Starting phenix.real_space_refine on Thu Jan 23 23:40:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j0o_35907/01_2025/8j0o_35907.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j0o_35907/01_2025/8j0o_35907.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j0o_35907/01_2025/8j0o_35907.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j0o_35907/01_2025/8j0o_35907.map" model { file = "/net/cci-nas-00/data/ceres_data/8j0o_35907/01_2025/8j0o_35907.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j0o_35907/01_2025/8j0o_35907.cif" } resolution = 3.32 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= 0.035 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 13430 2.51 5 N 3565 2.21 5 O 3891 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 20986 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 949, 7544 Classifications: {'peptide': 949} Link IDs: {'PTRANS': 43, 'TRANS': 905} Chain breaks: 2 Chain: "B" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2438 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 4, 'TRANS': 291} Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2086 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 12, 'TRANS': 245} Chain: "D" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1222 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} Chain breaks: 1 Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 817 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "F" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "G" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1114 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 12, 'TRANS': 126} Chain: "H" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1559 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 8, 'TRANS': 186} Chain breaks: 1 Chain: "J" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1146 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 7, 'TRANS': 141} Chain breaks: 1 Chain: "K" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2162 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.57, per 1000 atoms: 0.60 Number of scatterers: 20986 At special positions: 0 Unit cell: (142.79, 212.55, 123.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3891 8.00 N 3565 7.00 C 13430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Links applied BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG L 1 " - " ASN A 818 " " NAG M 1 " - " ASN A 913 " " NAG N 1 " - " ASN J 182 " Time building additional restraints: 4.82 Conformation dependent library (CDL) restraints added in 2.8 seconds 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4914 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 27 sheets defined 35.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 479 through 510 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 655 through 666 Processing helix chain 'A' and resid 887 through 894 removed outlier: 3.753A pdb=" N ASN A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 993 removed outlier: 3.897A pdb=" N ILE A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 9 Processing helix chain 'B' and resid 11 through 26 Processing helix chain 'B' and resid 29 through 44 removed outlier: 3.809A pdb=" N GLU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 66 removed outlier: 3.831A pdb=" N ILE B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 83 removed outlier: 3.792A pdb=" N ALA B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 102 through 117 removed outlier: 3.855A pdb=" N ALA B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 135 removed outlier: 3.575A pdb=" N ARG B 124 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 removed outlier: 3.739A pdb=" N ALA B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 168 removed outlier: 3.586A pdb=" N TRP B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.582A pdb=" N PHE B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.789A pdb=" N CYS B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 203 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 223 removed outlier: 3.732A pdb=" N LYS B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 242 removed outlier: 3.817A pdb=" N LEU B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 271 removed outlier: 3.550A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 297 removed outlier: 3.740A pdb=" N SER B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 4.029A pdb=" N LEU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 39 Processing helix chain 'C' and resid 45 through 64 Processing helix chain 'C' and resid 69 through 82 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 101 through 113 removed outlier: 4.493A pdb=" N MET C 110 " --> pdb=" O MET C 106 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 132 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 148 through 153 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.842A pdb=" N PHE C 177 " --> pdb=" O PHE C 173 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 179 " --> pdb=" O ASN C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 188 removed outlier: 4.206A pdb=" N SER C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.540A pdb=" N LEU C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET C 242 " --> pdb=" O GLU C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 237 through 242' Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.626A pdb=" N LYS C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 256 " --> pdb=" O PHE C 252 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLN C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 73 removed outlier: 3.755A pdb=" N VAL D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA D 73 " --> pdb=" O CYS D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 91 removed outlier: 3.658A pdb=" N ILE D 80 " --> pdb=" O PRO D 76 " (cutoff:3.500A) Proline residue: D 81 - end of helix Processing helix chain 'D' and resid 95 through 114 removed outlier: 3.611A pdb=" N ALA D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP D 107 " --> pdb=" O CYS D 103 " (cutoff:3.500A) Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 115 through 124 removed outlier: 3.809A pdb=" N THR D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 155 removed outlier: 3.506A pdb=" N PHE D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 134 " --> pdb=" O PHE D 130 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 135 " --> pdb=" O LEU D 131 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN D 140 " --> pdb=" O TYR D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 166 removed outlier: 3.628A pdb=" N TRP D 164 " --> pdb=" O HIS D 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 34 removed outlier: 3.550A pdb=" N LEU E 33 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 64 removed outlier: 3.641A pdb=" N GLY E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL E 61 " --> pdb=" O CYS E 57 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 78 removed outlier: 4.208A pdb=" N ASN E 78 " --> pdb=" O GLU E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 86 removed outlier: 3.545A pdb=" N LEU E 84 " --> pdb=" O THR E 80 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASN E 86 " --> pdb=" O ASP E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 102 removed outlier: 3.904A pdb=" N VAL E 99 " --> pdb=" O HIS E 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 45 removed outlier: 3.507A pdb=" N VAL F 19 " --> pdb=" O SER F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 71 removed outlier: 3.545A pdb=" N ALA F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 78 removed outlier: 3.823A pdb=" N TYR F 77 " --> pdb=" O ARG F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 86 Processing helix chain 'F' and resid 90 through 108 removed outlier: 3.738A pdb=" N LEU F 98 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE F 99 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N MET F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 63 removed outlier: 4.019A pdb=" N SER G 63 " --> pdb=" O GLN G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 178 removed outlier: 3.916A pdb=" N LEU G 171 " --> pdb=" O MET G 167 " (cutoff:3.500A) Proline residue: G 172 - end of helix Processing helix chain 'H' and resid 7 through 21 removed outlier: 3.583A pdb=" N TYR H 21 " --> pdb=" O HIS H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 83 removed outlier: 3.840A pdb=" N LEU H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 119 removed outlier: 4.097A pdb=" N GLY H 118 " --> pdb=" O ARG H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 177 Processing helix chain 'H' and resid 185 through 192 Processing helix chain 'H' and resid 199 through 210 Processing helix chain 'J' and resid 91 through 104 removed outlier: 3.624A pdb=" N LEU J 104 " --> pdb=" O ASP J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 140 Processing helix chain 'J' and resid 197 through 207 removed outlier: 3.740A pdb=" N PHE J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 20 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.545A pdb=" N CYS A 933 " --> pdb=" O VAL A 947 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 43 removed outlier: 4.485A pdb=" N VAL A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 92 removed outlier: 4.172A pdb=" N ALA A 89 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 99 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 108 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET A 107 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU A 120 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER A 109 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 135 removed outlier: 3.883A pdb=" N TRP A 163 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N HIS A 155 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU A 161 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.809A pdb=" N LYS A 201 " --> pdb=" O GLN A 211 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN A 211 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ASN A 203 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE A 209 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 230 removed outlier: 3.754A pdb=" N GLY A 228 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 236 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 247 " --> pdb=" O ARG A 257 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 275 through 277 removed outlier: 3.923A pdb=" N ARG A 275 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 292 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE A 291 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 303 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU A 302 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 321 through 326 removed outlier: 3.518A pdb=" N LEU A 321 " --> pdb=" O MET A 336 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 377 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR A 389 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 12.691A pdb=" N LEU A 379 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 12.184A pdb=" N LEU A 387 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 405 through 412 removed outlier: 3.506A pdb=" N TYR A 406 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 418 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 412 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 430 through 433 removed outlier: 6.797A pdb=" N LEU A 430 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER A 444 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N PHE A 432 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 458 removed outlier: 3.915A pdb=" N CYS A 454 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 544 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP A 557 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLU A 549 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ILE A 555 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 569 through 576 removed outlier: 6.666A pdb=" N GLN A 586 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 625 through 633 removed outlier: 8.530A pdb=" N LEU A 627 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE A 643 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU A 629 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LEU A 641 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL A 639 " --> pdb=" O VAL A 631 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 694 through 699 removed outlier: 6.120A pdb=" N LEU A 694 " --> pdb=" O ARG A 685 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG A 685 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TRP A 696 " --> pdb=" O GLY A 683 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY D 180 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 705 through 711 removed outlier: 7.159A pdb=" N VAL A 744 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL A 710 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 742 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE A 757 " --> pdb=" O VAL A 774 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N VAL A 774 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 759 " --> pdb=" O SER A 772 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N SER A 772 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU A 761 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR J 191 " --> pdb=" O SER A 772 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 723 through 725 Processing sheet with id=AB9, first strand: chain 'A' and resid 778 through 786 removed outlier: 5.002A pdb=" N TRP A 796 " --> pdb=" O PRO A 781 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG A 802 " --> pdb=" O ASN A 797 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 821 through 822 removed outlier: 3.536A pdb=" N PHE A 822 " --> pdb=" O GLU D 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 847 through 849 Processing sheet with id=AC3, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.814A pdb=" N THR C 138 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 84 through 89 removed outlier: 3.725A pdb=" N ASP G 88 " --> pdb=" O PHE G 45 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N PHE G 45 " --> pdb=" O ASP G 88 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU G 138 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET G 140 " --> pdb=" O ARG G 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 75 through 77 removed outlier: 3.616A pdb=" N ARG G 66 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY G 92 " --> pdb=" O ILE G 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 6 removed outlier: 6.704A pdb=" N VAL H 31 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N CYS H 57 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU H 29 " --> pdb=" O CYS H 57 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ASN H 27 " --> pdb=" O PRO H 59 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE H 61 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ALA H 25 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL H 26 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ALA H 32 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILE H 89 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA H 123 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR