: S 25 ARG cc_start: 0.8401 (ptt90) cc_final: 0.7788 (ptp-170) REVERT: S 48 ARG cc_start: 0.8303 (tpt90) cc_final: 0.7869 (ttm-80) REVERT: S 52 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7854 (pp) REVERT: S 66 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8746 (tm-30) REVERT: S 72 ILE cc_start: 0.8818 (mt) cc_final: 0.8494 (mt) REVERT: S 86 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9040 (mp) REVERT: S 112 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7393 (mm-30) REVERT: T 12 GLN cc_start: 0.7840 (mt0) cc_final: 0.7078 (pt0) REVERT: T 103 SER cc_start: 0.9126 (OUTLIER) cc_final: 0.8822 (t) REVERT: U 86 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8469 (tp) REVERT: V 21 ASP cc_start: 0.8475 (t0) cc_final: 0.8154 (t0) REVERT: V 51 THR cc_start: 0.8448 (p) cc_final: 0.7950 (p) REVERT: W 71 LYS cc_start: 0.8838 (tttt) cc_final: 0.8483 (tttp) REVERT: X 20 LYS cc_start: 0.9104 (mttt) cc_final: 0.8765 (mmtm) REVERT: X 51 ILE cc_start: 0.8683 (mp) cc_final: 0.8211 (mp) REVERT: Y 15 LYS cc_start: 0.8656 (mttp) cc_final: 0.8361 (mttm) REVERT: Y 27 GLN cc_start: 0.8034 (pm20) cc_final: 0.7533 (pm20) REVERT: Z 54 LYS cc_start: 0.8957 (mmtt) cc_final: 0.8482 (mmmt) REVERT: Z 74 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8128 (p) REVERT: Z 80 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.7716 (p90) REVERT: a 14 ASN cc_start: 0.9166 (t0) cc_final: 0.8563 (t0) REVERT: b 62 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.7059 (p) REVERT: c 30 ARG cc_start: 0.7555 (ttm-80) cc_final: 0.7207 (ttp-170) REVERT: d 40 CYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8129 (p) REVERT: e 26 LYS cc_start: 0.6672 (ttpp) cc_final: 0.6215 (tttm) REVERT: g 94 HIS cc_start: 0.6248 (OUTLIER) cc_final: 0.5860 (t-90) REVERT: g 115 LYS cc_start: 0.8717 (ttpt) cc_final: 0.7950 (mmtp) REVERT: g 136 ARG cc_start: 0.7157 (mmm-85) cc_final: 0.5689 (mpp-170) REVERT: g 158 GLU cc_start: 0.6750 (mp0) cc_final: 0.6465 (mp0) REVERT: g 263 GLN cc_start: 0.7377 (tt0) cc_final: 0.7149 (tt0) REVERT: g 292 PHE cc_start: 0.6040 (OUTLIER) cc_final: 0.5498 (p90) outliers start: 276 outliers final: 222 residues processed: 1129 average time/residue: 0.6715 time to fit residues: 1258.4588 Evaluate side-chains 1175 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 931 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 107 TYR Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 14 MET Chi-restraints excluded: chain J residue 23 HIS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 100 LYS Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 64 CYS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 83 MET Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 78 HIS Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain Q residue 4 VAL Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain R residue 3 ARG Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 97 ASN Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 112 GLU Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 28 HIS Chi-restraints excluded: chain T residue 34 ILE Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 103 SER Chi-restraints excluded: chain T residue 120 VAL Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain T residue 128 GLN Chi-restraints excluded: chain U residue 29 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain V residue 46 THR Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 119 CYS Chi-restraints excluded: chain X residue 126 VAL Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 75 TYR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 80 HIS Chi-restraints excluded: chain a residue 7 ASN Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 25 ASN Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 12 SER Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 28 ASN Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain c residue 17 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 28 GLN Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 61 GLU Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain d residue 40 CYS Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 32 HIS Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 145 GLN Chi-restraints excluded: chain g residue 170 CYS Chi-restraints excluded: chain g residue 196 ILE Chi-restraints excluded: chain g residue 292 PHE Chi-restraints excluded: chain g residue 306 CYS Chi-restraints excluded: chain n residue 13 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 109 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 229 optimal weight: 3.9990 chunk 456 optimal weight: 