H 92 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE H 125 " --> pdb=" O TYR H 92 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL H 127 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS H 153 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 83 through 87 removed outlier: 6.277A pdb=" N LYS J 70 " --> pdb=" O HIS J 58 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS J 58 " --> pdb=" O LYS J 70 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY J 72 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU J 56 " --> pdb=" O GLY J 72 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU J 55 " --> pdb=" O PRO J 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 156 through 162 removed outlier: 6.761A pdb=" N HIS J 149 " --> pdb=" O VAL J 157 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL J 159 " --> pdb=" O THR J 147 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR J 147 " --> pdb=" O VAL J 159 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL J 161 " --> pdb=" O GLN J 145 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLN J 145 " --> pdb=" O VAL J 161 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL J 150 " --> pdb=" O GLN J 188 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 26 through 34 removed outlier: 3.642A pdb=" N ILE K 243 " --> pdb=" O LEU K 263 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS K 256 " --> pdb=" O GLU K 280 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU K 280 " --> pdb=" O LYS K 256 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU K 26 " --> pdb=" O LEU K 275 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU K 277 " --> pdb=" O LEU K 26 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2847 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.38 Time building geometry restraints manager: 5.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 21179 1.54 - 1.86: 275 1.86 - 2.19: 0 2.19 - 2.51: 0 2.51 - 2.83: 2 Bond restraints: 21456 Sorted by residual: bond pdb=" N PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 1.473 2.828 -1.355 1.40e-02 5.10e+03 9.37e+03 bond pdb=" N PRO A 630 " pdb=" CD PRO A 630 " ideal model delta sigma weight residual 1.473 2.759 -1.286 1.40e-02 5.10e+03 8.44e+03 bond pdb=" N PRO A 260 " pdb=" CD PRO A 260 " ideal model delta sigma weight residual 1.473 1.803 -0.330 1.40e-02 5.10e+03 5.56e+02 bond pdb=" N PRO E 88 " pdb=" CD PRO E 88 " ideal model delta sigma weight residual 1.473 1.698 -0.225 1.40e-02 5.10e+03 2.58e+02 bond pdb=" N PRO G 90 " pdb=" CD PRO G 90 " ideal model delta sigma weight residual 1.473 1.683 -0.210 1.40e-02 5.10e+03 2.24e+02 ... (remaining 21451 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.84: 29051 9.84 - 19.68: 12 19.68 - 29.51: 1 29.51 - 39.35: 0 39.35 - 49.19: 4 Bond angle restraints: 29068 Sorted by residual: angle pdb=" N PRO C 83 " pdb=" CD PRO C 83 " pdb=" CG PRO C 83 " ideal model delta sigma weight residual 103.20 54.01 49.19 1.50e+00 4.44e-01 1.08e+03 angle pdb=" CA PRO C 83 " pdb=" N PRO C 83 " pdb=" CD PRO C 83 " ideal model delta sigma weight residual 112.00 68.27 43.73 1.40e+00 5.10e-01 9.76e+02 angle pdb=" CA PRO A 630 " pdb=" N PRO A 630 " pdb=" CD PRO A 630 " ideal model delta sigma weight residual 112.00 68.51 43.49 1.40e+00 5.10e-01 9.65e+02 angle pdb=" N PRO A 630 " pdb=" CD PRO A 630 " pdb=" CG PRO A 630 " ideal model delta sigma weight residual 103.20 62.67 40.53 1.50e+00 4.44e-01 7.30e+02 angle pdb=" CA PRO A 260 " pdb=" N PRO A 260 " pdb=" CD PRO A 260 " ideal model delta sigma weight residual 112.00 91.02 20.98 1.40e+00 5.10e-01 2.25e+02 ... (remaining 29063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 11378 21.52 - 43.04: 1274 43.04 - 64.55: 217 64.55 - 86.07: 49 86.07 - 107.59: 19 Dihedral angle restraints: 12937 sinusoidal: 5312 harmonic: 7625 Sorted by residual: dihedral pdb=" CA LEU A 929 " pdb=" C LEU A 929 " pdb=" N GLU A 930 " pdb=" CA GLU A 930 " ideal model delta harmonic sigma weight residual 180.00 147.31 32.69 0 5.00e+00 4.00e-02 4.28e+01 dihedral pdb=" CA PHE A 581 " pdb=" C PHE A 581 " pdb=" N PRO A 582 " pdb=" CA PRO A 582 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLY B 67 " pdb=" C GLY B 67 " pdb=" N ARG B 68 " pdb=" CA ARG B 68 " ideal model delta harmonic sigma weight residual 180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 12934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3030 0.088 - 0.177: 241 0.177 - 0.265: 3 0.265 - 0.353: 4 0.353 - 0.442: 1 Chirality restraints: 3279 Sorted by residual: chirality pdb=" CG LEU H 16 " pdb=" CB LEU H 16 " pdb=" CD1 LEU H 16 " pdb=" CD2 LEU H 16 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3276 not shown) Planarity restraints: 3682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 82 " -0.229 5.00e-02 4.00e+02 2.42e-01 9.38e+01 pdb=" N PRO C 83 " 0.406 5.00e-02 4.00e+02 pdb=" CA PRO C 83 " -0.118 5.00e-02 4.00e+02 pdb=" CD PRO C 83 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 629 " -0.217 5.00e-02 4.00e+02 2.27e-01 8.21e+01 pdb=" N PRO A 630 " 0.380 5.00e-02 4.00e+02 pdb=" CA PRO A 630 " -0.096 5.00e-02 4.00e+02 pdb=" CD PRO A 630 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 259 " 0.116 5.00e-02 4.00e+02 1.46e-01 3.43e+01 pdb=" N PRO A 260 " -0.251 5.00e-02 4.00e+02 pdb=" CA PRO A 260 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 260 " 0.067 5.00e-02 4.00e+02 ... (remaining 3679 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 96 2.51 - 3.11: 14136 3.11 - 3.71: 30174 3.71 - 4.30: 39668 4.30 - 4.90: 67826 Nonbonded interactions: 151900 Sorted by model distance: nonbonded pdb=" O GLU H 201 " pdb=" OE2 GLU H 201 " model vdw 1.915 3.040 nonbonded pdb=" NH1 ARG B 224 " pdb=" SD MET C 251 " model vdw 1.990 3.480 nonbonded pdb=" O GLU D 175 " pdb=" OE1 GLU D 175 " model vdw 2.055 3.040 nonbonded pdb=" O MET A 505 " pdb=" CE MET A 505 " model vdw 2.062 3.460 nonbonded pdb=" NH2 ARG B 224 " pdb=" CE MET C 251 " model vdw 2.108 3.540 ... (remaining 151895 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 Found NCS groups: ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 2.270 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: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 45.240 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.080 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2216 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 : 0.014 1.355 21456 Z= 0.569 Angle : 0.970 49.189 29068 Z= 0.567 Chirality : 0.045 0.442 3279 Planarity : 0.008 0.242 3679 Dihedral : 18.117 107.591 8023 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.36 % Favored : 91.37 % Rotamer: Outliers : 0.40 % Allowed : 28.40 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.16), residues: 2597 helix: 1.26 (0.18), residues: 859 sheet: 0.32 (0.20), residues: 665 loop : -3.37 (0.15), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP H 164 HIS 0.014 0.001 HIS D 160 PHE 0.042 0.001 PHE A 581 TYR 0.025 0.001 TYR E 91 ARG 0.011 0.001 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 533 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 310 LEU cc_start: 0.6008 (mp) cc_final: 0.5467 (pt) REVERT: C 222 TRP cc_start: 0.6412 (t60) cc_final: 0.6146 (t60) REVERT: F 90 ILE cc_start: 0.6958 (mt) cc_final: 0.6747 (mp) REVERT: G 47 ILE cc_start: 0.6516 (mt) cc_final: 0.5986 (mt) REVERT: G 162 MET cc_start: 0.4922 (ptp) cc_final: 0.4597 (ttp) REVERT: H 7 THR cc_start: 0.5261 (p) cc_final: 0.5012 (p) outliers start: 9 outliers final: 0 residues processed: 540 average time/residue: 0.3927 time to fit residues: 306.8374 Evaluate side-chains 299 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 201 optimal weight: 0.0670 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 overall best weight: 1.2522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 222 HIS ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 GLN A 575 GLN A 625 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 783 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN B 238 HIS C 39 GLN C 53 GLN C 64 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 HIS ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN G 124 ASN G 163 ASN ** H 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN H 195 ASN H 199 ASN ** J 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.098405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.080665 restraints weight = 82141.399| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 4.92 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3705 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 21456 Z= 0.286 Angle : 0.822 13.773 29068 Z= 0.401 Chirality : 0.046 0.282 3279 Planarity : 0.006 0.076 3679 Dihedral : 6.574 58.022 3028 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 8.24 % Favored : 91.49 % Rotamer: Outliers : 5.10 % Allowed : 27.30 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.16), residues: 2597 helix: 1.22 (0.18), residues: 884 sheet: 0.39 (0.20), residues: 678 loop : -3.27 (0.16), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 127 HIS 0.015 0.002 HIS A 294 PHE 0.022 0.002 PHE G 160 TYR 0.034 0.002 TYR E 58 ARG 0.008 0.001 ARG F 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 321 time to evaluate : 2.349 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: A 375 ILE cc_start: 0.6012 (mt) cc_final: 0.5685 (mt) REVERT: A 442 LEU cc_start: 0.0434 (OUTLIER) cc_final: -0.0039 (tp) REVERT: A 707 ILE cc_start: 0.4870 (OUTLIER) cc_final: 0.4668 (mm) REVERT: A 847 MET cc_start: 0.0581 (OUTLIER) cc_final: 0.0357 (ptt) REVERT: B 32 GLN cc_start: 0.7357 (tp40) cc_final: 0.7145 (tt0) REVERT: B 183 MET cc_start: -0.0658 (ttt) cc_final: -0.1413 (mmm) REVERT: B 234 MET cc_start: 0.5225 (ptt) cc_final: 0.4812 (ptp) REVERT: C 70 LYS cc_start: 0.8133 (tptm) cc_final: 0.7657 (tppt) REVERT: C 74 LEU cc_start: 0.8481 (mt) cc_final: 0.8067 (tt) REVERT: C 203 MET cc_start: 0.0674 (OUTLIER) cc_final: -0.0234 (mmt) REVERT: C 210 MET cc_start: 0.2555 (mmm) cc_final: 0.2238 (mmm) REVERT: C 226 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6483 (tm-30) REVERT: D 49 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8205 (p0) REVERT: E 85 ARG cc_start: 0.3761 (ttt-90) cc_final: 0.3515 (ttt-90) REVERT: F 90 ILE cc_start: 0.7056 (mt) cc_final: 0.6825 (mp) REVERT: G 47 ILE cc_start: 0.6513 (mt) cc_final: 0.6308 (mt) REVERT: G 117 LYS cc_start: 0.6359 (tptt) cc_final: 0.5809 (tptt) REVERT: G 124 ASN cc_start: 0.7110 (OUTLIER) cc_final: 0.5991 (t0) REVERT: G 162 MET cc_start: 0.6882 (ptp) cc_final: 0.5851 (ttp) REVERT: H 14 MET cc_start: 0.4849 (tmm) cc_final: 0.4319 (tmm) REVERT: H 94 GLN cc_start: 0.5423 (OUTLIER) cc_final: 0.4755 (tm-30) REVERT: H 151 TRP cc_start: 0.7190 (OUTLIER) cc_final: 0.6626 (t-100) REVERT: H 166 GLU cc_start: 0.8495 (mp0) cc_final: 0.8256 (mp0) REVERT: J 69 ARG cc_start: 0.4310 (tmt170) cc_final: 0.4091 (tmt170) REVERT: J 74 LEU cc_start: -0.0140 (OUTLIER) cc_final: -0.0716 (tt) REVERT: K 154 GLN cc_start: 0.8692 (tt0) cc_final: 0.8457 (tm-30) REVERT: K 189 GLU cc_start: 0.7797 (mp0) cc_final: 0.7371 (mp0) REVERT: K 251 LEU cc_start: 0.2324 (OUTLIER) cc_final: 0.2092 (tp) outliers start: 116 outliers final: 36 residues processed: 412 average time/residue: 0.3570 time to fit residues: 222.0258 Evaluate side-chains 307 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 261 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 454 CYS Chi-restraints excluded: chain A residue 611 TRP Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 238 HIS Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 203 MET Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 151 TRP Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 245 LEU Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 28 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 51 optimal weight: 0.0050 overall best weight: 1.0596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS A 533 GLN ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 HIS C 230 HIS G 124 ASN H 94 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 HIS K 124 ASN K 154 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.098997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.081845 restraints weight = 83287.503| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 5.03 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3965 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21456 Z= 0.225 Angle : 0.749 12.843 29068 Z= 0.362 Chirality : 0.045 0.494 3279 Planarity : 0.005 0.062 3679 Dihedral : 5.341 55.997 3028 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.97 % Favored : 91.72 % Rotamer: Outliers : 4.66 % Allowed : 28.00 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.16), residues: 2597 helix: 1.40 (0.18), residues: 881 sheet: 0.47 (0.20), residues: 686 loop : -3.25 (0.15), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 74 HIS 0.017 0.001 HIS B 238 PHE 0.023 0.002 PHE H 119 TYR 0.018 0.002 TYR H 144 ARG 0.014 0.001 ARG E 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 296 time to evaluate : 2.253 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: A 96 ASP cc_start: 0.7512 (m-30) cc_final: 0.6953 (t70) REVERT: A 177 MET cc_start: 0.6364 (mtt) cc_final: 0.6072 (mtt) REVERT: A 294 HIS cc_start: 0.6227 (t-170) cc_final: 0.5379 (t-90) REVERT: A 442 LEU cc_start: 0.0733 (OUTLIER) cc_final: 0.0440 (mp) REVERT: A 470 GLU cc_start: 0.8661 (mt-10) cc_final: 0.6909 (mt-10) REVERT: A 533 GLN cc_start: 0.1913 (OUTLIER) cc_final: 0.1695 (mp-120) REVERT: A 689 ASP cc_start: 0.4152 (t0) cc_final: 0.3541 (t0) REVERT: B 32 GLN cc_start: 0.7370 (tp40) cc_final: 0.7138 (tt0) REVERT: B 42 ASN cc_start: 0.4769 (m-40) cc_final: 0.4510 (m110) REVERT: B 120 ASN cc_start: 0.2832 (OUTLIER) cc_final: 0.2595 (t0) REVERT: B 230 PHE cc_start: 0.5686 (m-80) cc_final: 0.5427 (m-80) REVERT: C 70 LYS cc_start: 0.8083 (tptm) cc_final: 0.7575 (tppt) REVERT: C 74 LEU cc_start: 0.8624 (mt) cc_final: 0.8165 (tt) REVERT: C 81 ASN cc_start: 0.5743 (t0) cc_final: 0.5350 (t0) REVERT: C 151 MET cc_start: 0.4278 (mmt) cc_final: 0.3598 (tpp) REVERT: C 165 TRP cc_start: 0.5556 (OUTLIER) cc_final: 0.5120 (m100) REVERT: C 210 MET cc_start: 0.2981 (mmm) cc_final: 0.2619 (mmm) REVERT: F 90 ILE cc_start: 0.7002 (mt) cc_final: 0.6775 (mp) REVERT: G 45 PHE cc_start: 0.7753 (OUTLIER) cc_final: 0.7476 (t80) REVERT: G 118 MET cc_start: -0.1300 (pmm) cc_final: -0.1541 (pmm) REVERT: G 124 ASN cc_start: 0.7365 (OUTLIER) cc_final: 0.6199 (t0) REVERT: G 162 MET cc_start: 0.7048 (ptp) cc_final: 0.5887 (ttp) REVERT: H 94 GLN cc_start: 0.5427 (OUTLIER) cc_final: 0.4959 (tm130) REVERT: H 132 PHE cc_start: 0.4300 (t80) cc_final: 0.4024 (t80) REVERT: H 166 GLU cc_start: 0.8449 (mp0) cc_final: 0.8030 (mp0) REVERT: J 69 ARG cc_start: 0.4763 (tmt170) cc_final: 0.4514 (tmt170) REVERT: J 74 LEU cc_start: 0.0688 (OUTLIER) cc_final: 0.0230 (tt) REVERT: K 9 ASP cc_start: 0.8249 (t70) cc_final: 0.7775 (p0) REVERT: K 166 GLN cc_start: 0.8049 (tp-100) cc_final: 0.7643 (tp-100) REVERT: K 251 LEU cc_start: 0.2384 (OUTLIER) cc_final: 0.2048 (tp) outliers start: 106 outliers final: 45 residues processed: 376 average time/residue: 0.3400 time to fit residues: 196.6153 Evaluate side-chains 307 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 253 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 533 GLN Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain C residue 165 TRP Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 125 TYR Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 221 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 123 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 186 optimal weight: 4.9990 chunk 137 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 256 optimal weight: 3.