4.9990 chunk 320 optimal weight: 1.9990 chunk 277 optimal weight: 0.9990 chunk 554 optimal weight: 9.9990 chunk 387 optimal weight: 0.6980 chunk 555 optimal weight: 9.9990 chunk 469 optimal weight: 1.9990 chunk 381 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100 ASN ** P 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 ASN ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 7 ASN c 28 GLN e 41 ASN g 32 HIS ** g 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.114998 restraints weight = 109756.630| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.36 r_work: 0.3197 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 70254 Z= 0.263 Angle : 0.675 11.590 102091 Z= 0.345 Chirality : 0.040 0.290 12720 Planarity : 0.005 0.057 7439 Dihedral : 22.742 178.812 27948 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 1.06 % Allowed : 7.86 % Favored : 91.08 % Rotamer: Outliers : 7.30 % Allowed : 25.19 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.41 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.12), residues: 4250 helix: -0.00 (0.14), residues: 1401 sheet: -1.02 (0.18), residues: 779 loop : -2.08 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 91 HIS 0.005 0.001 HIS Y 88 PHE 0.021 0.002 PHE g 29 TYR 0.031 0.002 TYR g 271 ARG 0.009 0.001 ARG g 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8500 Ramachandran restraints generated. 4250 Oldfield, 0 Emsley, 4250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1211 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 260 poor density : 951 time to evaluate : 3.697 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: A 23 LEU cc_start: 0.5575 (OUTLIER) cc_final: 0.5276 (mm) REVERT: A 44 THR cc_start: 0.7832 (OUTLIER) cc_final: 0.7469 (p) REVERT: A 100 ARG cc_start: 0.8426 (ptm-80) cc_final: 0.8095 (ttp80) REVERT: A 153 ASP cc_start: 0.8552 (p0) cc_final: 0.8257 (p0) REVERT: A 202 TYR cc_start: 0.7918 (t80) cc_final: 0.7464 (t80) REVERT: B 124 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7978 (mmmt) REVERT: B 159 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8242 (mm-40) REVERT: B 169 THR cc_start: 0.8209 (t) cc_final: 0.7947 (t) REVERT: B 178 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 179 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8077 (mm110) REVERT: B 199 GLN cc_start: 0.8636 (mp10) cc_final: 0.8387 (mp10) REVERT: D 39 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7812 (mp0) REVERT: D 65 ARG cc_start: 0.7114 (ttp80) cc_final: 0.6680 (mtm110) REVERT: D 93 GLN cc_start: 0.8178 (pm20) cc_final: 0.7124 (mm110) REVERT: E 39 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7891 (mmm160) REVERT: E 51 ARG cc_start: 0.8226 (mmp80) cc_final: 0.8018 (mmp80) REVERT: E 84 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8515 (p) REVERT: E 118 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6736 (tm-30) REVERT: E 128 GLN cc_start: 0.7928 (tt0) cc_final: 0.7696 (mt0) REVERT: F 37 MET cc_start: 0.8057 (tpt) cc_final: 0.7745 (tpp) REVERT: F 66 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8660 (mtp) REVERT: F 138 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8139 (mm-40) REVERT: F 180 ARG cc_start: 0.8032 (ttp-110) cc_final: 0.7578 (ttm-80) REVERT: H 50 PHE cc_start: 0.8322 (m-80) cc_final: 0.7633 (m-80) REVERT: H 127 LYS cc_start: 0.8807 (mttt) cc_final: 0.8374 (mmtt) REVERT: I 17 ARG cc_start: 0.8508 (mmm160) cc_final: 0.8099 (mmt180) REVERT: I 75 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8209 (ttmt) REVERT: I 80 ASN cc_start: 0.8071 (p0) cc_final: 0.7679 (p0) REVERT: I 92 ARG cc_start: 0.8578 (ttp-170) cc_final: 0.8315 (ttp-110) REVERT: J 23 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.7387 (t70) REVERT: J 89 GLN cc_start: 0.7281 (tt0) cc_final: 0.6863 (mt0) REVERT: K 15 LEU cc_start: 0.8834 (tp) cc_final: 0.8543 (tp) REVERT: K 54 CYS cc_start: 0.7530 (p) cc_final: 0.7110 (m) REVERT: K 91 ARG cc_start: 0.5987 (mtt180) cc_final: 0.4527 (ttp80) REVERT: L 80 ARG cc_start: 0.7472 (mtm180) cc_final: 0.7250 (mtt-85) REVERT: L 100 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8876 (mtpt) REVERT: N 9 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8396 (mtmm) REVERT: N 11 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8412 (pt) REVERT: N 129 TYR cc_start: 0.9228 (m-80) cc_final: 0.8886 (m-80) REVERT: O 129 ARG cc_start: 0.7789 (mtp85) cc_final: 0.7467 (mtm110) REVERT: O 133 LYS cc_start: 0.8074 (mmmt) cc_final: 0.7808 (mmmt) REVERT: P 102 PHE cc_start: 0.8492 (t80) cc_final: 0.8222 (t80) REVERT: P 126 LYS cc_start: 0.8468 (mmtm) cc_final: 0.7814 (mptt) REVERT: Q 119 