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 GLN A 625 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 HIS A 786 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 GLN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 159 HIS B 253 ASN ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN G 163 ASN ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.098982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.082144 restraints weight = 84651.421| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 5.43 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4141 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21456 Z= 0.210 Angle : 0.740 11.978 29068 Z= 0.354 Chirality : 0.043 0.215 3279 Planarity : 0.005 0.062 3679 Dihedral : 5.036 57.608 3028 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.43 % Favored : 91.26 % Rotamer: Outliers : 4.57 % Allowed : 28.48 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.16), residues: 2597 helix: 1.36 (0.18), residues: 883 sheet: 0.51 (0.19), residues: 687 loop : -3.23 (0.16), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 165 HIS 0.016 0.001 HIS B 238 PHE 0.037 0.002 PHE D 85 TYR 0.021 0.002 TYR A 636 ARG 0.010 0.001 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 292 time to evaluate : 2.482 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: A 96 ASP cc_start: 0.7548 (m-30) cc_final: 0.6968 (t70) REVERT: A 107 MET cc_start: 0.5597 (ppp) cc_final: 0.5319 (tmm) REVERT: A 177 MET cc_start: 0.6677 (mtt) cc_final: 0.6316 (mtt) REVERT: A 442 LEU cc_start: 0.1353 (OUTLIER) cc_final: 0.1009 (mp) REVERT: A 632 MET cc_start: 0.3579 (tpp) cc_final: 0.3232 (tpp) REVERT: A 726 MET cc_start: 0.5376 (ppp) cc_final: 0.5098 (ppp) REVERT: A 889 GLN cc_start: 0.6885 (tm-30) cc_final: 0.6651 (tm-30) REVERT: B 32 GLN cc_start: 0.7239 (tp40) cc_final: 0.6988 (tt0) REVERT: B 120 ASN cc_start: 0.2900 (OUTLIER) cc_final: 0.2002 (t0) REVERT: C 6 LEU cc_start: 0.7816 (mm) cc_final: 0.7584 (mm) REVERT: C 70 LYS cc_start: 0.8169 (tptm) cc_final: 0.7646 (tppt) REVERT: C 74 LEU cc_start: 0.8649 (mt) cc_final: 0.8190 (tt) REVERT: C 130 MET cc_start: 0.5965 (tmm) cc_final: 0.5720 (tmm) REVERT: C 135 PHE cc_start: 0.4109 (OUTLIER) cc_final: 0.2283 (t80) REVERT: C 151 MET cc_start: 0.4127 (mmt) cc_final: 0.3422 (tpp) REVERT: C 182 ILE cc_start: 0.3584 (mm) cc_final: 0.3236 (mm) REVERT: C 210 MET cc_start: 0.3285 (mmm) cc_final: 0.2862 (mmm) REVERT: C 226 GLU cc_start: 0.7198 (mm-30) cc_final: 0.5197 (tp30) REVERT: C 251 MET cc_start: 0.4949 (tmm) cc_final: 0.4647 (tmm) REVERT: D 49 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8450 (p0) REVERT: D 105 MET cc_start: 0.7407 (mmt) cc_final: 0.7063 (mmt) REVERT: F 90 ILE cc_start: 0.7162 (mt) cc_final: 0.6932 (mp) REVERT: G 45 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7397 (t80) REVERT: G 118 MET cc_start: -0.1495 (pmm) cc_final: -0.1743 (pmm) REVERT: G 124 ASN cc_start: 0.7532 (OUTLIER) cc_final: 0.6192 (t0) REVERT: G 162 MET cc_start: 0.6997 (ptp) cc_final: 0.6360 (ttm) REVERT: H 70 MET cc_start: 0.3536 (ptt) cc_final: 0.3258 (ptt) REVERT: H 94 GLN cc_start: 0.5349 (OUTLIER) cc_final: 0.5014 (tm130) REVERT: H 132 PHE cc_start: 0.4566 (t80) cc_final: 0.4311 (t80) REVERT: H 163 ASP cc_start: 0.6762 (p0) cc_final: 0.6295 (p0) REVERT: H 166 GLU cc_start: 0.8388 (mp0) cc_final: 0.7845 (mp0) REVERT: J 74 LEU cc_start: 0.0996 (OUTLIER) cc_final: 0.0389 (tt) REVERT: K 9 ASP cc_start: 0.8105 (t70) cc_final: 0.7683 (p0) REVERT: K 166 GLN cc_start: 0.8143 (tp-100) cc_final: 0.7632 (tp-100) REVERT: K 251 LEU cc_start: 0.2346 (OUTLIER) cc_final: 0.1957 (tp) outliers start: 104 outliers final: 61 residues processed: 370 average time/residue: 0.3257 time to fit residues: 188.9432 Evaluate side-chains 331 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 261 time to evaluate : 2.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 839 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 165 TRP Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 124 ASN Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 50 HIS Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 9 optimal weight: 3.9990 chunk 208 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 253 optimal weight: 20.0000 chunk 167 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 166 optimal weight: 0.0970 chunk 142 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 786 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN B 167 ASN ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 ASN K 154 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.097994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.081587 restraints weight = 86295.874| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 5.01 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4570 moved from start: 0.7441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 21456 Z= 0.269 Angle : 0.794 13.422 29068 Z= 0.390 Chirality : 0.045 0.239 3279 Planarity : 0.006 0.115 3679 Dihedral : 4.958 59.797 3028 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.28 % Favored : 91.41 % Rotamer: Outliers : 5.36 % Allowed : 27.56 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.16), residues: 2597 helix: 1.06 (0.17), residues: 886 sheet: 0.42 (0.20), residues: 670 loop : -3.05 (0.16), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 163 HIS 0.011 0.001 HIS B 238 PHE 0.043 0.002 PHE D 85 TYR 0.028 0.002 TYR B 147 ARG 0.009 0.001 ARG H 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 318 time to evaluate : 2.310 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: A 177 MET cc_start: 0.6716 (mtt) cc_final: 0.6261 (mtt) REVERT: A 442 LEU cc_start: 0.2453 (OUTLIER) cc_final: 0.2160 (mp) REVERT: A 632 MET cc_start: 0.4250 (tpp) cc_final: 0.3695 (tpp) REVERT: A 847 MET cc_start: 0.3625 (tmm) cc_final: 0.3081 (tmm) REVERT: A 848 GLU cc_start: 0.5984 (pm20) cc_final: 0.5615 (pm20) REVERT: A 889 GLN cc_start: 0.7258 (tm-30) cc_final: 0.6974 (tm-30) REVERT: B 33 ILE cc_start: 0.5861 (mt) cc_final: 0.5656 (mt) REVERT: B 120 ASN cc_start: 0.4357 (OUTLIER) cc_final: 0.3979 (t0) REVERT: C 67 TYR cc_start: 0.5692 (m-10) cc_final: 0.5274 (m-10) REVERT: C 74 LEU cc_start: 0.8677 (mt) cc_final: 0.8179 (tt) REVERT: C 135 PHE cc_start: 0.4882 (OUTLIER) cc_final: 0.3075 (t80) REVERT: C 147 ARG cc_start: 0.2043 (mtt180) cc_final: 0.0148 (tmm-80) REVERT: C 151 MET cc_start: 0.4596 (mmt) cc_final: 0.3861 (tpp) REVERT: C 182 ILE cc_start: 0.3980 (mm) cc_final: 0.3686 (mm) REVERT: G 45 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7718 (t80) REVERT: G 77 PHE cc_start: 0.6505 (t80) cc_final: 0.6262 (t80) REVERT: G 106 ASP cc_start: 0.5990 (p0) cc_final: 0.5789 (p0) REVERT: G 117 LYS cc_start: 0.6858 (tptt) cc_final: 0.6542 (tptt) REVERT: G 118 MET cc_start: -0.0971 (pmm) cc_final: -0.1424 (pmm) REVERT: G 140 MET cc_start: 0.4217 (mmt) cc_final: 0.4014 (mmm) REVERT: G 162 MET cc_start: 0.7442 (ptp) cc_final: 0.5981 (ttp) REVERT: H 94 GLN cc_start: 0.5787 (OUTLIER) cc_final: 0.5263 (tm-30) REVERT: H 132 PHE cc_start: 0.5143 (t80) cc_final: 0.4771 (t80) REVERT: H 163 ASP cc_start: 0.6996 (p0) cc_final: 0.6567 (p0) REVERT: H 166 GLU cc_start: 0.8499 (mp0) cc_final: 0.7949 (mp0) REVERT: J 74 LEU cc_start: 0.1907 (OUTLIER) cc_final: 0.1230 (tt) REVERT: J 179 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6354 (tm-30) REVERT: K 9 ASP cc_start: 0.8229 (t70) cc_final: 0.7724 (p0) REVERT: K 251 LEU cc_start: 0.2090 (OUTLIER) cc_final: 0.1836 (tp) outliers start: 122 outliers final: 62 residues processed: 410 average time/residue: 0.3205 time to fit residues: 203.6140 Evaluate side-chains 338 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 269 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain A residue 955 VAL Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain C residue 222 TRP Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 196 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 163 optimal weight: 0.5980 chunk 155 optimal weight: 0.6980 chunk 145 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 197 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 137 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 625 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.098619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.082301 restraints weight = 86892.288| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 5.04 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4608 moved from start: 0.7999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21456 Z= 0.204 Angle : 0.765 11.468 29068 Z= 0.366 Chirality : 0.044 0.213 3279 Planarity : 0.005 0.075 3679 Dihedral : 4.717 58.621 3028 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.32 % Favored : 91.34 % Rotamer: Outliers : 3.52 % Allowed : 29.93 % Favored : 66.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2597 helix: 1.19 (0.18), residues: 886 sheet: 0.59 (0.20), residues: 673 loop : -2.98 (0.16), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 992 HIS 0.009 0.001 HIS B 238 PHE 0.025 0.002 PHE E 101 TYR 0.022 0.002 TYR B 8 ARG 0.007 0.001 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 295 time to evaluate : 2.370 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: A 177 MET cc_start: 0.6746 (mtt) cc_final: 0.6218 (mtt) REVERT: A 442 LEU cc_start: 0.2418 (OUTLIER) cc_final: 0.1968 (mp) REVERT: A 847 MET cc_start: 0.3574 (tmm) cc_final: 0.2579 (tmm) REVERT: A 848 GLU cc_start: 0.6080 (pm20) cc_final: 0.4921 (pp20) REVERT: A 871 LEU cc_start: 0.3905 (OUTLIER) cc_final: 0.3655 (pp) REVERT: A 889 GLN cc_start: 0.7250 (tm-30) cc_final: 0.6986 (tm-30) REVERT: B 183 MET cc_start: -0.0357 (mmt) cc_final: -0.1175 (mmt) REVERT: C 67 TYR cc_start: 0.5670 (m-10) cc_final: 0.5365 (m-10) REVERT: C 70 LYS cc_start: 0.7807 (tptp) cc_final: 0.7149 (tppt) REVERT: C 135 PHE cc_start: 0.4732 (OUTLIER) cc_final: 0.2447 (t80) REVERT: C 147 ARG cc_start: 0.2003 (mtt180) cc_final: 0.0037 (mtp85) REVERT: C 151 MET cc_start: 0.4560 (mmt) cc_final: 0.3385 (tpp) REVERT: D 49 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8345 (p0) REVERT: D 137 LEU cc_start: 0.8122 (tp) cc_final: 0.7840 (mt) REVERT: G 45 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.7908 (t80) REVERT: G 117 LYS cc_start: 0.6834 (tptt) cc_final: 0.6328 (tptt) REVERT: G 118 MET cc_start: -0.0686 (pmm) cc_final: -0.1189 (pmm) REVERT: G 130 GLU cc_start: 0.8575 (mp0) cc_final: 0.8358 (mp0) REVERT: G 140 MET cc_start: 0.4159 (mmt) cc_final: 0.3923 (mmm) REVERT: G 162 MET cc_start: 0.7351 (ptp) cc_final: 0.5996 (ttp) REVERT: H 94 GLN cc_start: 0.5932 (OUTLIER) cc_final: 0.5566 (tm-30) REVERT: H 163 ASP cc_start: 0.6913 (p0) cc_final: 0.6469 (p0) REVERT: H 166 GLU cc_start: 0.8500 (mp0) cc_final: 0.7906 (mp0) REVERT: J 74 LEU cc_start: 0.1943 (OUTLIER) cc_final: 0.1713 (tp) REVERT: K 9 ASP cc_start: 0.8545 (t70) cc_final: 0.7953 (p0) REVERT: K 154 GLN cc_start: 0.8893 (pt0) cc_final: 0.8165 (mm-40) REVERT: K 166 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7810 (tp-100) REVERT: K 251 LEU cc_start: 0.1832 (OUTLIER) cc_final: 0.1505 (tp) outliers start: 80 outliers final: 51 residues processed: 359 average time/residue: 0.3264 time to fit residues: 183.7426 Evaluate side-chains 328 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 269 time to evaluate : 2.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 196 SER Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 182 THR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 61 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.098251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.082139 restraints weight = 87406.641| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 5.06 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4871 moved from start: 0.8811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21456 Z= 0.222 Angle : 0.760 11.978 29068 Z= 0.367 Chirality : 0.044 0.205 3279 Planarity : 0.005 0.100 3679 Dihedral : 4.733 58.467 3028 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.97 % Favored : 91.72 % Rotamer: Outliers : 4.09 % Allowed : 29.49 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.16), residues: 2597 helix: 1.25 (0.18), residues: 881 sheet: 0.55 (0.20), residues: 670 loop : -2.93 (0.16), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP H 197 HIS 0.028 0.001 HIS A 174 PHE 0.028 0.002 PHE G 77 TYR 0.020 0.002 TYR K 62 ARG 0.017 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 311 time to evaluate : 2.396 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: A 117 LEU cc_start: 0.6788 (tp) cc_final: 0.6566 (tp) REVERT: A 177 MET cc_start: 0.6824 (mtt) cc_final: 0.6348 (mtt) REVERT: A 310 LEU cc_start: 0.6542 (mm) cc_final: 0.6069 (pp) REVERT: A 442 LEU cc_start: 0.2574 (OUTLIER) cc_final: 0.2158 (mp) REVERT: A 861 LEU cc_start: 0.7285 (tt) cc_final: 0.7004 (tp) REVERT: A 889 GLN cc_start: 0.7445 (tm-30) cc_final: 0.7190 (tm-30) REVERT: B 95 MET cc_start: 0.2210 (mpp) cc_final: 0.1824 (mmp) REVERT: B 120 ASN cc_start: 0.4464 (OUTLIER) cc_final: 0.4168 (t0) REVERT: B 183 MET cc_start: 0.0076 (mmt) cc_final: -0.0675 (mmt) REVERT: C 29 MET cc_start: 0.6517 (ppp) cc_final: 0.6173 (ppp) REVERT: C 67 TYR cc_start: 0.5878 (m-10) cc_final: 0.5343 (m-10) REVERT: C 70 LYS cc_start: 0.7937 (tptp) cc_final: 0.7201 (tppt) REVERT: C 135 PHE cc_start: 0.5615 (OUTLIER) cc_final: 0.3170 (t80) REVERT: C 147 ARG cc_start: 0.2242 (mtt180) cc_final: 0.0502 (ttp-170) REVERT: C 151 MET cc_start: 0.4618 (mmt) cc_final: 0.3539 (tpp) REVERT: C 210 MET cc_start: 0.3309 (mmm) cc_final: 0.2836 (mmm) REVERT: D 49 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8377 (p0) REVERT: D 142 MET cc_start: 0.5132 (tpt) cc_final: 0.4831 (tmm) REVERT: E 9 LEU cc_start: 0.7558 (tp) cc_final: 0.7349 (tp) REVERT: F 89 LEU cc_start: 0.7401 (mt) cc_final: 0.6995 (pp) REVERT: G 45 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8036 (t80) REVERT: G 117 LYS cc_start: 0.6941 (tptt) cc_final: 0.6737 (tptt) REVERT: G 118 MET cc_start: -0.0770 (pmm) cc_final: -0.1512 (pmm) REVERT: G 130 GLU cc_start: 0.8542 (mp0) cc_final: 0.8209 (mp0) REVERT: G 162 MET cc_start: 0.7441 (ptp) cc_final: 0.5897 (ttp) REVERT: H 94 GLN cc_start: 0.6039 (OUTLIER) cc_final: 0.5592 (tm-30) REVERT: H 132 PHE cc_start: 0.5622 (t80) cc_final: 0.5265 (t80) REVERT: H 163 ASP cc_start: 0.6880 (p0) cc_final: 0.6450 (p0) REVERT: H 166 GLU cc_start: 0.8548 (mp0) cc_final: 0.7978 (mp0) REVERT: J 74 LEU cc_start: 0.2265 (OUTLIER) cc_final: 0.1989 (tp) REVERT: J 151 ASP cc_start: 0.4901 (m-30) cc_final: 0.4052 (t0) REVERT: J 185 VAL cc_start: 0.8183 (t) cc_final: 0.7907 (p) REVERT: K 166 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8009 (tp-100) REVERT: K 189 GLU cc_start: 0.8766 (mp0) cc_final: 0.8234 (tp30) REVERT: K 251 LEU cc_start: 0.1841 (OUTLIER) cc_final: 0.1519 (tp) outliers start: 93 outliers final: 64 residues processed: 386 average time/residue: 0.3224 time to fit residues: 194.3195 Evaluate side-chains 357 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 285 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 222 HIS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 410 PHE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 853 GLU Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 951 LYS Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 127 LYS Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 164 HIS Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 243 ILE Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 16 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 ASN ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN B 169 HIS B 242 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** F 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 HIS H 94 GLN ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.097600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.081681 restraints weight = 91204.356| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 5.16 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5434 moved from start: 1.0486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 21456 Z= 0.312 Angle : 0.870 11.939 29068 Z= 0.427 Chirality : 0.047 0.476 3279 Planarity : 0.006 0.072 3679 Dihedral : 5.151 59.226 3028 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.78 % Favored : 90.87 % Rotamer: Outliers : 4.57 % Allowed : 30.02 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.99 (0.16), residues: 2597 helix: 1.01 (0.18), residues: 884 sheet: 0.40 (0.20), residues: 661 loop : -2.97 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 15 HIS 0.026 0.002 HIS A 222 PHE 0.034 0.003 PHE E 101 TYR 0.020 0.002 TYR K 62 ARG 0.027 0.001 ARG H 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 341 time to evaluate : 2.234 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: A 80 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7082 (mmtm) REVERT: A 90 MET cc_start: 0.8331 (tmm) cc_final: 0.8104 (tmm) REVERT: A 100 VAL cc_start: 0.7716 (t) cc_final: 0.6261 (t) REVERT: A 177 MET cc_start: 0.7154 (mtt) cc_final: 0.6619 (mtt) REVERT: A 310 LEU cc_start: 0.6939 (mm) cc_final: 0.6288 (pp) REVERT: A 632 MET cc_start: 0.3316 (tpp) cc_final: 0.2980 (tpp) REVERT: A 848 GLU cc_start: 0.7615 (pp20) cc_final: 0.7328 (pp20) REVERT: A 889 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 938 TYR cc_start: 0.7984 (p90) cc_final: 0.7612 (p90) REVERT: A 957 LYS cc_start: 0.6154 (mtmt) cc_final: 0.5831 (ptpt) REVERT: B 120 ASN cc_start: 0.5078 (OUTLIER) cc_final: 0.4578 (t0) REVERT: B 183 MET cc_start: 0.1296 (mmt) cc_final: 0.0581 (mmt) REVERT: B 226 MET cc_start: 0.4747 (OUTLIER) cc_final: 0.4313 (tpp) REVERT: C 67 TYR cc_start: 0.5959 (m-10) cc_final: 0.5575 (m-10) REVERT: C 70 LYS cc_start: 0.8066 (tptp) cc_final: 0.7775 (tptp) REVERT: C 110 MET cc_start: 0.0197 (ttp) cc_final: -0.0095 (ttp) REVERT: C 147 ARG cc_start: 0.2479 (mtt180) cc_final: 0.1490 (ttp-170) REVERT: C 151 MET cc_start: 0.5520 (mmt) cc_final: 0.4687 (tpp) REVERT: C 210 MET cc_start: 0.3909 (mmm) cc_final: 0.3404 (mmm) REVERT: G 45 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8507 (t80) REVERT: G 95 VAL cc_start: 0.8011 (t) cc_final: 0.7796 (p) REVERT: G 117 LYS cc_start: 0.7212 (tptt) cc_final: 0.6916 (tptt) REVERT: G 118 MET cc_start: 0.0545 (pmm) cc_final: -0.0035 (pmm) REVERT: G 140 MET cc_start: 0.5827 (mmm) cc_final: 0.5604 (tpt) REVERT: H 94 GLN cc_start: 0.6418 (OUTLIER) cc_final: 0.6163 (tm-30) REVERT: H 151 TRP cc_start: 0.6985 (OUTLIER) cc_final: 0.6774 (t-100) REVERT: H 163 ASP cc_start: 0.6910 (p0) cc_final: 0.6579 (p0) REVERT: H 166 GLU cc_start: 0.8638 (mp0) cc_final: 0.8042 (mp0) REVERT: H 207 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8598 (pp) REVERT: J 151 ASP cc_start: 0.5531 (m-30) cc_final: 0.4914 (t0) REVERT: J 185 VAL cc_start: 0.8309 (t) cc_final: 0.8058 (p) REVERT: K 9 ASP cc_start: 0.8750 (t0) cc_final: 0.8119 (p0) REVERT: K 154 GLN cc_start: 0.9112 (pt0) cc_final: 0.8277 (mm-40) REVERT: K 166 GLN cc_start: 0.8801 (mm-40) cc_final: 0.8149 (tp-100) REVERT: K 251 LEU cc_start: 0.2460 (OUTLIER) cc_final: 0.2202 (tp) outliers start: 104 outliers final: 68 residues processed: 415 average time/residue: 0.3177 time to fit residues: 206.8039 Evaluate side-chains 382 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 306 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 75 TRP Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 443 TRP Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 860 HIS Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 911 ASN Chi-restraints excluded: chain A residue 919 MET Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 33 TYR Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 96 ARG Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain H residue 94 GLN Chi-restraints excluded: chain H residue 151 TRP Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 245 LEU Chi-restraints excluded: chain K residue 251 LEU Chi-restraints excluded: chain K residue 281 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 57 optimal weight: 3.9990 chunk 224 optimal weight: 0.0770 chunk 199 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 189 optimal weight: 0.7980 chunk 119 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 249 optimal weight: 0.7980 chunk 252 optimal weight: 30.0000 chunk 169 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 786 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 ASN ** H 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.097631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.081655 restraints weight = 90775.561| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 5.22 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5585 moved from start: 1.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 21456 Z= 0.257 Angle : 0.855 16.082 29068 Z= 0.407 Chirality : 0.046 0.231 3279 Planarity : 0.005 0.057 3679 Dihedral : 4.954 59.643 3028 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.24 % Favored : 91.45 % Rotamer: Outliers : 3.21 % Allowed : 31.87 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.95 (0.16), residues: 2597 helix: 1.01 (0.18), residues: 881 sheet: 0.38 (0.20), residues: 667 loop : -2.88 (0.16), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 110 HIS 0.016 0.002 HIS A 174 PHE 0.041 0.002 PHE C 148 TYR 0.028 0.002 TYR H 93 ARG 0.013 0.001 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 348 time to evaluate : 2.386 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: A 90 MET cc_start: 0.8318 (tmm) cc_final: 0.7988 (tmm) REVERT: A 177 MET cc_start: 0.7053 (mtt) cc_final: 0.6497 (mtt) REVERT: A 221 GLN cc_start: 0.7198 (pm20) cc_final: 0.6929 (pp30) REVERT: A 310 LEU cc_start: 0.6950 (mm) cc_final: 0.6299 (pp) REVERT: A 632 MET cc_start: 0.3054 (tpp) cc_final: 0.2725 (tpp) REVERT: A 847 MET cc_start: 0.8603 (mmm) cc_final: 0.8336 (mmm) REVERT: A 930 GLU cc_start: 0.5524 (tp30) cc_final: 0.5295 (tp30) REVERT: A 938 TYR cc_start: 0.8308 (p90) cc_final: 0.8029 (p90) REVERT: B 226 MET cc_start: 0.4440 (OUTLIER) cc_final: 0.4091 (tpp) REVERT: B 234 MET cc_start: 0.6452 (ptt) cc_final: 0.6063 (ppp) REVERT: C 67 TYR cc_start: 0.5885 (m-10) cc_final: 0.5369 (m-10) REVERT: C 70 LYS cc_start: 0.8062 (tptp) cc_final: 0.7389 (tppt) REVERT: C 147 ARG cc_start: 0.2653 (mtt180) cc_final: 0.1646 (ttp-170) REVERT: C 151 MET cc_start: 0.5561 (mmt) cc_final: 0.4708 (tpp) REVERT: C 184 SER cc_start: 0.8232 (p) cc_final: 0.7960 (m) REVERT: C 210 MET cc_start: 0.3944 (mmm) cc_final: 0.3475 (mmm) REVERT: G 45 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.8651 (t80) REVERT: G 95 VAL cc_start: 0.8196 (t) cc_final: 0.7895 (p) REVERT: G 118 MET cc_start: 0.0536 (pmm) cc_final: -0.0104 (pmm) REVERT: G 140 MET cc_start: 0.6493 (mmm) cc_final: 0.6280 (mmm) REVERT: H 163 ASP cc_start: 0.6934 (p0) cc_final: 0.6604 (p0) REVERT: H 166 GLU cc_start: 0.8674 (mp0) cc_final: 0.8077 (mp0) REVERT: H 174 LEU cc_start: 0.8165 (mt) cc_final: 0.7954 (mt) REVERT: H 197 TRP cc_start: 0.3944 (p-90) cc_final: 0.3660 (p-90) REVERT: J 151 ASP cc_start: 0.5683 (m-30) cc_final: 0.5037 (t0) REVERT: J 185 VAL cc_start: 0.8413 (t) cc_final: 0.8183 (p) REVERT: K 9 ASP cc_start: 0.8763 (t0) cc_final: 0.8158 (p0) REVERT: K 154 GLN cc_start: 0.9086 (pt0) cc_final: 0.8205 (mm110) REVERT: K 166 GLN cc_start: 0.8822 (mm110) cc_final: 0.8421 (tp-100) REVERT: K 189 GLU cc_start: 0.8815 (mp0) cc_final: 0.8460 (tp30) REVERT: K 251 LEU cc_start: 0.2249 (OUTLIER) cc_final: 0.1848 (tp) outliers start: 73 outliers final: 48 residues processed: 401 average time/residue: 0.3293 time to fit residues: 204.5494 Evaluate side-chains 366 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 315 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 909 PHE Chi-restraints excluded: chain A residue 911 ASN Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain D residue 176 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain H residue 26 VAL Chi-restraints excluded: chain J residue 111 ARG Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 194 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 245 LEU Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 132 optimal weight: 0.0870 chunk 43 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 81 optimal weight: 0.0020 chunk 179 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 191 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.4566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 HIS A 634 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.098100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.081843 restraints weight = 91271.826| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 5.85 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5625 moved from start: 1.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21456 Z= 0.213 Angle : 0.851 15.031 29068 Z= 0.404 Chirality : 0.045 0.220 3279 Planarity : 0.005 0.058 3679 Dihedral : 4.837 58.838 3028 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.74 % Favored : 91.95 % Rotamer: Outliers : 2.51 % Allowed : 33.01 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.16), residues: 2597 helix: 1.02 (0.18), residues: 882 sheet: 0.57 (0.20), residues: 657 loop : -2.89 (0.16), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 110 HIS 0.015 0.001 HIS A 580 PHE 0.040 0.002 PHE G 77 TYR 0.020 0.001 TYR F 96 ARG 0.015 0.001 ARG C 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5194 Ramachandran restraints generated. 2597 Oldfield, 0 Emsley, 2597 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 331 time to evaluate : 2.748 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: A 90 MET cc_start: 0.8283 (tmm) cc_final: 0.7991 (tmm) REVERT: A 221 GLN cc_start: 0.7016 (pm20) cc_final: 0.6728 (pp30) REVERT: A 310 LEU cc_start: 0.7017 (mm) cc_final: 0.6331 (pp) REVERT: A 538 MET cc_start: 0.5249 (ptp) cc_final: 0.4662 (ptp) REVERT: A 573 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7587 (pmm) REVERT: A 632 MET cc_start: 0.3002 (tpp) cc_final: 0.2771 (tpp) REVERT: A 774 VAL cc_start: 0.4603 (t) cc_final: 0.4323 (p) REVERT: A 907 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7655 (pm20) REVERT: A 919 MET cc_start: 0.7080 (mmp) cc_final: 0.6830 (mmp) REVERT: B 120 ASN cc_start: 0.5507 (OUTLIER) cc_final: 0.5012 (t0) REVERT: B 234 MET cc_start: 0.6469 (ptt) cc_final: 0.6078 (ptp) REVERT: C 36 ILE cc_start: 0.6774 (mt) cc_final: 0.6361 (mt) REVERT: C 70 LYS cc_start: 0.8115 (tptp) cc_final: 0.7442 (tppt) REVERT: C 147 ARG cc_start: 0.2804 (mtt180) cc_final: 0.1837 (ttp80) REVERT: C 148 PHE cc_start: 0.8435 (t80) cc_final: 0.8208 (t80) REVERT: C 151 MET cc_start: 0.5625 (mmt) cc_final: 0.4883 (tpp) REVERT: C 184 SER cc_start: 0.8097 (p) cc_final: 0.7806 (m) REVERT: C 210 MET cc_start: 0.3971 (mmm) cc_final: 0.3508 (mmm) REVERT: F 89 LEU cc_start: 0.7917 (mt) cc_final: 0.7532 (pp) REVERT: G 45 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8700 (t80) REVERT: G 95 VAL cc_start: 0.7960 (t) cc_final: 0.7708 (p) REVERT: G 118 MET cc_start: 0.0480 (pmm) cc_final: 0.0264 (pmm) REVERT: G 140 MET cc_start: 0.6759 (mmm) cc_final: 0.6517 (mmm) REVERT: H 163 ASP cc_start: 0.7092 (p0) cc_final: 0.6731 (p0) REVERT: H 166 GLU cc_start: 0.8708 (mp0) cc_final: 0.8158 (mp0) REVERT: H 174 LEU cc_start: 0.8184 (mt) cc_final: 0.7974 (mt) REVERT: H 203 ASN cc_start: 0.8010 (m-40) cc_final: 0.7774 (p0) REVERT: J 69 ARG cc_start: 0.6750 (mtm180) cc_final: 0.6517 (mtm180) REVERT: J 151 ASP cc_start: 0.5653 (m-30) cc_final: 0.5046 (t0) REVERT: K 9 ASP cc_start: 0.8763 (t0) cc_final: 0.8130 (p0) REVERT: K 154 GLN cc_start: 0.9090 (pt0) cc_final: 0.8226 (mm110) REVERT: K 166 GLN cc_start: 0.8892 (mm110) cc_final: 0.8439 (tp-100) REVERT: K 189 GLU cc_start: 0.8753 (mp0) cc_final: 0.8467 (tp30) REVERT: K 251 LEU cc_start: 0.2015 (OUTLIER) cc_final: 0.1777 (tp) outliers start: 57 outliers final: 45 residues processed: 370 average time/residue: 0.3086 time to fit residues: 181.4288 Evaluate side-chains 368 residues out of total 2275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 319 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 530 PHE Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain A residue 671 PHE Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 793 TYR Chi-restraints excluded: chain A residue 863 ILE Chi-restraints excluded: chain A residue 911 ASN Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 PHE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain G residue 45 PHE Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 103 TYR Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 142 SER Chi-restraints excluded: chain G residue 149 PHE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain J residue 111 ARG Chi-restraints excluded: chain J residue 162 VAL Chi-restraints excluded: chain J residue 171 HIS Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 245 LEU Chi-restraints excluded: chain K residue 251 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 36 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 78 optimal weight: 0.0870 chunk 216 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS ** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 HIS ** E 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 ASN ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.099274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.082099 restraints weight = 91183.224| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 6.04 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5768 moved from start: 1.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21456 Z= 0.215 Angle : 0.861 17.737 29068 Z= 0.406 Chirality : 0.046 0.233 3279 Planarity : 0.005 0.060 3679 Dihedral : 4.781 59.157 3028 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.82 % Favored : 91.88 % Rotamer: Outliers : 2.64 % Allowed : 33.67 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2597 helix: 1.10 (0.18), residues: 876 sheet: 0.60 (0.20), residues: 660 loop : -2.81 (0.16), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 110 HIS 0.021 0.001 HIS A 580 PHE 0.035 0.002 PHE G 77 TYR 0.023 0.002 TYR F 96 ARG 0.012 0.001 ARG C 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9381.98 seconds wall clock time: 167 minutes 50.35 seconds (10070.35 seconds total)