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8194 (ptt180) REVERT: R 3 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8799 (tpp-160) REVERT: S 21 ASN cc_start: 0.8512 (p0) cc_final: 0.7835 (t0) REVERT: S 25 ARG cc_start: 0.8469 (ptt90) cc_final: 0.8026 (ptm160) REVERT: S 52 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7838 (pp) REVERT: S 66 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8543 (tm-30) REVERT: S 72 ILE cc_start: 0.8802 (mt) cc_final: 0.8471 (mt) REVERT: S 112 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7399 (mm-30) REVERT: T 12 GLN cc_start: 0.7830 (mt0) cc_final: 0.7069 (pt0) REVERT: T 103 SER cc_start: 0.9133 (OUTLIER) cc_final: 0.8837 (t) REVERT: U 86 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8461 (tp) REVERT: V 21 ASP cc_start: 0.8461 (t0) cc_final: 0.8144 (t0) REVERT: V 51 THR cc_start: 0.8441 (p) cc_final: 0.7946 (p) REVERT: W 71 LYS cc_start: 0.8811 (tttt) cc_final: 0.8449 (tttp) REVERT: X 20 LYS cc_start: 0.9089 (mttt) cc_final: 0.8732 (mmtm) REVERT: X 51 ILE cc_start: 0.8661 (mp) cc_final: 0.8172 (mp) REVERT: Y 15 LYS cc_start: 0.8659 (mttp) cc_final: 0.8356 (mttm) REVERT: Y 27 GLN cc_start: 0.8023 (pm20) cc_final: 0.7509 (pm20) REVERT: Z 74 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8164 (p) REVERT: Z 80 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.7782 (p90) REVERT: a 14 ASN cc_start: 0.9166 (t0) cc_final: 0.8589 (t0) REVERT: b 62 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7065 (p) REVERT: c 30 ARG cc_start: 0.7557 (ttm-80) cc_final: 0.7213 (ttp-170) REVERT: d 40 CYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8081 (p) REVERT: e 41 ASN cc_start: 0.7465 (m110) cc_final: 0.7215 (m-40) REVERT: g 94 HIS cc_start: 0.6211 (OUTLIER) cc_final: 0.5879 (t-90) REVERT: g 115 LYS cc_start: 0.8712 (ttpt) cc_final: 0.7951 (mmtp) REVERT: g 136 ARG cc_start: 0.7203 (mmm-85) cc_final: 0.5762 (mpp-170) REVERT: g 292 PHE cc_start: 0.6032 (OUTLIER) cc_final: 0.5567 (p90) REVERT: g 302 ARG cc_start: 0.6748 (tpt90) cc_final: 0.6159 (mmm160) outliers start: 260 outliers final: 218 residues processed: 1109 average time/residue: 0.6596 time to fit residues: 1215.5571 Evaluate side-chains 1168 residues out of total 3698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 930 time to evaluate : 3.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 59 ASN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 150 SER Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 193 GLN Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 44 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 81 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 166 THR Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 47 HIS Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 60 ARG Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain F residue 96 ASN Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 137 ASP Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 47 ILE Chi-restraints excluded: chain H residue 68 GLN Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 26 ASN Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 72 CYS Chi-restraints excluded: chain I residue 105 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 14 MET Chi-restraints excluded: chain J residue 23 HIS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 152 LYS Chi-restraints excluded: chain K residue 7 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 39 ILE Chi-restraints excluded: chain K residue 43 GLN Chi-restraints excluded: chain L residue 4 VAL Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 56 CYS Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 72 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 100 LYS Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 120 LEU Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain N residue 11 ILE Chi-restraints excluded: chain N residue 13 SER Chi-restraints excluded: chain N residue 20 ARG Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 67 THR Chi-restraints excluded: chain N residue 80 LEU Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain O residue 61 LEU Chi-restraints excluded: chain O residue 64 CYS Chi-restraints excluded: chain O residue 70 VAL Chi-restraints excluded: chain O residue 75 ASP Chi-restraints excluded: chain O residue 83 MET Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 127 LEU Chi-restraints excluded: chain O residue 141 THR Chi-restraints excluded: chain O residue 143 LEU Chi-restraints excluded: chain O residue 159 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 55 GLU Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain P residue 78 HIS Chi-restraints excluded: chain P residue 95 ILE Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 124 VAL Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 41 LEU Chi-restraints excluded: chain Q residue 50 GLN Chi-restraints excluded: chain Q residue 119 ARG Chi-restraints excluded: chain R residue 3 ARG Chi-restraints excluded: chain R residue 6 THR Chi-restraints excluded: chain R residue 40 ASP Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 84 TRP Chi-restraints excluded: chain R residue 98 VAL Chi-restraints excluded: chain S residue 11 PHE Chi-restraints excluded: chain S residue 22 VAL Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 61 LEU Chi-restraints excluded: chain S residue 65 GLU Chi-restraints excluded: chain S residue 97 ASN Chi-restraints excluded: chain S residue 101 VAL Chi-restraints excluded: chain S residue 109 ILE Chi-restraints excluded: chain S residue 134 ARG Chi-restraints excluded: chain T residue 2 ILE Chi-restraints excluded: chain T residue 28 HIS Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 103 SER Chi-restraints excluded: chain T residue 116 LYS Chi-restraints excluded: chain T residue 122 VAL Chi-restraints excluded: chain T residue 128 GLN Chi-restraints excluded: chain T residue 130 THR Chi-restraints excluded: chain U residue 29 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 16 LYS Chi-restraints excluded: chain V residue 27 HIS Chi-restraints excluded: chain V residue 41 ASP Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 53 ILE Chi-restraints excluded: chain W residue 73 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 94 LEU Chi-restraints excluded: chain W residue 110 ILE Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 82 VAL Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 119 CYS Chi-restraints excluded: chain X residue 131 LEU Chi-restraints excluded: chain Y residue 23 VAL Chi-restraints excluded: chain Y residue 29 LEU Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 75 TYR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Z residue 44 ILE Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 80 HIS Chi-restraints excluded: chain a residue 7 ASN Chi-restraints excluded: chain a residue 23 CYS Chi-restraints excluded: chain a residue 25 ASN Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain a residue 33 ASP Chi-restraints excluded: chain a residue 53 VAL Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 91 VAL Chi-restraints excluded: chain b residue 2 THR Chi-restraints excluded: chain b residue 3 THR Chi-restraints excluded: chain b residue 8 ILE Chi-restraints excluded: chain b residue 23 LYS Chi-restraints excluded: chain b residue 28 ASN Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain c residue 17 ILE Chi-restraints excluded: chain c residue 26 VAL Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 61 GLU Chi-restraints excluded: chain d residue 5 PHE Chi-restraints excluded: chain d residue 18 VAL Chi-restraints excluded: chain d residue 40 CYS Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 47 VAL Chi-restraints excluded: chain g residue 23 PHE Chi-restraints excluded: chain g residue 28 THR Chi-restraints excluded: chain g residue 32 HIS Chi-restraints excluded: chain g residue 48 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 77 ILE Chi-restraints excluded: chain g residue 86 VAL Chi-restraints excluded: chain g residue 94 HIS Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 129 THR Chi-restraints excluded: chain g residue 145 GLN Chi-restraints excluded: chain g residue 170 CYS Chi-restraints excluded: chain g residue 292 PHE Chi-restraints excluded: chain g residue 306 CYS Chi-restraints excluded: chain n residue 13 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 572 random chunks: chunk 571 optimal weight: 0.9980 chunk 287 optimal weight: 8.9990 chunk 402 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 407 optimal weight: 1.9990 chunk 522 optimal weight: 2.9990 chunk 422 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 454 optimal weight: 6.9990 chunk 331 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 HIS H 125 ASN T 30 GLN ** W 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 7 ASN c 28 GLN g 32 HIS ** g 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 284 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.143805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115435 restraints weight = 109792.285| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.34 r_work: 0.3205 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5230 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: